From f4d3030cab2108fe7f9a5d60a8b84434dc10e8fb Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Thu, 30 Apr 2026 16:10:35 -0600 Subject: [PATCH 01/24] fix: adapt ma_io to per-annotation strand and renamed MA record API The molecular_annotation crate moved strand from AnnotationType to per-Annotation and replaced from_ma_record/write_ma_record with from_record + from_tags / to_record. Update src/utils/ma_io.rs and tests/molecular_annotation.rs to call sites. read_ma_tags now extracts MA/AL/AQ/AN aux fields explicitly and feeds them through MolecularAnnotations::from_tags, then attaches AlignedBlocks for liftover. --- src/utils/ma_io.rs | 263 ++++++++++++++++++++++++++++++++++ tests/molecular_annotation.rs | 249 ++++++++++++++++++++++++++++++++ 2 files changed, 512 insertions(+) create mode 100644 src/utils/ma_io.rs create mode 100644 tests/molecular_annotation.rs diff --git a/src/utils/ma_io.rs b/src/utils/ma_io.rs new file mode 100644 index 00000000..1c2f9aca --- /dev/null +++ b/src/utils/ma_io.rs @@ -0,0 +1,263 @@ +//! MA-spec annotation I/O bridge for fibertools-rs. +//! +//! `read_annotations` returns a [`MolecularAnnotations`] for any input record: +//! the spec `MA`/`AL`/`AQ`/`AN` tags take precedence; otherwise the legacy +//! fibertools-rs tags (`ns`/`nl` for nucleosomes, `as`/`al`/`aq` for MSPs) are +//! parsed inline. Pre-FIRE BAMs have no `aq` and so produce `msp+` (no +//! quality). Post-FIRE BAMs map `aq` onto the linear-scaled `msp+Q` quality. +//! +//! `write_annotations` always emits the spec tags. When `legacy` is set, it +//! additionally writes the corresponding `ns`/`nl`/`as`/`al`/`aq` tags so +//! downstream tooling that hasn't migrated yet still sees what it expects. + +use anyhow::{bail, Result}; +use molecular_annotation::{Annotation, MolecularAnnotations, QualitySpec, Strand}; +use rust_htslib::bam::{self, record::Aux}; + +/// Annotation type names used by fibertools-rs. +pub const NUC_TYPE: &str = "nuc"; +pub const MSP_TYPE: &str = "msp"; + +/// Legacy fibertools-rs tags. Listed here so callers (and the writer below) +/// have one place to look up which tags this module produces/consumes. +pub const LEGACY_NUC_MSP_TAGS: &[&[u8]] = &[b"ns", b"nl", b"as", b"al", b"aq"]; + +/// Read annotations from a BAM record. +/// +/// Prefers spec MA tags; falls back to legacy `ns`/`nl`/`as`/`al`/`aq`. Always +/// returns a populated [`MolecularAnnotations`] (with read length and aligned +/// blocks set) — even if no annotation tags are present. +pub fn read_annotations(record: &bam::Record) -> Result { + if let Some(annot) = read_ma_tags(record)? { + return Ok(annot); + } + read_legacy_nuc_msp(record) +} + +fn read_ma_tags(record: &bam::Record) -> Result> { + let ma = match record.aux(b"MA") { + Ok(Aux::String(s)) => s.to_string(), + _ => return Ok(None), + }; + let aq: Option> = match record.aux(b"AQ") { + Ok(Aux::ArrayU8(arr)) => Some(arr.iter().collect()), + _ => None, + }; + let an: Option = match record.aux(b"AN") { + Ok(Aux::String(s)) => Some(s.to_string()), + _ => None, + }; + let al: Vec = match record.aux(b"AL") { + Ok(Aux::ArrayU32(arr)) => arr.iter().collect(), + Ok(Aux::ArrayI32(arr)) => arr.iter().map(|v| v as u32).collect(), + _ => Vec::new(), + }; + let mut annot = MolecularAnnotations::from_tags(&ma, &al, aq.as_deref(), an.as_deref()) + .map_err(|e| anyhow::anyhow!("MA tag parse error: {e}"))?; + annot.set_aligned_blocks_raw( + molecular_annotation::AlignedBlocks::from_record(record), + record.is_reverse(), + ); + Ok(Some(annot)) +} + +fn read_legacy_nuc_msp(record: &bam::Record) -> Result { + let mut annot = MolecularAnnotations::from_record(record); + + let ns = u32_array(record, b"ns"); + let nl = u32_array(record, b"nl"); + let a_starts = u32_array(record, b"as"); + let a_lens = u32_array(record, b"al"); + let aq = u8_array(record, b"aq"); + + if let (Some(ns), Some(nl)) = (ns.as_ref(), nl.as_ref()) { + if ns.len() != nl.len() { + bail!( + "legacy ns ({}) and nl ({}) length mismatch", + ns.len(), + nl.len() + ); + } + if !ns.is_empty() { + let nuc = annot.add_annotation_type(NUC_TYPE, QualitySpec::none()); + for (s, l) in ns.iter().zip(nl.iter()) { + nuc.add(*s, *l, Strand::Forward, vec![], None); + } + } + } + + if let (Some(starts), Some(lens)) = (a_starts.as_ref(), a_lens.as_ref()) { + if starts.len() != lens.len() { + bail!( + "legacy as ({}) and al ({}) length mismatch", + starts.len(), + lens.len() + ); + } + let q_spec = if aq.is_some() { + "Q".parse::()? + } else { + QualitySpec::none() + }; + if let Some(ref q) = aq { + if q.len() != starts.len() { + bail!( + "legacy aq ({}) and as ({}) length mismatch", + q.len(), + starts.len() + ); + } + } + if !starts.is_empty() { + let msp = annot.add_annotation_type(MSP_TYPE, q_spec); + for (i, (s, l)) in starts.iter().zip(lens.iter()).enumerate() { + let qualities = aq.as_ref().map(|q| vec![q[i]]).unwrap_or_default(); + msp.add(*s, *l, Strand::Forward, qualities, None); + } + } + } + + Ok(annot) +} + +/// Write annotations to a BAM record. +/// +/// Always emits the MA-spec tags. When `legacy` is set, also emits the +/// fibertools-rs legacy `ns`/`nl`/`as`/`al`/`aq` tags for `nuc` and `msp` +/// annotation types. When not set, any pre-existing legacy tags are stripped +/// so the output is MA-only. +pub fn write_annotations(record: &mut bam::Record, annot: &MolecularAnnotations, legacy: bool) { + for tag in LEGACY_NUC_MSP_TAGS { + record.remove_aux(tag).ok(); + } + annot.to_record(record); + if legacy { + write_legacy_nuc_msp(record, annot); + } +} + +fn write_legacy_nuc_msp(record: &mut bam::Record, annot: &MolecularAnnotations) { + if let Some(nuc) = annot.get_type(NUC_TYPE) { + push_starts_lens(record, b"ns", b"nl", &nuc.annotations); + } + if let Some(msp) = annot.get_type(MSP_TYPE) { + push_starts_lens(record, b"as", b"al", &msp.annotations); + if msp.quality_spec.num_qualities() == 1 && msp.quality_spec.has_quality() { + let aq: Vec = msp + .annotations + .iter() + .map(|a| a.qualities.first().copied().unwrap_or(0)) + .collect(); + if !aq.is_empty() { + record.push_aux(b"aq", Aux::ArrayU8((&aq).into())).ok(); + } + } + } +} + +fn push_starts_lens( + record: &mut bam::Record, + starts_tag: &[u8], + lens_tag: &[u8], + items: &[Annotation], +) { + if items.is_empty() { + return; + } + let starts: Vec = items.iter().map(|a| a.start).collect(); + let lens: Vec = items.iter().map(|a| a.length).collect(); + record + .push_aux(starts_tag, Aux::ArrayU32((&starts).into())) + .ok(); + record + .push_aux(lens_tag, Aux::ArrayU32((&lens).into())) + .ok(); +} + +/// Convenience for callers that still operate on raw `i64` arrays of +/// nucleosome and MSP coordinates. Returns +/// `(nuc_starts, nuc_lengths, msp_starts, msp_lengths, msp_qual)` derived +/// from whichever tag set is present (MA wins over legacy). +/// +/// Coordinates are in molecular orientation — the same convention as the +/// legacy `ns`/`nl`/`as`/`al` tags. `msp_qual` is empty when there are no +/// MSP qualities (pre-FIRE state); otherwise one byte per MSP. +pub fn extract_nuc_msp_arrays( + record: &bam::Record, +) -> Result<(Vec, Vec, Vec, Vec, Vec)> { + let annot = read_annotations(record)?; + let (nuc_starts, nuc_lengths) = annot + .get_type(NUC_TYPE) + .map(|t| { + ( + t.annotations.iter().map(|a| a.start as i64).collect(), + t.annotations.iter().map(|a| a.length as i64).collect(), + ) + }) + .unwrap_or_default(); + let (msp_starts, msp_lengths, msp_qual) = annot + .get_type(MSP_TYPE) + .map(|t| { + let starts: Vec = t.annotations.iter().map(|a| a.start as i64).collect(); + let lens: Vec = t.annotations.iter().map(|a| a.length as i64).collect(); + let qs: Vec = if t.quality_spec.has_quality() { + t.annotations + .iter() + .map(|a| a.qualities.first().copied().unwrap_or(0)) + .collect() + } else { + Vec::new() + }; + (starts, lens, qs) + }) + .unwrap_or_default(); + Ok((nuc_starts, nuc_lengths, msp_starts, msp_lengths, msp_qual)) +} + +/// Build a [`MolecularAnnotations`] for `nuc` and `msp` annotation types from +/// raw `u32` start/length arrays in molecular orientation, plus an optional +/// per-MSP linear quality array. Convenience for producers that have already +/// computed coordinates and want to hand them to [`write_annotations`]. +pub fn build_nuc_msp_annotations( + record: &bam::Record, + nuc_starts: &[u32], + nuc_lengths: &[u32], + msp_starts: &[u32], + msp_lengths: &[u32], + msp_qual: Option<&[u8]>, +) -> MolecularAnnotations { + let mut annot = MolecularAnnotations::from_record(record); + if !nuc_starts.is_empty() { + let nuc = annot.add_annotation_type(NUC_TYPE, QualitySpec::none()); + for (s, l) in nuc_starts.iter().zip(nuc_lengths.iter()) { + nuc.add(*s, *l, Strand::Forward, vec![], None); + } + } + if !msp_starts.is_empty() { + let q_spec = match msp_qual { + Some(_) => "Q".parse::().expect("Q parses"), + None => QualitySpec::none(), + }; + let msp = annot.add_annotation_type(MSP_TYPE, q_spec); + for (i, (s, l)) in msp_starts.iter().zip(msp_lengths.iter()).enumerate() { + let q = msp_qual.map(|q| vec![q[i]]).unwrap_or_default(); + msp.add(*s, *l, Strand::Forward, q, None); + } + } + annot +} + +fn u32_array(record: &bam::Record, tag: &[u8]) -> Option> { + match record.aux(tag) { + Ok(Aux::ArrayU32(arr)) => Some(arr.iter().collect()), + Ok(Aux::ArrayI32(arr)) => Some(arr.iter().map(|v| v as u32).collect()), + _ => None, + } +} + +fn u8_array(record: &bam::Record, tag: &[u8]) -> Option> { + match record.aux(tag) { + Ok(Aux::ArrayU8(arr)) => Some(arr.iter().collect()), + _ => None, + } +} diff --git a/tests/molecular_annotation.rs b/tests/molecular_annotation.rs new file mode 100644 index 00000000..650dd821 --- /dev/null +++ b/tests/molecular_annotation.rs @@ -0,0 +1,249 @@ +//! Integration tests for the MA-spec ↔ legacy fibertools tag conversion. +//! +//! Uses BAM fixtures already in `tests/data/`. Validates that: +//! - Reading legacy `ns/nl/as/al/aq` produces the same MolecularAnnotations +//! shape (counts, coords, qualities) as direct raw tag access. +//! - Writing MA tags then reading them back yields equal annotations. +//! - `--legacy=true` produces both MA and legacy tags; `--legacy=false` +//! strips legacy tags from the output. +//! - Reverse-aligned records keep coordinates in molecular orientation. +//! - Records with both MA and legacy tags resolve to the MA version. + +use std::path::PathBuf; + +use fibertools_rs::utils::ma_io::{read_annotations, write_annotations, MSP_TYPE, NUC_TYPE}; +use molecular_annotation::{MolecularAnnotations, QualitySpec, Strand}; +use rust_htslib::bam::record::Aux; +use rust_htslib::bam::{self, Read}; + +fn fixture_path(name: &str) -> PathBuf { + PathBuf::from(env!("CARGO_MANIFEST_DIR")) + .join("tests/data") + .join(name) +} + +fn read_records(name: &str) -> Vec { + let mut reader = + bam::Reader::from_path(fixture_path(name)).unwrap_or_else(|e| panic!("open {name}: {e}")); + reader.records().collect::>().unwrap() +} + +fn raw_u32(record: &bam::Record, tag: &[u8]) -> Option> { + match record.aux(tag) { + Ok(Aux::ArrayU32(arr)) => Some(arr.iter().collect()), + Ok(Aux::ArrayI32(arr)) => Some(arr.iter().map(|v| v as u32).collect()), + _ => None, + } +} + +fn raw_u8(record: &bam::Record, tag: &[u8]) -> Option> { + match record.aux(tag) { + Ok(Aux::ArrayU8(arr)) => Some(arr.iter().collect()), + _ => None, + } +} + +const FIXTURES: &[&str] = &["msp_nuc.bam", "nuc_example.bam", "all.bam"]; + +#[test] +fn legacy_read_matches_raw_tags() { + for fixture in FIXTURES { + for record in read_records(fixture) { + let annot = read_annotations(&record).unwrap(); + let raw_ns = raw_u32(&record, b"ns").unwrap_or_default(); + let raw_nl = raw_u32(&record, b"nl").unwrap_or_default(); + let raw_as = raw_u32(&record, b"as").unwrap_or_default(); + let raw_al = raw_u32(&record, b"al").unwrap_or_default(); + let raw_aq = raw_u8(&record, b"aq"); + + if let Some(nuc) = annot.get_type(NUC_TYPE) { + let starts: Vec = nuc.annotations.iter().map(|a| a.start).collect(); + let lens: Vec = nuc.annotations.iter().map(|a| a.length).collect(); + assert_eq!(starts, raw_ns, "{fixture}: nuc starts"); + assert_eq!(lens, raw_nl, "{fixture}: nuc lengths"); + } + + if let Some(msp) = annot.get_type(MSP_TYPE) { + let starts: Vec = msp.annotations.iter().map(|a| a.start).collect(); + let lens: Vec = msp.annotations.iter().map(|a| a.length).collect(); + assert_eq!(starts, raw_as, "{fixture}: msp starts"); + assert_eq!(lens, raw_al, "{fixture}: msp lengths"); + + if let Some(q) = raw_aq { + let qs: Vec = msp.annotations.iter().map(|a| a.qualities[0]).collect(); + assert_eq!(qs, q, "{fixture}: msp qualities"); + assert!(msp.quality_spec.has_quality(), "{fixture}: aq → Q-spec"); + } else { + assert!(!msp.quality_spec.has_quality(), "{fixture}: no aq → no Q"); + } + } + } + } +} + +#[test] +fn ma_write_then_read_roundtrips() { + for fixture in FIXTURES { + for record in read_records(fixture) { + let original = read_annotations(&record).unwrap(); + let mut converted = record.clone(); + write_annotations(&mut converted, &original, false); + + // Legacy tags must be gone after non-legacy write. + for tag in [b"ns", b"nl", b"as", b"al", b"aq"] { + assert!( + converted.aux(tag).is_err(), + "{fixture}: legacy {} should be stripped", + std::str::from_utf8(tag).unwrap() + ); + } + + let round = read_annotations(&converted).unwrap(); + assert_eq!( + round.annotation_types, original.annotation_types, + "{fixture}: MA round-trip" + ); + } + } +} + +#[test] +fn legacy_write_emits_both_tag_sets() { + for fixture in FIXTURES { + for record in read_records(fixture) { + let original = read_annotations(&record).unwrap(); + let mut both = record.clone(); + write_annotations(&mut both, &original, true); + + // MA tag present. + assert!(both.aux(b"MA").is_ok(), "{fixture}: MA expected"); + + // Legacy tags also present where applicable. + if original.get_type(NUC_TYPE).is_some() { + assert!(both.aux(b"ns").is_ok(), "{fixture}: ns expected"); + assert!(both.aux(b"nl").is_ok(), "{fixture}: nl expected"); + } + if original.get_type(MSP_TYPE).is_some() { + assert!(both.aux(b"as").is_ok(), "{fixture}: as expected"); + assert!(both.aux(b"al").is_ok(), "{fixture}: al expected"); + } + } + } +} + +#[test] +fn legacy_write_inverse_roundtrip() { + // fixture → legacy write into a fresh record (with MA stripped) → re-read + // via the legacy path → equal annotations. + for fixture in FIXTURES { + for record in read_records(fixture) { + let original = read_annotations(&record).unwrap(); + let mut fresh = record.clone(); + // Wipe everything, then write legacy-only. + for tag in [ + b"MA", b"AL", b"AQ", b"AN", b"ns", b"nl", b"as", b"al", b"aq", + ] { + fresh.remove_aux(tag).ok(); + } + write_annotations(&mut fresh, &original, true); + // Strip MA so the read path falls back to legacy. + fresh.remove_aux(b"MA").ok(); + fresh.remove_aux(b"AL").ok(); + fresh.remove_aux(b"AQ").ok(); + fresh.remove_aux(b"AN").ok(); + + let round = read_annotations(&fresh).unwrap(); + assert_eq!( + round.annotation_types, original.annotation_types, + "{fixture}: legacy inverse roundtrip" + ); + } + } +} + +#[test] +fn ma_takes_precedence_over_legacy() { + // Build a record with both MA and legacy tags, with intentionally + // divergent values, and confirm the MA version wins. + let mut record = read_records("msp_nuc.bam").into_iter().next().unwrap(); + let legacy = read_annotations(&record).unwrap(); + let read_length = legacy.read_length; + + // Construct a different MA payload; write it without stripping legacy. + let mut alt = MolecularAnnotations::new(read_length); + alt.add_annotation_type(MSP_TYPE, QualitySpec::none()) + .add(0, 10, Strand::Forward, vec![], None) + .add(50, 5, Strand::Forward, vec![], None); + alt.to_record(&mut record); + + let resolved = read_annotations(&record).unwrap(); + let resolved_msp = resolved.get_type(MSP_TYPE).expect("msp expected"); + let alt_msp = alt.get_type(MSP_TYPE).unwrap(); + assert_eq!( + resolved_msp.annotations, alt_msp.annotations, + "MA must win over legacy" + ); + assert_ne!( + resolved_msp.annotations.len(), + legacy.get_type(MSP_TYPE).unwrap().annotations.len(), + "sanity: legacy and alt diverge" + ); +} + +#[test] +fn reverse_strand_keeps_molecular_coords() { + let reverse: Vec<_> = read_records("all.bam") + .into_iter() + .filter(|r| r.is_reverse()) + .collect(); + assert!(!reverse.is_empty(), "expected reverse records in all.bam"); + + for record in reverse { + let raw_ns = raw_u32(&record, b"ns").unwrap_or_default(); + let annot = read_annotations(&record).unwrap(); + if let Some(nuc) = annot.get_type(NUC_TYPE) { + let starts: Vec = nuc.annotations.iter().map(|a| a.start).collect(); + assert_eq!( + starts, raw_ns, + "reverse record: stored starts equal raw ns (molecular orientation)" + ); + + // Library's get_bam_coords flips for reverse-aligned reads. + let bam_coords = annot.get_bam_coords(NUC_TYPE).unwrap(); + for (i, (bs, be)) in bam_coords.iter().enumerate() { + let mol_start = nuc.annotations[i].start; + let mol_end = mol_start + nuc.annotations[i].length; + let len = annot.read_length; + assert_eq!(*bs, len - mol_end); + assert_eq!(*be, len - mol_start); + } + } + } +} + +#[test] +fn missing_annotations_yield_empty_container() { + let mut blank = read_records("nuc_example.bam").into_iter().next().unwrap(); + for tag in [ + b"MA", b"AL", b"AQ", b"AN", b"ns", b"nl", b"as", b"al", b"aq", + ] { + blank.remove_aux(tag).ok(); + } + let annot = read_annotations(&blank).unwrap(); + assert_eq!(annot.total_annotation_count(), 0); + assert_eq!(annot.read_length, blank.seq_len() as u32); +} + +#[test] +fn mismatched_legacy_lengths_returns_error() { + let mut record = read_records("nuc_example.bam").into_iter().next().unwrap(); + record.remove_aux(b"ns").ok(); + record.remove_aux(b"nl").ok(); + record + .push_aux(b"ns", Aux::ArrayU32((&vec![1u32, 2, 3]).into())) + .unwrap(); + record + .push_aux(b"nl", Aux::ArrayU32((&vec![10u32, 20]).into())) + .unwrap(); + assert!(read_annotations(&record).is_err()); +} From e6712b8744341ce404ec47dc4478607c53959d19 Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Thu, 30 Apr 2026 16:17:25 -0600 Subject: [PATCH 02/24] docs: refresh ma_io module overview Updates the module-level doc comment to reflect the post-Phase-0 API shape, the planned producer/consumer split for nuc/msp/fire, and the in-memory-only m6a/cpg story (MM/ML stays the on-disk truth). --- src/utils/ma_io.rs | 24 ++++++++++++++++-------- 1 file changed, 16 insertions(+), 8 deletions(-) diff --git a/src/utils/ma_io.rs b/src/utils/ma_io.rs index 1c2f9aca..424e4ddf 100644 --- a/src/utils/ma_io.rs +++ b/src/utils/ma_io.rs @@ -1,14 +1,22 @@ //! MA-spec annotation I/O bridge for fibertools-rs. //! -//! `read_annotations` returns a [`MolecularAnnotations`] for any input record: -//! the spec `MA`/`AL`/`AQ`/`AN` tags take precedence; otherwise the legacy -//! fibertools-rs tags (`ns`/`nl` for nucleosomes, `as`/`al`/`aq` for MSPs) are -//! parsed inline. Pre-FIRE BAMs have no `aq` and so produce `msp+` (no -//! quality). Post-FIRE BAMs map `aq` onto the linear-scaled `msp+Q` quality. +//! Reading: prefers MA/AL/AQ/AN; falls back to legacy `ns/nl/as/al/aq` if no +//! MA tag is present. Returns a populated [`MolecularAnnotations`] (read +//! length and aligned blocks set) even when no annotation tags exist. //! -//! `write_annotations` always emits the spec tags. When `legacy` is set, it -//! additionally writes the corresponding `ns`/`nl`/`as`/`al`/`aq` tags so -//! downstream tooling that hasn't migrated yet still sees what it expects. +//! Writing: always emits MA-spec tags. With `legacy=true` it additionally +//! emits legacy `ns/nl/as/al/aq` for `nuc` and `msp` types so pre-MA +//! consumers (older pyft, IGV decorators) keep working during the +//! migration. With `legacy=false` any pre-existing legacy tags are stripped. +//! +//! Annotation type names produced by fibertools-rs: +//! - `nuc` (forward strand, no quality) +//! - `msp` (forward strand, no quality pre-FIRE; `Q` post-FIRE) +//! - `fire` (forward strand, `P` phred quality) +//! +//! `m6a` and `cpg` types may appear *in memory* on a [`MolecularAnnotations`] +//! populated by `BaseMods::populate_ma`, but are NEVER read or written here: +//! their on-disk source of truth is `MM`/`ML`. use anyhow::{bail, Result}; use molecular_annotation::{Annotation, MolecularAnnotations, QualitySpec, Strand}; From d5900bac8a09a382ec8fc1a4dcdf20856c706cb0 Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Thu, 30 Apr 2026 16:18:18 -0600 Subject: [PATCH 03/24] feat: ma_io fire+P builder and extractor Adds FIRE_TYPE constant, build_annotations (nuc/msp/fire-aware), and extract_fire_arrays. build_nuc_msp_annotations is preserved as a thin wrapper so existing producers keep compiling until they migrate to the fire-aware builder. --- src/utils/ma_io.rs | 98 +++++++++++++++++++++++++++++++++++----------- 1 file changed, 75 insertions(+), 23 deletions(-) diff --git a/src/utils/ma_io.rs b/src/utils/ma_io.rs index 424e4ddf..107935d6 100644 --- a/src/utils/ma_io.rs +++ b/src/utils/ma_io.rs @@ -25,6 +25,7 @@ use rust_htslib::bam::{self, record::Aux}; /// Annotation type names used by fibertools-rs. pub const NUC_TYPE: &str = "nuc"; pub const MSP_TYPE: &str = "msp"; +pub const FIRE_TYPE: &str = "fire"; /// Legacy fibertools-rs tags. Listed here so callers (and the writer below) /// have one place to look up which tags this module produces/consumes. @@ -222,39 +223,90 @@ pub fn extract_nuc_msp_arrays( Ok((nuc_starts, nuc_lengths, msp_starts, msp_lengths, msp_qual)) } -/// Build a [`MolecularAnnotations`] for `nuc` and `msp` annotation types from -/// raw `u32` start/length arrays in molecular orientation, plus an optional -/// per-MSP linear quality array. Convenience for producers that have already -/// computed coordinates and want to hand them to [`write_annotations`]. -pub fn build_nuc_msp_annotations( +/// Build a [`MolecularAnnotations`] for nuc/msp/fire types from raw arrays in +/// molecular orientation. Each input is optional; passing `None` skips that +/// type. Coordinates and lengths are paired positionally. +/// +/// - `nuc`: `(starts, lengths)` — no quality. +/// - `msp`: `(starts, lengths, optional Q-scaled qualities)`. With qualities +/// present, the type uses `msp+Q`; without, `msp+` (no quality). +/// - `fire`: `(starts, lengths, phred-scaled qualities)`. Always `fire+P`. +pub fn build_annotations( record: &bam::Record, - nuc_starts: &[u32], - nuc_lengths: &[u32], - msp_starts: &[u32], - msp_lengths: &[u32], - msp_qual: Option<&[u8]>, + nuc: Option<(&[u32], &[u32])>, + msp: Option<(&[u32], &[u32], Option<&[u8]>)>, + fire: Option<(&[u32], &[u32], &[u8])>, ) -> MolecularAnnotations { let mut annot = MolecularAnnotations::from_record(record); - if !nuc_starts.is_empty() { - let nuc = annot.add_annotation_type(NUC_TYPE, QualitySpec::none()); - for (s, l) in nuc_starts.iter().zip(nuc_lengths.iter()) { - nuc.add(*s, *l, Strand::Forward, vec![], None); + if let Some((starts, lens)) = nuc { + if !starts.is_empty() { + let t = annot.add_annotation_type(NUC_TYPE, QualitySpec::none()); + for (s, l) in starts.iter().zip(lens.iter()) { + t.add(*s, *l, Strand::Forward, vec![], None); + } } } - if !msp_starts.is_empty() { - let q_spec = match msp_qual { - Some(_) => "Q".parse::().expect("Q parses"), - None => QualitySpec::none(), - }; - let msp = annot.add_annotation_type(MSP_TYPE, q_spec); - for (i, (s, l)) in msp_starts.iter().zip(msp_lengths.iter()).enumerate() { - let q = msp_qual.map(|q| vec![q[i]]).unwrap_or_default(); - msp.add(*s, *l, Strand::Forward, q, None); + if let Some((starts, lens, q)) = msp { + if !starts.is_empty() { + let qspec = match q { + Some(_) => "Q".parse::().expect("Q parses"), + None => QualitySpec::none(), + }; + let t = annot.add_annotation_type(MSP_TYPE, qspec); + for (i, (s, l)) in starts.iter().zip(lens.iter()).enumerate() { + let qv = q.map(|q| vec![q[i]]).unwrap_or_default(); + t.add(*s, *l, Strand::Forward, qv, None); + } + } + } + if let Some((starts, lens, phred)) = fire { + if !starts.is_empty() { + let t = + annot.add_annotation_type(FIRE_TYPE, "P".parse::().expect("P parses")); + for (i, (s, l)) in starts.iter().zip(lens.iter()).enumerate() { + t.add(*s, *l, Strand::Forward, vec![phred[i]], None); + } } } annot } +/// Backwards-compatible wrapper around [`build_annotations`]. Existing +/// nuc/msp producers can keep calling this until they migrate to the +/// fire-aware [`build_annotations`]. +pub fn build_nuc_msp_annotations( + record: &bam::Record, + nuc_starts: &[u32], + nuc_lengths: &[u32], + msp_starts: &[u32], + msp_lengths: &[u32], + msp_qual: Option<&[u8]>, +) -> MolecularAnnotations { + let nuc = (!nuc_starts.is_empty()).then_some((nuc_starts, nuc_lengths)); + let msp = (!msp_starts.is_empty()).then_some((msp_starts, msp_lengths, msp_qual)); + build_annotations(record, nuc, msp, None) +} + +/// Convenience: read fire annotations as raw arrays in molecular orientation. +/// Returns `(starts, lengths, phred_qualities)`. All three are empty if the +/// record has no `fire` MA type. +pub fn extract_fire_arrays(record: &bam::Record) -> Result<(Vec, Vec, Vec)> { + let annot = read_annotations(record)?; + Ok(annot + .get_type(FIRE_TYPE) + .map(|t| { + let starts = t.annotations.iter().map(|a| a.start).collect(); + let lens = t.annotations.iter().map(|a| a.length).collect(); + let phred = t + .annotations + .iter() + .map(|a| a.qualities.first().copied().unwrap_or(0)) + .collect(); + (starts, lens, phred) + }) + .unwrap_or_default()) +} + fn u32_array(record: &bam::Record, tag: &[u8]) -> Option> { match record.aux(tag) { Ok(Aux::ArrayU32(arr)) => Some(arr.iter().collect()), From 3ce18f3f2d6f0066df40c74782c43abe13593134 Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Wed, 6 May 2026 11:05:15 -0600 Subject: [PATCH 04/24] feat: integrate MA spec into all subcommands This wires up nuc,msp, and fire annotations to go thru MA spec. Does not cover m6a/cpg. --- Cargo.toml | 3 +- src/cli/fire_opts.rs | 5 + src/cli/nucleosome_opts.rs | 4 + src/cli/predict_opts.rs | 5 + src/fiber.rs | 10 +- src/subcommands/add_nucleosomes.rs | 2 +- src/subcommands/fire.rs | 45 +++++++-- src/subcommands/mock_fire.rs | 23 ++--- src/subcommands/predict_m6a.rs | 21 +++- src/utils.rs | 1 + src/utils/basemods.rs | 7 ++ src/utils/ma_io.rs | 153 +++++++++++++++++++++-------- src/utils/nucleosome.rs | 30 ++---- 13 files changed, 214 insertions(+), 95 deletions(-) diff --git a/Cargo.toml b/Cargo.toml index ec2b245a..f93646de 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -50,7 +50,7 @@ ordered-float = "3.4.0" rayon = "1.10" linear-map = "1.2.0" regex = "1.9.1" -rust-htslib = "0.46" +rust-htslib = "0.47" serde = { version = "1.0.104", features = ["derive"], optional = false } @@ -69,6 +69,7 @@ burn = { version = "0.18.0", optional = true, features = [ num = "0.4.3" rand = "0.8.5" noodles = { version = "0.100.0", features = ["fasta", "bed"] } +molecular-annotation = { path = "../Molecular-annotation-spec/rust", features = ["htslib"] } [build-dependencies] burn-import = { version = "0.18.0", default-features = false, features = [ diff --git a/src/cli/fire_opts.rs b/src/cli/fire_opts.rs index 63160359..cce04c98 100644 --- a/src/cli/fire_opts.rs +++ b/src/cli/fire_opts.rs @@ -56,6 +56,10 @@ pub struct FireOptions { /// Optional path to a FDR table #[clap(long, env)] pub fdr_table: Option, + /// Also emit legacy ns/nl/as/al/aq tags alongside the MA-spec tags + /// (`MA`/`AQ`/`AN`). Default: only MA-spec tags are written. + #[clap(long)] + pub legacy_tags: bool, } impl Default for FireOptions { @@ -76,6 +80,7 @@ impl Default for FireOptions { min_msp_length_for_positive_fire_call: 85, model: None, fdr_table: None, + legacy_tags: false, } } } diff --git a/src/cli/nucleosome_opts.rs b/src/cli/nucleosome_opts.rs index 8cb9e2fc..9d342470 100644 --- a/src/cli/nucleosome_opts.rs +++ b/src/cli/nucleosome_opts.rs @@ -48,4 +48,8 @@ pub struct AddNucleosomeOptions { pub out: String, #[clap(flatten)] pub nuc: NucleosomeParameters, + /// Also emit legacy ns/nl/as/al/aq tags alongside the MA-spec tags + /// (`MA`/`AQ`/`AN`). Default: only MA-spec tags are written. + #[clap(long)] + pub legacy_tags: bool, } diff --git a/src/cli/predict_opts.rs b/src/cli/predict_opts.rs index eaf00683..81e52bec 100644 --- a/src/cli/predict_opts.rs +++ b/src/cli/predict_opts.rs @@ -29,6 +29,10 @@ pub struct PredictM6AOptions { /// Skip the actual prediction step to allow for testing the speed of other parts of the code #[clap(long, help_heading = "Developer-Options", hide = true)] pub fake: bool, + /// Also emit legacy ns/nl/as/al/aq tags alongside the MA-spec tags + /// (`MA`/`AQ`/`AN`). Default: only MA-spec tags are written. + #[clap(long)] + pub legacy_tags: bool, } impl std::default::Default for PredictM6AOptions { @@ -42,6 +46,7 @@ impl std::default::Default for PredictM6AOptions { all_calls: false, batch_size: 1, fake: false, + legacy_tags: false, } } } diff --git a/src/fiber.rs b/src/fiber.rs index 5f74a1de..f5d81627 100644 --- a/src/fiber.rs +++ b/src/fiber.rs @@ -37,13 +37,13 @@ impl FiberseqData { } .to_string(); - let nuc_starts = get_u32_tag(&record, b"ns"); - let msp_starts = get_u32_tag(&record, b"as"); - let nuc_length = get_u32_tag(&record, b"nl"); - let msp_length = get_u32_tag(&record, b"al"); + let (nuc_starts, nuc_length, msp_starts, msp_length, msp_qual) = + crate::utils::ma_io::extract_nuc_msp_arrays(&record).unwrap_or_else(|e| { + log::warn!("Failed to read annotations: {e}"); + Default::default() + }); let nuc = Ranges::new(&record, nuc_starts, None, Some(nuc_length)); let mut msp = Ranges::new(&record, msp_starts, None, Some(msp_length)); - let msp_qual = get_u8_tag(&record, b"aq"); if !msp_qual.is_empty() { msp.set_qual(msp_qual); } diff --git a/src/subcommands/add_nucleosomes.rs b/src/subcommands/add_nucleosomes.rs index 66a4e6d2..5219bdec 100644 --- a/src/subcommands/add_nucleosomes.rs +++ b/src/subcommands/add_nucleosomes.rs @@ -22,7 +22,7 @@ pub fn add_nucleosomes_to_bam(nuc_opts: &mut AddNucleosomeOptions) { let fd = FiberseqData::new(record.clone(), None, &nuc_opts.input.filters); //let m6a = fd.base_mods.forward_m6a(); let m6a = fd.m6a.forward_starts(); - add_nucleosomes_to_record(record, &m6a, &nuc_opts.nuc); + add_nucleosomes_to_record(record, &m6a, &nuc_opts.nuc, nuc_opts.legacy_tags); record }) .collect(); diff --git a/src/subcommands/fire.rs b/src/subcommands/fire.rs index 99aab79c..b4b188bc 100644 --- a/src/subcommands/fire.rs +++ b/src/subcommands/fire.rs @@ -1,10 +1,9 @@ use super::decorator::get_fire_color; use crate::cli::FireOptions; use crate::fiber::FiberseqData; -use crate::utils::bio_io; +use crate::utils::{bio_io, ma_io}; use crate::*; use anyhow; -use bam::record::{Aux, AuxArray}; use gbdt::gradient_boost::GBDT; use itertools::Itertools; use rayon::prelude::*; @@ -15,18 +14,40 @@ pub fn add_fire_to_rec( fire_opts: &FireOptions, model: &GBDT, precision_table: &MapPrecisionValues, + legacy: bool, ) { let fire_feats = FireFeats::new(rec, fire_opts); let mut precisions = fire_feats.predict_with_xgb(model, precision_table); + // FIRE produces precisions in MSP-iteration (BAM) order. Convert to + // molecular orientation so they pair with the molecular-ordered MSP + // coords that go into the MA tag. if rec.record.is_reverse() { precisions.reverse(); } - let aux_array: AuxArray = (&precisions).into(); - let aux_array_field = Aux::ArrayU8(aux_array); - rec.record.remove_aux(b"aq").unwrap_or(()); // remove any existing ML field - rec.record - .push_aux(b"aq", aux_array_field) - .expect("Cannot add FIRE precision to bam"); + + let mut annot = match ma_io::read_annotations(&rec.record) { + Ok(a) => a, + Err(e) => { log::warn!("FIRE: failed to read annotations: {e}"); return; } + }; + + let Some(msp) = annot.get_type(ma_io::MSP_TYPE) else { + log::warn!("FIRE: no msp annotations on record; skipping"); + return; + }; + if msp.annotations.len() != precisions.len() { + log::warn!( + "FIRE precision count ({}) does not match MSP count ({}); skipping", + precisions.len(), msp.annotations.len(), + ); + return; + } + + let starts: Vec = msp.annotations.iter().map(|a| a.start).collect(); + let lens: Vec = msp.annotations.iter().map(|a| a.length).collect(); + ma_io::add_fire_annotations(&mut annot, &starts, &lens, &precisions); + + ma_io::write_annotations(&mut rec.record, &annot, legacy); + log::trace!("precisions: {precisions:?}"); } @@ -65,7 +86,13 @@ pub fn add_fire_to_bam(fire_opts: &mut FireOptions) -> Result<(), anyhow::Error> for recs in &fibers.chunks(2_000) { let mut recs: Vec = recs.collect(); recs.par_iter_mut().for_each(|r| { - add_fire_to_rec(r, fire_opts, &model, &precision_table); + add_fire_to_rec( + r, + fire_opts, + &model, + &precision_table, + fire_opts.legacy_tags, + ); }); for rec in recs { out.write(&rec.record)?; diff --git a/src/subcommands/mock_fire.rs b/src/subcommands/mock_fire.rs index af14512c..1ef9e099 100644 --- a/src/subcommands/mock_fire.rs +++ b/src/subcommands/mock_fire.rs @@ -1,8 +1,10 @@ use crate::cli::MockFireOptions; use crate::utils::bio_io::{self, read_bed_regions, BedRecord}; +use crate::utils::ma_io; use anyhow::{Context, Result}; +use molecular_annotation::MolecularAnnotations; use rust_htslib::bam::header::HeaderRecord; -use rust_htslib::bam::record::{Aux, Cigar, CigarString}; +use rust_htslib::bam::record::{Cigar, CigarString}; use rust_htslib::bam::{Header, HeaderView, Record}; use std::collections::HashMap; @@ -120,20 +122,11 @@ fn create_mock_fire_record( quals.push(quality); } - // Add the MSP start positions (as tag) - record - .push_aux(b"as", Aux::ArrayU32((&starts).into())) - .context("Failed to add 'as' tag (MSP starts)")?; - - // Add the MSP lengths (al tag) - record - .push_aux(b"al", Aux::ArrayU32((&lengths).into())) - .context("Failed to add 'al' tag (MSP lengths)")?; - - // Add the FIRE quality scores (aq tag) - this is what makes them FIRE elements - record - .push_aux(b"aq", Aux::ArrayU8((&quals).into())) - .context("Failed to add 'aq' tag (FIRE quality scores)")?; + // Build MA-spec annotations and emit. Mock FIRE only produces MSPs with + // the FIRE precision (Q-scaled) quality; no nucleosomes are populated. + let mut annot = MolecularAnnotations::from_record(&record); + ma_io::add_fire_annotations(&mut annot, &starts, &lengths, &quals); + ma_io::write_annotations(&mut record, &annot, false); Ok(record) } diff --git a/src/subcommands/predict_m6a.rs b/src/subcommands/predict_m6a.rs index 4360518c..aa63996b 100644 --- a/src/subcommands/predict_m6a.rs +++ b/src/subcommands/predict_m6a.rs @@ -47,12 +47,14 @@ where pub nuc_opts: cli::NucleosomeParameters, pub burn_models: m6a_burn::BurnModels, pub fake: bool, + pub legacy_tags: bool, } impl PredictOptions where B: Backend, { + #[allow(clippy::too_many_arguments)] #[allow(clippy::too_many_arguments)] pub fn new( keep: bool, @@ -62,6 +64,7 @@ where batch_size: usize, nuc_opts: cli::NucleosomeParameters, fake: bool, + legacy_tags: bool, ) -> Self { // set up a precision table let mut map = BTreeMap::new(); @@ -80,6 +83,7 @@ where nuc_opts, burn_models: m6a_burn::BurnModels::new(&polymerase), fake, + legacy_tags, }; options.add_model().expect("Error loading model"); options @@ -247,7 +251,12 @@ where let modified_bases_forward = cur_basemods.m6a().forward_starts(); // adding the nucleosomes - nucleosome::add_nucleosomes_to_record(record, &modified_bases_forward, &opts.nuc_opts); + nucleosome::add_nucleosomes_to_record( + record, + &modified_bases_forward, + &opts.nuc_opts, + opts.legacy_tags, + ); // clear the existing data if !opts.keep { @@ -517,6 +526,7 @@ pub fn read_bam_into_fiberdata(opts: &mut PredictM6AOptions) { opts.batch_size, opts.nuc.clone(), opts.fake, + opts.legacy_tags, ); // get default fire options let fire_opts = crate::cli::FireOptions::default(); @@ -541,6 +551,7 @@ pub fn read_bam_into_fiberdata(opts: &mut PredictM6AOptions) { predict_options.batch_size, predict_options.nuc_opts.clone(), predict_options.fake, + predict_options.legacy_tags, ); PredictOptions::predict_m6a_on_records(&thread_opts, records) }) @@ -555,7 +566,13 @@ pub fn read_bam_into_fiberdata(opts: &mut PredictM6AOptions) { let mut fd_recs = FiberseqData::from_records(chunk, &opts.input.header_view(), &opts.input.filters); fd_recs.par_iter_mut().for_each(|fd| { - crate::subcommands::fire::add_fire_to_rec(fd, &fire_opts, &model, &precision_table); + crate::subcommands::fire::add_fire_to_rec( + fd, + &fire_opts, + &model, + &precision_table, + opts.legacy_tags, + ); }); // write to output diff --git a/src/utils.rs b/src/utils.rs index 3efb17b6..6f35b107 100644 --- a/src/utils.rs +++ b/src/utils.rs @@ -6,6 +6,7 @@ pub mod bio_io; pub mod fibertig; pub mod fire; pub mod input_bam; +pub mod ma_io; pub mod nucleosome; pub mod panspec; // test modules for expressions diff --git a/src/utils/basemods.rs b/src/utils/basemods.rs index 07ab0476..3bdc0395 100644 --- a/src/utils/basemods.rs +++ b/src/utils/basemods.rs @@ -11,6 +11,13 @@ use std::collections::HashMap; use std::convert::TryFrom; +/// A group of base modification calls of one (base, strand, modification_type) +/// triple — for example, "all m6A calls on adenines on the forward strand." +/// +/// Per-call positions and qualities live in `ranges`. This reuses the +/// `Ranges`/`FiberAnnotations` infrastructure (rather than a separate type) +/// to share the position-flipping, quality-filtering, and reference-liftover +/// logic. Each call is stored as a 1bp range; the `length` field is always 1. #[derive(Eq, PartialEq, Debug, PartialOrd, Ord, Clone)] pub struct BaseMod { pub modified_base: u8, diff --git a/src/utils/ma_io.rs b/src/utils/ma_io.rs index 107935d6..fe292d73 100644 --- a/src/utils/ma_io.rs +++ b/src/utils/ma_io.rs @@ -132,9 +132,18 @@ fn read_legacy_nuc_msp(record: &bam::Record) -> Result { /// Write annotations to a BAM record. /// /// Always emits the MA-spec tags. When `legacy` is set, also emits the -/// fibertools-rs legacy `ns`/`nl`/`as`/`al`/`aq` tags for `nuc` and `msp` -/// annotation types. When not set, any pre-existing legacy tags are stripped -/// so the output is MA-only. +/// fibertools-rs legacy `ns`/`nl`/`as`/`al`/`aq` tags so pre-MA consumers +/// (older pyft, IGV decorators) keep working during the migration. +/// +/// The legacy mapping: +/// - `nuc` → `ns`/`nl` +/// - `msp` → `as`/`al` +/// - `fire` → `aq` (paired with the `as`/`al` from `msp`, since pre-MA +/// fibertools stored FIRE precisions as MSP qualities). When no `fire` +/// type is present, `aq` falls back to `msp`'s own quality if it has one. +/// +/// When `legacy` is not set, any pre-existing legacy tags are stripped so +/// the output is MA-only. pub fn write_annotations(record: &mut bam::Record, annot: &MolecularAnnotations, legacy: bool) { for tag in LEGACY_NUC_MSP_TAGS { record.remove_aux(tag).ok(); @@ -149,14 +158,45 @@ fn write_legacy_nuc_msp(record: &mut bam::Record, annot: &MolecularAnnotations) if let Some(nuc) = annot.get_type(NUC_TYPE) { push_starts_lens(record, b"ns", b"nl", &nuc.annotations); } + + // Legacy convention: pre-MA fibertools wrote FIRE precisions onto the + // MSP `aq` tag — there was no separate FIRE tag. So legacy MSP output + // takes coords from MSP and quality from FIRE when FIRE is present; + // otherwise it falls back to MSP's own quality (when present), or no + // `aq` at all (pre-FIRE state). if let Some(msp) = annot.get_type(MSP_TYPE) { push_starts_lens(record, b"as", b"al", &msp.annotations); - if msp.quality_spec.num_qualities() == 1 && msp.quality_spec.has_quality() { - let aq: Vec = msp - .annotations - .iter() - .map(|a| a.qualities.first().copied().unwrap_or(0)) - .collect(); + + let aq: Option> = if let Some(fire) = annot.get_type(FIRE_TYPE) { + // Sanity: legacy convention assumes FIRE coords mirror MSP coords. + // If they don't, the `aq` array we emit won't align with `as`/`al`. + debug_assert_eq!( + fire.annotations.len(), + msp.annotations.len(), + "legacy aq emission requires fire and msp to have matching counts" + ); + if fire.annotations.len() == msp.annotations.len() { + Some( + fire.annotations + .iter() + .map(|a| a.qualities.first().copied().unwrap_or(0)) + .collect(), + ) + } else { + None + } + } else if msp.quality_spec.num_qualities() == 1 && msp.quality_spec.has_quality() { + Some( + msp.annotations + .iter() + .map(|a| a.qualities.first().copied().unwrap_or(0)) + .collect(), + ) + } else { + None + }; + + if let Some(aq) = aq { if !aq.is_empty() { record.push_aux(b"aq", Aux::ArrayU8((&aq).into())).ok(); } @@ -223,14 +263,68 @@ pub fn extract_nuc_msp_arrays( Ok((nuc_starts, nuc_lengths, msp_starts, msp_lengths, msp_qual)) } -/// Build a [`MolecularAnnotations`] for nuc/msp/fire types from raw arrays in -/// molecular orientation. Each input is optional; passing `None` skips that -/// type. Coordinates and lengths are paired positionally. +/// Add `nuc` annotations (forward strand, no quality) to `annot`. +/// +/// No-op if `starts` is empty. `starts` and `lens` must be the same length +/// and paired positionally. +pub fn add_nuc_annotations( + annot: &mut MolecularAnnotations, + starts: &[u32], + lens: &[u32], +) { + if starts.is_empty() { + return; + } + let t = annot.add_annotation_type(NUC_TYPE, QualitySpec::none()); + for (s, l) in starts.iter().zip(lens.iter()) { + t.add(*s, *l, Strand::Forward, vec![], None); + } +} + +/// Add `msp` annotations (forward strand) to `annot`. +/// +/// With `qualities` present, the type uses `msp+Q`; without, `msp+` (no +/// quality). No-op if `starts` is empty. All input slices must be the same +/// length and paired positionally. +pub fn add_msp_annotations( + annot: &mut MolecularAnnotations, + starts: &[u32], + lens: &[u32], + qualities: Option<&[u8]>, +) { + if starts.is_empty() { + return; + } + let qspec = match qualities { + Some(_) => "Q".parse::().expect("Q parses"), + None => QualitySpec::none(), + }; + let t = annot.add_annotation_type(MSP_TYPE, qspec); + for (i, (s, l)) in starts.iter().zip(lens.iter()).enumerate() { + let qv = qualities.map(|q| vec![q[i]]).unwrap_or_default(); + t.add(*s, *l, Strand::Forward, qv, None); + } +} + +/// Add `fire` annotations (forward strand, phred quality) to `annot`. /// -/// - `nuc`: `(starts, lengths)` — no quality. -/// - `msp`: `(starts, lengths, optional Q-scaled qualities)`. With qualities -/// present, the type uses `msp+Q`; without, `msp+` (no quality). -/// - `fire`: `(starts, lengths, phred-scaled qualities)`. Always `fire+P`. +/// No-op if `starts` is empty. All input slices must be the same length and +/// paired positionally. +pub fn add_fire_annotations( + annot: &mut MolecularAnnotations, + starts: &[u32], + lens: &[u32], + phred: &[u8], +) { + if starts.is_empty() { + return; + } + let t = annot.add_annotation_type(FIRE_TYPE, "P".parse::().expect("P parses")); + for (i, (s, l)) in starts.iter().zip(lens.iter()).enumerate() { + t.add(*s, *l, Strand::Forward, vec![phred[i]], None); + } +} + pub fn build_annotations( record: &bam::Record, nuc: Option<(&[u32], &[u32])>, @@ -239,34 +333,13 @@ pub fn build_annotations( ) -> MolecularAnnotations { let mut annot = MolecularAnnotations::from_record(record); if let Some((starts, lens)) = nuc { - if !starts.is_empty() { - let t = annot.add_annotation_type(NUC_TYPE, QualitySpec::none()); - for (s, l) in starts.iter().zip(lens.iter()) { - t.add(*s, *l, Strand::Forward, vec![], None); - } - } + add_nuc_annotations(&mut annot, starts, lens); } if let Some((starts, lens, q)) = msp { - if !starts.is_empty() { - let qspec = match q { - Some(_) => "Q".parse::().expect("Q parses"), - None => QualitySpec::none(), - }; - let t = annot.add_annotation_type(MSP_TYPE, qspec); - for (i, (s, l)) in starts.iter().zip(lens.iter()).enumerate() { - let qv = q.map(|q| vec![q[i]]).unwrap_or_default(); - t.add(*s, *l, Strand::Forward, qv, None); - } - } + add_msp_annotations(&mut annot, starts, lens, q); } if let Some((starts, lens, phred)) = fire { - if !starts.is_empty() { - let t = - annot.add_annotation_type(FIRE_TYPE, "P".parse::().expect("P parses")); - for (i, (s, l)) in starts.iter().zip(lens.iter()).enumerate() { - t.add(*s, *l, Strand::Forward, vec![phred[i]], None); - } - } + add_fire_annotations(&mut annot, starts, lens, phred); } annot } diff --git a/src/utils/nucleosome.rs b/src/utils/nucleosome.rs index e9b59914..9bbb92a6 100644 --- a/src/utils/nucleosome.rs +++ b/src/utils/nucleosome.rs @@ -1,8 +1,7 @@ use crate::cli::NucleosomeParameters; -use rust_htslib::{ - bam, - bam::record::{Aux, AuxArray}, -}; +use crate::utils::ma_io; +use molecular_annotation::MolecularAnnotations; +use rust_htslib::bam; pub fn find_nucleosomes(m6a: &[i64], options: &NucleosomeParameters) -> Vec<(i64, i64)> { let mut nucs = vec![]; @@ -189,13 +188,8 @@ pub fn add_nucleosomes_to_record( record: &mut bam::Record, m6a: &[i64], options: &NucleosomeParameters, + legacy: bool, ) { - record.remove_aux(b"ns").unwrap_or(()); - record.remove_aux(b"nl").unwrap_or(()); - record.remove_aux(b"as").unwrap_or(()); - record.remove_aux(b"al").unwrap_or(()); - record.remove_aux(b"aq").unwrap_or(()); - let nucs = if options.allowed_m6a_skips < 0 { find_nucleosomes(m6a, options) } else { @@ -205,18 +199,10 @@ pub fn add_nucleosomes_to_record( let (nuc_starts, nuc_lengths) = filter_for_end(record, &nucs, options.distance_from_end); let (msp_starts, msp_lengths) = filter_for_end(record, &msps, options.distance_from_end); - for (&tag, array) in - [b"ns", b"nl", b"as", b"al"] - .iter() - .zip([nuc_starts, nuc_lengths, msp_starts, msp_lengths]) - { - if array.is_empty() { - continue; - } - let aux_array: AuxArray = (&array).into(); - let aux_array_field = Aux::ArrayU32(aux_array); - record.push_aux(tag, aux_array_field).unwrap(); - } + let mut annot = MolecularAnnotations::from_record(record); + ma_io::add_nuc_annotations(&mut annot, &nuc_starts, &nuc_lengths); + ma_io::add_msp_annotations(&mut annot, &msp_starts, &msp_lengths, None); + ma_io::write_annotations(record, &annot, legacy); } #[cfg(test)] From 390150be87b8272052ecc664dc67ce667f5e12ff Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Mon, 11 May 2026 17:08:00 -0600 Subject: [PATCH 05/24] fix: faithful range lengths at indel boundaries Adopt MA spec's inward liftover semantics for query-space ranges. Legacy liftover_closest used inclusive endpoint matching (q_pos <= q_en), which mapped positions at block ends back into the previous block, over-extending ranges across deletions by 1bp. Inward semantics treat blocks as half-open, so a query position at the edge of a deletion lifts to the next aligned reference base. Nucleosome and MSP lengths now match the read's actual aligned footprint. Snapshot regenerated. --- src/utils/bamannotations.rs | 44 +++++++++++++------ .../regression__extract__extract_nuc.snap | 6 +-- .../regression__pileup__pileup_default.snap | 12 +++-- .../regression__pileup__pileup_m6a.snap | 12 +++-- .../regression__pileup__pileup_no_msp.snap | 15 ++++--- 5 files changed, 58 insertions(+), 31 deletions(-) diff --git a/src/utils/bamannotations.rs b/src/utils/bamannotations.rs index c154bfd1..43bbdaec 100644 --- a/src/utils/bamannotations.rs +++ b/src/utils/bamannotations.rs @@ -111,20 +111,38 @@ impl FiberAnnotations { .collect::>(); let (reference_starts, reference_ends, reference_lengths) = if single_bp_liftover { - lift_query_range_exact(record, &starts, &starts) + lift_query_range_exact(record, &starts, &starts).unwrap_or_else(|e| { + log::error!( + "Failed lifting over annotations in BAM record: {} aligned from {} to {}.", + String::from_utf8_lossy(record.qname()), + record.reference_start() + 1, + record.reference_end() + ); + log::error!("Failed to lift query range: {}", e); + panic!("Failed to lift query range: {}", e); + }) } else { - lift_query_range(record, &starts, &ends) - } - .unwrap_or_else(|e| { - log::error!( - "Failed lifting over annotations in BAM record: {} aligned from {} to {}.", - String::from_utf8_lossy(record.qname()), - record.reference_start() + 1, - record.reference_end() - ); - log::error!("Failed to lift query range: {}", e); - panic!("Failed to lift query range: {}", e); - }); + // MA spec inward semantics for multi-bp query-space ranges. + // Half-open block matching; endpoints in indel gaps snap inward + // toward the aligned region rather than to the nearer block edge. + let blocks = molecular_annotation::AlignedBlocks::from_record(record); + let mut rs_vec: Vec> = Vec::with_capacity(starts.len()); + let mut re_vec: Vec> = Vec::with_capacity(starts.len()); + let mut rl_vec: Vec> = Vec::with_capacity(starts.len()); + for (&s, &e) in starts.iter().zip(ends.iter()) { + let (rs, re) = blocks.lift_to_reference(s as u32, e as u32); + let rs = rs.map(|x| x as i64); + let re = re.map(|x| x as i64); + let rl = match (rs, re) { + (Some(s), Some(e)) => Some(e - s), + _ => None, + }; + rs_vec.push(rs); + re_vec.push(re); + rl_vec.push(rl); + } + (rs_vec, re_vec, rl_vec) + }; // Normalize extras into a Vec matching the other parallel vectors so // it can be zipped in and move with the annotation through the sort. diff --git a/tests/regression/snapshots/regression__extract__extract_nuc.snap b/tests/regression/snapshots/regression__extract__extract_nuc.snap index 6832ac88..88ae14de 100644 --- a/tests/regression/snapshots/regression__extract__extract_nuc.snap +++ b/tests/regression/snapshots/regression__extract__extract_nuc.snap @@ -5,12 +5,12 @@ expression: "select_bed12_cols(&out, BED12_COLS)" chrom start end name strand block_count block_sizes block_starts ptg000001l 306 15696 m54329U_210323_190418/5048829/ccs - 78 0,127,118,116,121,135,111,84,98,114,102,106,127,83,98,115,113,121,114,87,137,121,100,157,137,99,150,145,114,129,107,127,125,117,128,145,131,108,97,142,99,118,180,128,116,123,132,118,124,125,135,121,156,116,147,124,152,145,120,150,115,105,111,117,123,112,153,136,122,125,118,118,81,122,102,139,119,1 0,184,391,621,880,1058,1236,1511,1679,1871,2060,2246,2442,2674,2798,3032,3209,3437,3634,4028,4187,4350,4548,4923,5157,5352,5493,5680,5876,6035,6253,6473,6638,6873,7011,7192,7354,7521,7718,7946,8385,8547,8686,8912,9106,9251,9420,9637,9840,10016,10192,10397,10547,10778,10926,11097,11262,11425,11649,11770,11976,12182,12385,12537,12742,12952,13106,13260,13446,13703,13907,14110,14334,14479,14704,14918,15082,15389 ptg000001l 832 21833 m54329U_210323_190418/141691444/ccs + 85 0,174,181,275,86,194,156,188,195,161,352,164,160,101,80,320,143,202,155,233,157,176,158,552,178,164,167,78,90,556,678,307,497,145,150,345,155,169,180,158,139,252,159,530,78,307,501,185,183,159,387,177,307,184,178,171,375,164,157,169,177,166,107,417,488,162,371,162,170,159,142,191,399,320,178,188,146,158,329,157,153,108,246,688,1 0,154,329,531,807,908,1123,1282,1477,1687,1849,2249,2414,2593,2700,2816,3190,3334,3550,3709,3979,4151,4354,4533,5096,5304,5507,5681,5760,5868,6431,7140,7480,8010,8156,8362,8708,8884,9064,9280,9439,9583,9850,10017,10558,10637,10945,11447,11656,11879,12062,12473,12651,13004,13199,13393,13608,14010,14178,14392,14616,14806,15071,15202,15626,16150,16365,16737,16937,17108,17302,17478,17683,18083,18413,18619,18808,18955,19171,19504,19672,19833,19942,20189,21000 -ptg000001l 6745 20968 m54329U_210323_190418/175376495/ccs - 72 0,141,119,153,141,147,138,117,146,157,145,164,148,142,132,114,95,105,123,146,144,146,148,311,128,117,138,177,143,131,147,157,136,174,169,143,118,135,157,293,90,142,141,137,162,152,135,151,141,141,167,140,154,203,136,157,160,121,138,153,146,115,146,125,117,123,137,156,163,144,191,1 0,162,353,525,722,899,1066,1259,1480,1657,1879,2062,2236,2428,2619,2845,3020,3237,3475,3617,3795,3992,4221,4370,4745,4970,5147,5335,5580,5749,5946,6122,6348,6513,6718,6903,7099,7292,7482,7700,8110,8280,8466,8668,8857,9049,9268,9428,9639,9836,10036,10241,10439,10594,10853,11024,11218,11424,11591,11771,11981,12223,12399,12596,12780,13006,13200,13361,13568,13812,13968,14222 +ptg000001l 6745 20968 m54329U_210323_190418/175376495/ccs - 72 0,141,119,153,141,147,138,117,146,156,145,164,148,142,132,114,95,105,123,146,144,146,148,311,128,117,138,177,143,131,147,157,136,174,169,143,117,135,157,293,90,142,141,137,162,152,135,151,141,141,167,140,154,203,136,157,160,121,138,153,146,115,146,125,117,123,137,156,163,144,191,1 0,162,353,525,722,899,1066,1259,1480,1658,1879,2062,2236,2428,2619,2845,3020,3237,3475,3617,3795,3992,4221,4370,4745,4970,5147,5335,5580,5749,5946,6122,6348,6513,6718,6903,7100,7292,7482,7700,8110,8280,8466,8668,8857,9049,9268,9428,9639,9836,10036,10241,10439,10594,10853,11024,11218,11424,11591,11771,11981,12223,12399,12596,12780,13006,13200,13361,13568,13812,13968,14222 ptg000001l 13560 36197 m54329U_210323_190418/32113767/ccs - 115 0,169,139,115,117,135,130,111,109,84,136,139,107,119,127,164,145,144,133,303,130,156,155,145,131,119,117,136,145,121,115,129,130,104,160,143,162,143,147,138,167,157,131,166,136,133,160,136,162,170,129,108,86,127,164,136,109,117,94,131,125,130,159,164,90,118,150,154,145,159,134,146,106,122,132,140,162,150,116,147,138,169,113,146,137,118,89,114,135,129,147,171,137,152,128,124,147,142,142,139,147,177,161,133,146,140,146,166,114,148,175,140,157,146,1 0,190,360,563,759,963,1111,1335,1498,1608,1735,1895,2097,2305,2474,2613,2822,2983,3204,3387,3814,4009,4209,4388,4567,4792,5024,5218,5427,5655,5876,6048,6291,6479,6661,6853,7031,7227,7427,7636,7806,7992,8188,8356,8561,8751,8923,9143,9288,9455,9626,9921,10110,10242,10389,10611,10995,11218,11425,11660,11851,12074,12219,12406,12621,12820,12989,13170,13362,13585,13772,13933,14173,14370,14542,14752,14899,15114,15319,15548,15766,15958,16178,16364,16553,16798,17012,17193,17454,17657,17854,18010,18225,18423,18599,18834,19024,19238,19452,19634,19835,19988,20166,20432,20616,20845,21064,21220,21502,21666,21829,22069,22231,22412,22636 -ptg000001l 14275 40558 m54329U_210323_190418/66718332/ccs + 141 0,335,132,129,156,178,143,145,81,352,165,136,132,348,107,92,139,176,150,131,147,129,155,85,77,100,152,148,128,129,164,163,126,166,138,184,114,233,136,140,152,182,175,111,253,148,84,122,162,150,151,109,134,186,169,137,165,132,122,127,90,158,153,140,164,144,137,160,116,147,134,167,129,120,127,228,128,133,157,171,167,153,156,100,156,151,162,157,172,172,133,135,148,105,102,142,155,96,139,188,149,130,156,162,129,109,205,126,144,145,170,127,137,132,146,154,171,163,150,134,152,136,115,110,127,142,171,169,167,154,166,156,138,89,94,155,208,128,169,159,1 0,117,533,711,874,1061,1246,1412,1696,1787,2140,2306,2472,2700,3049,3242,3378,3541,3730,3897,4105,4266,4436,4683,4837,4915,5023,5200,5406,5579,5764,5935,6140,6314,6506,6645,6861,7057,7343,7527,7689,7853,8040,8222,8334,8591,8796,8944,9106,9272,9447,9687,9800,9978,10167,10392,10567,10767,10978,11179,11393,11508,11689,11911,12055,12248,12415,12576,12783,12969,13139,13290,13511,13687,13867,14037,14357,14521,14668,14828,15022,15213,15378,15602,15777,15991,16160,16329,16543,16734,16924,17084,17261,17474,17629,17816,17992,18254,18422,18564,18779,18989,19132,19292,19488,19692,19802,20046,20218,20365,20517,20728,20908,21090,21268,21437,21625,21801,21981,22231,22425,22635,22795,23030,23186,23409,23571,23776,24141,24356,24541,24708,24920,25059,25149,25288,25444,25696,25854,26024,26282 +ptg000001l 14275 40558 m54329U_210323_190418/66718332/ccs + 141 0,335,132,129,156,178,143,145,81,352,165,136,132,348,107,92,139,176,150,131,147,129,155,85,77,100,152,148,128,129,164,163,126,166,138,184,114,233,136,140,152,182,175,111,253,148,84,122,162,150,151,109,134,186,169,137,165,132,122,127,90,158,153,140,164,144,137,160,116,147,134,167,129,120,127,228,128,133,157,171,167,153,156,99,156,151,162,157,172,172,133,135,148,105,102,142,155,96,139,188,149,130,156,162,129,109,205,126,144,145,170,127,137,132,146,154,171,163,150,134,152,136,115,110,127,142,171,169,167,154,166,156,138,89,94,155,208,128,169,159,1 0,117,533,711,874,1061,1246,1412,1696,1787,2140,2306,2472,2700,3049,3242,3378,3541,3730,3897,4105,4266,4436,4683,4837,4915,5023,5200,5406,5579,5764,5935,6140,6314,6506,6645,6861,7057,7343,7527,7689,7853,8040,8222,8334,8591,8796,8944,9106,9272,9447,9687,9800,9978,10167,10392,10567,10767,10978,11179,11393,11508,11689,11911,12055,12248,12415,12576,12783,12969,13139,13290,13511,13687,13867,14037,14357,14521,14668,14828,15022,15213,15378,15603,15777,15991,16160,16329,16543,16734,16924,17084,17261,17474,17629,17816,17992,18254,18422,18564,18779,18989,19132,19292,19488,19692,19802,20046,20218,20365,20517,20728,20908,21090,21268,21437,21625,21801,21981,22231,22425,22635,22795,23030,23186,23409,23571,23776,24141,24356,24541,24708,24920,25059,25149,25288,25444,25696,25854,26024,26282 ptg000001l 16029 34725 m54329U_210323_190418/90833781/ccs - 92 0,114,114,136,128,192,141,172,127,129,132,126,113,112,139,109,166,143,125,132,115,159,147,317,208,153,147,157,157,117,147,156,134,269,151,96,168,160,148,152,127,142,120,157,119,110,106,166,172,85,126,112,145,145,151,129,113,148,99,121,161,150,159,110,118,113,130,138,109,147,152,144,126,115,129,215,167,516,150,122,116,138,177,134,138,163,143,154,114,133,118,1 0,151,347,552,747,890,1131,1288,1516,1720,1938,2121,2338,2517,2720,2929,3115,3330,3526,3733,3928,4115,4300,4518,4836,5072,5252,5430,5649,5884,6039,6231,6439,6640,6964,7204,7313,7516,7696,7903,8113,8303,8502,8691,8914,9122,9384,9559,9752,9986,10157,10346,10521,10722,10939,11154,11385,11582,11807,12003,12161,12393,12572,12790,12983,13175,13395,13602,13852,14044,14202,14426,14607,14805,15009,15139,15365,15573,16107,16357,16557,16749,16912,17120,17313,17511,17701,17864,18119,18285,18504,18695 ptg000001l 21207 39362 m54329U_210323_190418/114362450/ccs + 100 0,169,118,122,97,112,136,148,137,148,176,149,170,186,124,162,150,131,143,125,123,104,101,98,137,140,144,159,124,93,122,127,121,146,116,122,122,114,121,122,120,110,113,141,114,132,113,89,140,117,120,119,125,144,141,132,140,143,136,131,106,151,125,169,122,121,124,128,142,139,126,171,111,134,131,161,130,151,121,110,129,138,137,109,94,129,132,240,124,153,117,155,141,159,102,118,109,127,118,1 0,48,226,411,599,782,967,1174,1355,1511,1681,1874,2024,2204,2393,2518,2683,2868,3006,3169,3348,3537,3756,3932,4118,4324,4486,4686,4906,5098,5298,5512,5705,5887,6065,6281,6465,6669,7047,7234,7433,7612,7780,7932,8152,8318,8496,8692,8868,9068,9270,9436,9617,9754,9963,10120,10314,10483,10694,10834,11036,11211,11402,11528,11716,11883,12034,12200,12365,12546,12714,12884,13086,13244,13429,13574,13782,13960,14158,14348,14529,14693,14875,15054,15258,15410,15603,15803,16089,16277,16484,16654,16840,17019,17235,17404,17593,17747,17954,18154 -ptg000001l 23691 44729 m54329U_210323_190418/85459034/ccs + 104 0,148,132,120,126,136,153,111,134,109,136,175,104,86,117,125,119,124,100,83,128,122,117,108,129,135,146,129,151,118,100,130,139,122,103,91,75,135,125,142,154,116,125,99,160,279,173,108,139,137,134,247,110,136,127,149,147,116,124,140,138,170,145,123,147,107,110,117,146,87,146,140,146,141,169,154,134,128,135,124,121,163,98,129,107,260,94,102,142,145,144,149,110,113,138,120,135,140,153,126,148,136,107,1 0,82,290,495,674,837,1079,1277,1510,1738,1933,2094,2293,2614,2725,2934,3154,3329,3503,3737,3925,4354,4591,4767,4950,5143,5337,5535,5722,5960,6186,6361,6558,6784,7003,7178,7389,7549,7737,7915,8119,8340,8509,8727,8848,9057,9349,9566,9761,9924,10091,10370,10682,10866,11055,11221,11414,11624,11807,12002,12180,12350,12557,12774,12960,13202,13363,13579,13733,14194,14383,14566,14751,14967,15134,15304,15504,15694,15919,16116,16331,16493,16678,16878,17092,17265,17670,17860,18017,18201,18385,18569,18794,19005,19183,19391,19587,19776,19985,20201,20393,20568,20799,21037 +ptg000001l 23691 44729 m54329U_210323_190418/85459034/ccs + 104 0,148,132,120,126,136,153,111,134,109,136,175,104,86,117,125,119,124,100,83,128,122,117,108,129,135,146,129,151,118,100,130,139,122,103,91,75,135,125,142,154,116,125,99,160,279,173,108,139,137,134,247,110,136,127,149,147,116,124,140,138,170,145,123,146,107,110,117,146,87,146,140,146,141,169,154,134,128,135,124,121,163,98,129,107,260,94,102,142,145,144,149,110,113,138,120,135,140,153,126,148,136,107,1 0,82,290,495,674,837,1079,1277,1510,1738,1933,2094,2293,2614,2725,2934,3154,3329,3503,3737,3925,4354,4591,4767,4950,5143,5337,5535,5722,5960,6186,6361,6558,6784,7003,7178,7389,7549,7737,7915,8119,8340,8509,8727,8848,9057,9349,9566,9761,9924,10091,10370,10682,10866,11055,11221,11414,11624,11807,12002,12180,12350,12557,12774,12961,13202,13363,13579,13733,14194,14383,14566,14751,14967,15134,15304,15504,15694,15919,16116,16331,16493,16678,16878,17092,17265,17670,17860,18017,18201,18385,18569,18794,19005,19183,19391,19587,19776,19985,20201,20393,20568,20799,21037 ptg000001l 25050 34283 m54329U_210323_190418/43059336/ccs + 48 0,120,148,139,172,145,158,153,186,215,160,158,137,119,118,142,159,153,162,165,132,162,198,128,169,157,158,147,170,132,140,149,298,168,142,160,163,134,225,268,161,157,160,129,155,162,177,1 0,203,404,578,783,956,1164,1323,1487,1674,1890,2052,2222,2432,2614,2800,2975,3174,3372,3559,3769,3935,4103,4333,4480,4691,4904,5102,5263,5475,5667,5869,6077,6383,6552,6733,6922,7110,7245,7471,7747,7916,8099,8272,8454,8631,8875,9232 ptg000001l 25868 39722 m54329U_210323_190418/10290844/ccs - 71 0,185,144,164,162,175,128,156,168,126,148,100,135,163,169,142,134,139,144,136,151,88,149,134,139,152,134,155,196,152,171,176,167,144,145,155,125,139,115,131,146,183,150,182,163,190,159,162,135,131,169,103,86,167,128,316,156,152,116,144,140,139,138,139,109,150,132,148,148,173,1 0,98,327,472,669,856,1072,1285,1485,1672,1865,2094,2278,2449,2653,2851,3098,3248,3458,3614,3783,3981,4184,4381,4590,4744,4947,5146,5319,5544,5705,5915,6100,6313,6502,6676,6923,7110,7326,7535,7747,7942,8126,8325,8561,8780,8971,9206,9428,9599,9751,9981,10239,10333,10590,10769,11120,11326,11534,11730,11903,12084,12287,12505,12733,12875,13081,13268,13439,13588,13853 ptg000001l 28298 44111 m54329U_210323_190418/2491749/ccs - 76 0,130,129,106,122,118,100,105,126,99,94,135,134,135,191,147,128,136,105,119,89,115,135,118,134,109,150,118,85,114,79,116,111,92,108,100,126,120,114,127,120,113,122,96,105,109,102,110,112,83,126,114,113,118,130,86,95,121,129,114,103,138,129,106,102,112,109,105,110,149,126,115,130,135,160,1 0,201,427,607,805,981,1144,1355,1777,1977,2179,2331,2511,2705,2889,3108,3331,3487,3677,3869,4065,4303,4480,4668,4827,5044,5206,5439,5623,5834,6192,6473,6710,6885,7091,7267,7493,7663,7878,8060,8212,8486,8718,9114,9343,9501,9675,10068,10259,10678,10818,11062,11247,11417,11595,11787,12063,12206,12391,12559,12759,12964,13131,13334,13538,13742,13910,14095,14282,14451,14627,14889,15057,15310,15480,15812 diff --git a/tests/regression/snapshots/regression__pileup__pileup_default.snap b/tests/regression/snapshots/regression__pileup__pileup_default.snap index 441af8af..81150869 100644 --- a/tests/regression/snapshots/regression__pileup__pileup_default.snap +++ b/tests/regression/snapshots/regression__pileup__pileup_default.snap @@ -164,7 +164,8 @@ ptg000001l 8279 8312 3 0 -1 2 1 ptg000001l 8312 8371 3 0 -1 3 0 ptg000001l 8371 8394 3 0 -1 2 1 ptg000001l 8394 8402 3 0 -1 1 2 -ptg000001l 8402 8559 3 0 -1 2 1 +ptg000001l 8402 8403 3 0 -1 1 1 +ptg000001l 8403 8559 3 0 -1 2 1 ptg000001l 8559 8624 3 0 -1 1 2 ptg000001l 8624 8691 3 0 -1 2 1 ptg000001l 8691 8769 3 0 -1 3 0 @@ -314,7 +315,8 @@ ptg000001l 13752 13790 4 0 -1 4 0 ptg000001l 13790 13791 4 0 -1 3 1 ptg000001l 13791 13836 4 0 -1 2 2 ptg000001l 13836 13844 4 0 -1 3 1 -ptg000001l 13844 13874 4 0 -1 4 0 +ptg000001l 13844 13845 4 0 -1 3 0 +ptg000001l 13845 13874 4 0 -1 4 0 ptg000001l 13874 13919 4 0 -1 3 1 ptg000001l 13919 13920 4 0 -1 2 2 ptg000001l 13920 13962 4 0 -1 3 1 @@ -1128,7 +1130,8 @@ ptg000001l 29809 29816 8 0 -1 3 5 ptg000001l 29816 29849 8 0 -1 2 6 ptg000001l 29849 29851 8 0 -1 3 5 ptg000001l 29851 29877 8 0 -1 2 6 -ptg000001l 29877 29881 8 0 -1 4 4 +ptg000001l 29877 29878 8 0 -1 3 4 +ptg000001l 29878 29881 8 0 -1 4 4 ptg000001l 29881 29898 8 0 -1 5 3 ptg000001l 29898 29899 8 0 -1 4 4 ptg000001l 29899 29924 8 0 -1 5 3 @@ -1614,7 +1617,8 @@ ptg000001l 36617 36630 6 0 -1 4 2 ptg000001l 36630 36637 6 0 -1 3 3 ptg000001l 36637 36640 6 0 -1 4 2 ptg000001l 36640 36651 6 0 -1 3 3 -ptg000001l 36651 36700 6 0 -1 4 2 +ptg000001l 36651 36652 6 0 -1 3 2 +ptg000001l 36652 36700 6 0 -1 4 2 ptg000001l 36700 36732 6 0 -1 5 1 ptg000001l 36732 36746 6 0 -1 4 2 ptg000001l 36746 36784 6 0 -1 3 3 diff --git a/tests/regression/snapshots/regression__pileup__pileup_m6a.snap b/tests/regression/snapshots/regression__pileup__pileup_m6a.snap index cc338e38..383dd06c 100644 --- a/tests/regression/snapshots/regression__pileup__pileup_m6a.snap +++ b/tests/regression/snapshots/regression__pileup__pileup_m6a.snap @@ -1654,7 +1654,8 @@ ptg000001l 8396 8398 3 0 -1 1 2 0 ptg000001l 8398 8399 3 0 -1 1 2 1 ptg000001l 8399 8401 3 0 -1 1 2 0 ptg000001l 8401 8402 3 0 -1 1 2 2 -ptg000001l 8402 8405 3 0 -1 2 1 0 +ptg000001l 8402 8403 3 0 -1 1 1 0 +ptg000001l 8403 8405 3 0 -1 2 1 0 ptg000001l 8405 8406 3 0 -1 2 1 1 ptg000001l 8406 8408 3 0 -1 2 1 0 ptg000001l 8408 8409 3 0 -1 2 1 1 @@ -2857,7 +2858,8 @@ ptg000001l 13833 13835 4 0 -1 2 2 0 ptg000001l 13835 13836 4 0 -1 2 2 2 ptg000001l 13836 13843 4 0 -1 3 1 0 ptg000001l 13843 13844 4 0 -1 3 1 1 -ptg000001l 13844 13874 4 0 -1 4 0 0 +ptg000001l 13844 13845 4 0 -1 3 0 0 +ptg000001l 13845 13874 4 0 -1 4 0 0 ptg000001l 13874 13875 4 0 -1 3 1 1 ptg000001l 13875 13877 4 0 -1 3 1 0 ptg000001l 13877 13878 4 0 -1 3 1 1 @@ -8660,7 +8662,8 @@ ptg000001l 29869 29870 8 0 -1 2 6 0 ptg000001l 29870 29871 8 0 -1 2 6 3 ptg000001l 29871 29876 8 0 -1 2 6 0 ptg000001l 29876 29877 8 0 -1 2 6 6 -ptg000001l 29877 29880 8 0 -1 4 4 0 +ptg000001l 29877 29878 8 0 -1 3 4 0 +ptg000001l 29878 29880 8 0 -1 4 4 0 ptg000001l 29880 29881 8 0 -1 4 4 4 ptg000001l 29881 29884 8 0 -1 5 3 0 ptg000001l 29884 29885 8 0 -1 5 3 3 @@ -11880,7 +11883,8 @@ ptg000001l 36641 36645 6 0 -1 3 3 0 ptg000001l 36645 36646 6 0 -1 3 3 3 ptg000001l 36646 36650 6 0 -1 3 3 0 ptg000001l 36650 36651 6 0 -1 3 3 3 -ptg000001l 36651 36663 6 0 -1 4 2 0 +ptg000001l 36651 36652 6 0 -1 3 2 0 +ptg000001l 36652 36663 6 0 -1 4 2 0 ptg000001l 36663 36665 6 0 -1 4 2 1 ptg000001l 36665 36666 6 0 -1 4 2 0 ptg000001l 36666 36667 6 0 -1 4 2 1 diff --git a/tests/regression/snapshots/regression__pileup__pileup_no_msp.snap b/tests/regression/snapshots/regression__pileup__pileup_no_msp.snap index a09b68bb..dc69473f 100644 --- a/tests/regression/snapshots/regression__pileup__pileup_no_msp.snap +++ b/tests/regression/snapshots/regression__pileup__pileup_no_msp.snap @@ -160,8 +160,8 @@ ptg000001l 8252 8279 3 0 -1 3 ptg000001l 8279 8312 3 0 -1 2 ptg000001l 8312 8371 3 0 -1 3 ptg000001l 8371 8394 3 0 -1 2 -ptg000001l 8394 8402 3 0 -1 1 -ptg000001l 8402 8559 3 0 -1 2 +ptg000001l 8394 8403 3 0 -1 1 +ptg000001l 8403 8559 3 0 -1 2 ptg000001l 8559 8624 3 0 -1 1 ptg000001l 8624 8691 3 0 -1 2 ptg000001l 8691 8769 3 0 -1 3 @@ -309,8 +309,8 @@ ptg000001l 13750 13752 4 0 -1 3 ptg000001l 13752 13790 4 0 -1 4 ptg000001l 13790 13791 4 0 -1 3 ptg000001l 13791 13836 4 0 -1 2 -ptg000001l 13836 13844 4 0 -1 3 -ptg000001l 13844 13874 4 0 -1 4 +ptg000001l 13836 13845 4 0 -1 3 +ptg000001l 13845 13874 4 0 -1 4 ptg000001l 13874 13919 4 0 -1 3 ptg000001l 13919 13920 4 0 -1 2 ptg000001l 13920 13962 4 0 -1 3 @@ -1116,7 +1116,8 @@ ptg000001l 29809 29816 8 0 -1 3 ptg000001l 29816 29849 8 0 -1 2 ptg000001l 29849 29851 8 0 -1 3 ptg000001l 29851 29877 8 0 -1 2 -ptg000001l 29877 29881 8 0 -1 4 +ptg000001l 29877 29878 8 0 -1 3 +ptg000001l 29878 29881 8 0 -1 4 ptg000001l 29881 29898 8 0 -1 5 ptg000001l 29898 29899 8 0 -1 4 ptg000001l 29899 29924 8 0 -1 5 @@ -1599,8 +1600,8 @@ ptg000001l 36588 36617 6 0 -1 2 ptg000001l 36617 36630 6 0 -1 4 ptg000001l 36630 36637 6 0 -1 3 ptg000001l 36637 36640 6 0 -1 4 -ptg000001l 36640 36651 6 0 -1 3 -ptg000001l 36651 36700 6 0 -1 4 +ptg000001l 36640 36652 6 0 -1 3 +ptg000001l 36652 36700 6 0 -1 4 ptg000001l 36700 36732 6 0 -1 5 ptg000001l 36732 36746 6 0 -1 4 ptg000001l 36746 36784 6 0 -1 3 From 72e238e51de510c790878060333ed08f4f2901a2 Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Mon, 11 May 2026 17:29:36 -0600 Subject: [PATCH 06/24] refactor: derive FiberseqData accessors from MolecularAnnotations Replace direct field access (fiber.msp, fiber.nuc, etc.) with method accessors that return AnnotationTypeView<'_> derived from the spec's MolecularAnnotations. read_annotations + BaseMods::populate_ma now populate the spec object at construction with nuc/msp/fire from MA tags and m6a/cpg from ML/MM, so the spec is the source of truth for read-side coordinates. AnnotationTypeView delegates to the library's iter_type / AnnotationInfo for per-annotation iteration and ref-coord lifting, and provides Vec / Vec> column accessors for the legacy column-oriented call sites. No bespoke per-annotation wrapper struct; call sites read AnnotationInfo fields directly. Legacy Ranges fields on FiberseqData are retained for the centering path, which still mutates them; they'll be dropped after centering migrates to the spec's translate. All read-site call sites (decorator, fire, footprint, pileup, qc, validate, utils/fire) updated to call fiber.X() instead of fiber.X. Centering deliberately left on field access. --- src/fiber.rs | 112 ++++++++++++++++---------- src/subcommands/decorator.rs | 16 ++-- src/subcommands/fire.rs | 14 ++-- src/subcommands/footprint.rs | 20 ++--- src/subcommands/pileup.rs | 4 +- src/subcommands/qc.rs | 39 +++++----- src/subcommands/validate.rs | 6 +- src/utils/bamannotations.rs | 147 ++++++++++++++++++++++++++++++++++- src/utils/basemods.rs | 31 ++++++++ src/utils/fire.rs | 20 ++--- src/utils/input_bam.rs | 1 + 11 files changed, 307 insertions(+), 103 deletions(-) diff --git a/src/fiber.rs b/src/fiber.rs index f5d81627..fd3ca53e 100644 --- a/src/fiber.rs +++ b/src/fiber.rs @@ -3,9 +3,11 @@ use super::subcommands::center::CenteredFiberData; use super::utils::input_bam::FiberFilters; use super::*; use crate::utils::bamannotations::*; -use crate::utils::basemods::BaseMods; +use crate::utils::basemods::{BaseMods, CPG_TYPE, M6A_TYPE}; use crate::utils::bio_io::*; use crate::utils::ftexpression::apply_filter_fsd; +use crate::utils::ma_io::{MSP_TYPE, NUC_TYPE}; +use molecular_annotation::MolecularAnnotations; use rayon::prelude::*; use rust_htslib::bam::Read; use rust_htslib::{bam, bam::ext::BamRecordExtensions, bam::record::Aux, bam::HeaderView}; @@ -15,6 +17,7 @@ use std::fmt::Write; #[derive(Debug, Clone, PartialEq)] pub struct FiberseqData { pub record: bam::Record, + pub annotations: MolecularAnnotations, pub msp: Ranges, pub nuc: Ranges, pub m6a: Ranges, @@ -36,7 +39,10 @@ impl FiberseqData { "." } .to_string(); - + let mut annotations = crate::utils::ma_io::read_annotations(&record).unwrap_or_else(|e| { + log::warn!("Failed to read annotations: {e}"); + MolecularAnnotations::from_record(&record) + }); let (nuc_starts, nuc_length, msp_starts, msp_length, msp_qual) = crate::utils::ma_io::extract_nuc_msp_arrays(&record).unwrap_or_else(|e| { log::warn!("Failed to read annotations: {e}"); @@ -64,6 +70,7 @@ impl FiberseqData { // get fiberseq basemods let mut base_mods = BaseMods::new(&record, filters.min_ml_score); base_mods.filter_at_read_ends(filters.strip_starting_basemods); + base_mods.populate_ma(&mut annotations); //let (m6a, cpg) = FiberMods::new(&base_mods); let m6a = base_mods.m6a(); @@ -71,6 +78,7 @@ impl FiberseqData { let mut fsd = FiberseqData { record, + annotations, msp, nuc, m6a, @@ -127,6 +135,26 @@ impl FiberseqData { // GET FUNCTIONS // + /// View over `msp` annotations derived from `self.annotations`. + pub fn msp(&self) -> AnnotationTypeView<'_> { + AnnotationTypeView::new(&self.annotations, MSP_TYPE) + } + + /// View over `nuc` annotations derived from `self.annotations`. + pub fn nuc(&self) -> AnnotationTypeView<'_> { + AnnotationTypeView::new(&self.annotations, NUC_TYPE) + } + + /// View over `m6a` annotations derived from `self.annotations`. + pub fn m6a(&self) -> AnnotationTypeView<'_> { + AnnotationTypeView::new(&self.annotations, M6A_TYPE) + } + + /// View over `cpg` annotations derived from `self.annotations`. + pub fn cpg(&self) -> AnnotationTypeView<'_> { + AnnotationTypeView::new(&self.annotations, CPG_TYPE) + } + pub fn get_qname(&self) -> String { String::from_utf8_lossy(self.record.qname()).to_string() } @@ -176,6 +204,8 @@ impl FiberseqData { /// Validate that all MSP boundaries align with m6A positions after centering fn validate_msp_m6a_alignment(&self) { + // Legacy fields are used here because centering only mutates the + // legacy Ranges (Branch 2 will move centering onto the MA spec). let m6a_positions = self.m6a.starts(); let msp_boundaries: Vec = self .msp @@ -203,54 +233,50 @@ impl FiberseqData { // WRITE BED12 FUNCTIONS // pub fn write_msp(&self, reference: bool) -> String { + let msp = self.msp(); let (starts, _ends, lengths) = if reference { ( - self.msp.reference_starts(), - self.msp.reference_ends(), - self.msp.reference_lengths(), + msp.reference_starts(), + msp.reference_ends(), + msp.reference_lengths(), ) } else { - ( - self.msp.option_starts(), - self.msp.option_ends(), - self.msp.option_lengths(), - ) + (msp.option_starts(), msp.option_ends(), msp.option_lengths()) }; self.to_bed12(reference, &starts, &lengths, LINKER_COLOR) } pub fn write_nuc(&self, reference: bool) -> String { + let nuc = self.nuc(); let (starts, _ends, lengths) = if reference { ( - self.nuc.reference_starts(), - self.nuc.reference_ends(), - self.nuc.reference_lengths(), + nuc.reference_starts(), + nuc.reference_ends(), + nuc.reference_lengths(), ) } else { - ( - self.nuc.option_starts(), - self.nuc.option_ends(), - self.nuc.option_lengths(), - ) + (nuc.option_starts(), nuc.option_ends(), nuc.option_lengths()) }; self.to_bed12(reference, &starts, &lengths, NUC_COLOR) } pub fn write_m6a(&self, reference: bool) -> String { + let m6a = self.m6a(); let starts = if reference { - self.m6a.reference_starts() + m6a.reference_starts() } else { - self.m6a.option_starts() + m6a.option_starts() }; let lengths = vec![Some(1); starts.len()]; self.to_bed12(reference, &starts, &lengths, M6A_COLOR) } pub fn write_cpg(&self, reference: bool) -> String { + let cpg = self.cpg(); let starts = if reference { - self.cpg.reference_starts() + cpg.reference_starts() } else { - self.cpg.option_starts() + cpg.option_starts() }; let lengths = vec![Some(1); starts.len()]; self.to_bed12(reference, &starts, &lengths, CPG_COLOR) @@ -415,11 +441,15 @@ impl FiberseqData { .count() as i64; // get the info - let m6a_count = self.m6a.annotations.len(); - let m6a_qual = self.m6a.qual().iter().map(|a| Some(*a as i64)).collect(); - let cpg_count = self.cpg.annotations.len(); - let cpg_qual = self.cpg.qual().iter().map(|a| Some(*a as i64)).collect(); - let fire = self.msp.qual().iter().map(|a| Some(*a as i64)).collect(); + let m6a = self.m6a(); + let cpg = self.cpg(); + let msp = self.msp(); + let nuc = self.nuc(); + let m6a_count = m6a.len(); + let m6a_qual = m6a.qual().iter().map(|a| Some(*a as i64)).collect(); + let cpg_count = cpg.len(); + let cpg_qual = cpg.qual().iter().map(|a| Some(*a as i64)).collect(); + let fire = msp.qual().iter().map(|a| Some(*a as i64)).collect(); // write the features let mut rtn = String::with_capacity(0); @@ -453,8 +483,8 @@ impl FiberseqData { .unwrap(); } // add PB features - let total_nuc_bp = self.nuc.lengths().iter().sum::(); - let total_msp_bp = self.msp.lengths().iter().sum::(); + let total_nuc_bp = nuc.lengths().iter().sum::(); + let total_msp_bp = msp.lengths().iter().sum::(); rtn.write_fmt(format_args!( "{}\t{}\t{}\t{}\t{}\t{}\t{}\t", self.ec, rq, at_count, m6a_count, total_nuc_bp, total_msp_bp, cpg_count @@ -462,20 +492,20 @@ impl FiberseqData { .unwrap(); // add fiber features let vecs = [ - self.nuc.option_starts(), - self.nuc.option_lengths(), - self.nuc.reference_starts(), - self.nuc.reference_lengths(), - self.msp.option_starts(), - self.msp.option_lengths(), + nuc.option_starts(), + nuc.option_lengths(), + nuc.reference_starts(), + nuc.reference_lengths(), + msp.option_starts(), + msp.option_lengths(), fire, - self.msp.reference_starts(), - self.msp.reference_lengths(), - self.m6a.option_starts(), - self.m6a.reference_starts(), + msp.reference_starts(), + msp.reference_lengths(), + m6a.option_starts(), + m6a.reference_starts(), m6a_qual, - self.cpg.option_starts(), - self.cpg.reference_starts(), + cpg.option_starts(), + cpg.reference_starts(), cpg_qual, ]; for vec in &vecs { diff --git a/src/subcommands/decorator.rs b/src/subcommands/decorator.rs index fca92ac5..9a580979 100644 --- a/src/subcommands/decorator.rs +++ b/src/subcommands/decorator.rs @@ -166,9 +166,10 @@ pub fn fire_decorators(fiber: &FiberseqData) -> Vec> { map.insert(color, vec![]); } - let ref_starts = fiber.msp.reference_starts(); - let ref_lengths = fiber.msp.reference_lengths(); - let quals = fiber.msp.qual(); + let msp = fiber.msp(); + let ref_starts = msp.reference_starts(); + let ref_lengths = msp.reference_lengths(); + let quals = msp.qual(); for ((pos, length), qual) in ref_starts.iter().zip(ref_lengths.iter()).zip(quals.iter()) { if let (Some(p), Some(l)) = (pos, length) { @@ -201,10 +202,11 @@ pub fn fire_decorators(fiber: &FiberseqData) -> Vec> { } pub fn decorator_from_bam(fiber: &FiberseqData) -> (String, Vec>) { - let m6a_starts = fiber.m6a.reference_starts(); - let cpg_starts = fiber.cpg.reference_starts(); - let nuc_starts = fiber.nuc.reference_starts(); - let nuc_lengths = fiber.nuc.reference_lengths(); + let m6a_starts = fiber.m6a().reference_starts(); + let cpg_starts = fiber.cpg().reference_starts(); + let nuc = fiber.nuc(); + let nuc_starts = nuc.reference_starts(); + let nuc_lengths = nuc.reference_lengths(); let mut decorators = vec![ Decorator::new(fiber, &m6a_starts, None, M6A_COLOR, "m6A"), diff --git a/src/subcommands/fire.rs b/src/subcommands/fire.rs index b4b188bc..511c337f 100644 --- a/src/subcommands/fire.rs +++ b/src/subcommands/fire.rs @@ -111,15 +111,17 @@ pub fn fire_to_bed9(fire_opts: &FireOptions, bam: &mut bam::Reader) -> Result<() //out_buffer.write_all(header.as_bytes())?; for rec in fibers { - let msp_starts = rec.msp.reference_starts(); - let nuc_starts = rec.nuc.reference_starts(); + let msp = rec.msp(); + let nuc = rec.nuc(); + let msp_starts = msp.reference_starts(); + let nuc_starts = nuc.reference_starts(); let start_iter = msp_starts.iter().chain(nuc_starts.iter()); - let msp_ends = rec.msp.reference_ends(); - let nuc_ends = rec.nuc.reference_ends(); + let msp_ends = msp.reference_ends(); + let nuc_ends = nuc.reference_ends(); let end_iter = msp_ends.iter().chain(nuc_ends.iter()); - let msp_qual = rec.msp.qual(); - let nuc_qual = rec.nuc.qual(); + let msp_qual = msp.qual(); + let nuc_qual = nuc.qual(); let qual_iter = msp_qual.iter().chain(nuc_qual.iter()); let n_msps = msp_starts.len(); for (count, ((start, end), qual)) in start_iter.zip(end_iter).zip(qual_iter).enumerate() { diff --git a/src/subcommands/footprint.rs b/src/subcommands/footprint.rs index 122f71db..db7f32f1 100644 --- a/src/subcommands/footprint.rs +++ b/src/subcommands/footprint.rs @@ -155,14 +155,14 @@ impl<'a> Footprint<'a> { for fiber in self.fibers.iter() { let mut has_spanning_msp = false; let mut msp_qual = -1; - for msp in &fiber.msp { + for msp in &fiber.msp() { // skip if there is no mapping of the msp - match (msp.reference_start, msp.reference_end, msp.reference_length) { - (Some(rs), Some(re), Some(_rl)) => { - if self.motif.spans(rs, re) { + match (msp.ref_start, msp.ref_end) { + (Some(rs), Some(re)) => { + if self.motif.spans(rs as i64, re as i64) { self.n_spanning_msps += 1; has_spanning_msp = true; - msp_qual = msp.qual as i16; + msp_qual = msp.qualities.first().copied().unwrap_or(0) as i16; break; } } @@ -178,10 +178,10 @@ impl<'a> Footprint<'a> { // for each fiber, check if there is a nucleosome that overlaps with the motif for fiber in self.fibers.iter() { let mut has_overlapping_nucleosome = false; - for nuc in &fiber.nuc { - match (nuc.reference_start, nuc.reference_end, nuc.reference_length) { - (Some(rs), Some(re), Some(_rl)) => { - if self.motif.overlaps(rs, re) { + for nuc in &fiber.nuc() { + match (nuc.ref_start, nuc.ref_end) { + (Some(rs), Some(re)) => { + if self.motif.overlaps(rs as i64, re as i64) { self.n_overlapping_nucs += 1; has_overlapping_nucleosome = true; break; @@ -209,7 +209,7 @@ impl<'a> Footprint<'a> { // make a binary vector over the motif indicating the presence of an m6a let mut m6a_vec = vec![false; motif_end]; - for m6a in fiber.m6a.reference_starts().iter().flatten() { + for m6a in fiber.m6a().reference_starts().iter().flatten() { if m6a < &self.motif.start { continue; } diff --git a/src/subcommands/pileup.rs b/src/subcommands/pileup.rs index 52bb957a..598cd41e 100644 --- a/src/subcommands/pileup.rs +++ b/src/subcommands/pileup.rs @@ -365,8 +365,8 @@ impl<'a> FireTrack<'a> { // skip this fiber if it has no MSP/NUC information // and we are looking at fiber_coverage if self.fire_track_opts.fiber_coverage - && fiber.msp.reference_starts().is_empty() - && fiber.nuc.reference_starts().is_empty() + && fiber.msp().reference_starts().is_empty() + && fiber.nuc().reference_starts().is_empty() { return; } diff --git a/src/subcommands/qc.rs b/src/subcommands/qc.rs index 576a4155..be38ebe8 100644 --- a/src/subcommands/qc.rs +++ b/src/subcommands/qc.rs @@ -130,7 +130,7 @@ impl<'a> QcStats<'a> { // add the m6a to the working queue let mut m6a_vec: Vec = vec![0.0; fiber.record.seq_len()]; - for m6a in fiber.m6a.starts().iter() { + for m6a in fiber.m6a().starts().iter() { m6a_vec[*m6a as usize] = 1.0; } @@ -155,18 +155,20 @@ impl<'a> QcStats<'a> { } fn add_ranges(&mut self, fiber: &fiber::FiberseqData) { - Self::add_range_lengths(&mut self.msp_lengths, &fiber.msp); - Self::add_range_lengths(&mut self.nuc_lengths, &fiber.nuc); + let msp = fiber.msp(); + let nuc = fiber.nuc(); + Self::add_range_lengths(&mut self.msp_lengths, &msp.lengths()); + Self::add_range_lengths(&mut self.nuc_lengths, &nuc.lengths()); self.nuc_count - .entry(fiber.nuc.annotations.len() as i64) + .entry(nuc.len() as i64) .and_modify(|e| *e += 1) .or_insert(1); self.msp_count - .entry(fiber.msp.annotations.len() as i64) + .entry(msp.len() as i64) .and_modify(|e| *e += 1) .or_insert(1); // read length per nucleosome - let read_length = fiber.record.seq_len() as f32 / fiber.nuc.annotations.len() as f32; + let read_length = fiber.record.seq_len() as f32 / nuc.len() as f32; self.read_length_per_nuc .entry(ordered_float_10k_round(read_length)) .and_modify(|e| *e += 1) @@ -204,7 +206,7 @@ impl<'a> QcStats<'a> { } fn add_basemod_stats(&mut self, fiber: &fiber::FiberseqData) { - let m6a_count = fiber.m6a.annotations.len() as i64; + let m6a_count = fiber.m6a().len() as i64; self.m6a_count .entry(m6a_count) .and_modify(|e| *e += 1) @@ -226,31 +228,28 @@ impl<'a> QcStats<'a> { // cpg count self.cpg_count - .entry(fiber.cpg.annotations.len() as i64) + .entry(fiber.cpg().len() as i64) .and_modify(|e| *e += 1) .or_insert(1); } - fn add_range_lengths( - hashmap: &mut HashMap, - range: &crate::utils::bamannotations::Ranges, - ) { - for r in range.lengths().iter() { + fn add_range_lengths(hashmap: &mut HashMap, lengths: &[i64]) { + for r in lengths.iter() { hashmap.entry(*r).and_modify(|e| *e += 1).or_insert(1); } } /// calculate the m6a per MSP/FIRE element fn m6a_per_msp(&mut self, fiber: &fiber::FiberseqData) { - for annotation in fiber.msp.into_iter() { - let st = annotation.start; - let en = annotation.end; - let qual = annotation.qual; + let msp = fiber.msp(); + let m6a_starts = fiber.m6a().starts(); + for annotation in &msp { + let st = annotation.query_start as i64; + let en = annotation.query_end as i64; + let qual = annotation.qualities.first().copied().unwrap_or(0); let is_fire = qual >= 230; let msp_size = en - st; - let m6a_count = fiber - .m6a - .starts() + let m6a_count = m6a_starts .iter() .filter(|&&m6a_st| st <= m6a_st && m6a_st < en) .count() as i64; diff --git a/src/subcommands/validate.rs b/src/subcommands/validate.rs index 272c74bf..2d8fab47 100644 --- a/src/subcommands/validate.rs +++ b/src/subcommands/validate.rs @@ -33,9 +33,9 @@ pub fn validate_fiberseq_bam(opts: &mut ValidateOptions) -> Result<()> { let mut bam = opts.bam.bam_reader(); for fiber in opts.bam.fibers(&mut bam) { - let m6a_okay = !fiber.m6a.annotations.is_empty(); - let nuc_okay = !fiber.nuc.annotations.is_empty(); - n_fire_calls += fiber.msp.qual().iter().filter(|q| **q > 0).count(); + let m6a_okay = !fiber.m6a().is_empty(); + let nuc_okay = !fiber.nuc().is_empty(); + n_fire_calls += fiber.msp().qual().iter().filter(|q| **q > 0).count(); n_aligned += !fiber.record.is_unmapped() as usize; n_phased += fiber.record.aux(b"HP").is_ok() as usize; diff --git a/src/utils/bamannotations.rs b/src/utils/bamannotations.rs index 43bbdaec..0062fa6f 100644 --- a/src/utils/bamannotations.rs +++ b/src/utils/bamannotations.rs @@ -1,7 +1,7 @@ use crate::utils::bamlift::*; +use molecular_annotation::{AnnotationInfo, MolecularAnnotations}; use rust_htslib::bam; use rust_htslib::bam::ext::BamRecordExtensions; - #[derive(Debug, Clone, PartialEq, Eq, Ord, PartialOrd)] pub struct FiberAnnotation { pub start: i64, @@ -125,7 +125,15 @@ impl FiberAnnotations { // MA spec inward semantics for multi-bp query-space ranges. // Half-open block matching; endpoints in indel gaps snap inward // toward the aligned region rather than to the nearer block edge. - let blocks = molecular_annotation::AlignedBlocks::from_record(record); + // + // Build AlignedBlocks directly from aligned_block_pairs to match + // the legacy lift's exact source (the spec's `from_record` skips + // records that report is_unmapped, which fibertig synthetic test + // records can hit even with a valid CIGAR). + let pairs = record.aligned_block_pairs().map(|([qs, qe], [rs, re])| { + ([qs as u32, qe as u32], [rs as u32, re as u32]) + }); + let blocks = molecular_annotation::AlignedBlocks::from_pairs(pairs, seq_len as u32); let mut rs_vec: Vec> = Vec::with_capacity(starts.len()); let mut re_vec: Vec> = Vec::with_capacity(starts.len()); let mut rl_vec: Vec> = Vec::with_capacity(starts.len()); @@ -210,6 +218,14 @@ impl FiberAnnotations { } } + pub fn len(&self) -> usize { + self.annotations.len() + } + + pub fn is_empty(&self) -> bool { + self.annotations.is_empty() + } + // Backward compatibility methods pub fn starts(&self) -> Vec { self.annotations.iter().map(|a| a.start).collect() @@ -639,3 +655,130 @@ impl<'a> Iterator for FiberAnnotationsIterator<'a> { // Backward compatibility alias pub type RangesIterator<'a> = FiberAnnotationsIterator<'a>; + + +/// View over a specific annotation type, providing the column-oriented +/// surface fibertools historically got from `FiberAnnotations` while +/// delegating per-annotation iteration to the library's +/// [`AnnotationInfo`]. +/// +/// Stays valid when the type is absent: every accessor returns an empty +/// `Vec` / zero count, so call sites avoid `Option` plumbing. +/// +/// All accessors and the per-annotation iterator yield results in +/// **BAM-orient ascending** order. The spec stores annotations in +/// molecular order; for reverse-aligned reads we reverse so consumers +/// (BED12 blocks, pileup intervals, TSV columns) get ascending output. +pub struct AnnotationTypeView<'a> { + annot: &'a MolecularAnnotations, + type_name: &'a str, +} + +impl<'a> AnnotationTypeView<'a> { + pub(crate) fn new(annot: &'a MolecularAnnotations, type_name: &'a str) -> Self { + Self { annot, type_name } + } + + pub fn len(&self) -> usize { + self.annot + .get_type(self.type_name) + .map(|t| t.annotations.len()) + .unwrap_or(0) + } + pub fn is_empty(&self) -> bool { + self.len() == 0 + } + + /// Materialize the annotation infos for this type in BAM-orient + /// ascending order. Computes reference coords once and amortizes that + /// cost across all column accessors and iter consumers. + fn bam_ordered(&self) -> Vec> { + let Some(it) = self.annot.iter_type(self.type_name) else { + return Vec::new(); + }; + let mut v: Vec> = it.collect(); + if self.annot.is_reverse_aligned() { + v.reverse(); + } + v + } + + pub fn starts(&self) -> Vec { + self.bam_ordered() + .into_iter() + .map(|a| a.query_start as i64) + .collect() + } + pub fn ends(&self) -> Vec { + self.bam_ordered() + .into_iter() + .map(|a| a.query_end as i64) + .collect() + } + pub fn option_starts(&self) -> Vec> { + self.bam_ordered() + .into_iter() + .map(|a| Some(a.query_start as i64)) + .collect() + } + pub fn option_ends(&self) -> Vec> { + self.bam_ordered() + .into_iter() + .map(|a| Some(a.query_end as i64)) + .collect() + } + pub fn option_lengths(&self) -> Vec> { + self.bam_ordered() + .into_iter() + .map(|a| Some((a.query_end - a.query_start) as i64)) + .collect() + } + pub fn lengths(&self) -> Vec { + self.bam_ordered() + .into_iter() + .map(|a| (a.query_end - a.query_start) as i64) + .collect() + } + pub fn qual(&self) -> Vec { + self.bam_ordered() + .into_iter() + .map(|a| a.qualities.first().copied().unwrap_or(0)) + .collect() + } + pub fn reference_starts(&self) -> Vec> { + self.bam_ordered() + .into_iter() + .map(|a| a.ref_start.map(|x| x as i64)) + .collect() + } + pub fn reference_ends(&self) -> Vec> { + self.bam_ordered() + .into_iter() + .map(|a| a.ref_end.map(|x| x as i64)) + .collect() + } + pub fn reference_lengths(&self) -> Vec> { + self.bam_ordered() + .into_iter() + .map(|a| match (a.ref_start, a.ref_end) { + (Some(s), Some(e)) => Some((e - s) as i64), + _ => None, + }) + .collect() + } + + /// Iterate per-annotation in BAM-orient ascending order, yielding the + /// library's [`AnnotationInfo`] view directly. Call sites read fields + /// like `info.query_start`, `info.ref_start`, `info.qualities`. + pub fn iter(&self) -> std::vec::IntoIter> { + self.bam_ordered().into_iter() + } +} + +impl<'a> IntoIterator for &AnnotationTypeView<'a> { + type Item = AnnotationInfo<'a>; + type IntoIter = std::vec::IntoIter>; + fn into_iter(self) -> Self::IntoIter { + self.iter() + } +} diff --git a/src/utils/basemods.rs b/src/utils/basemods.rs index 3bdc0395..d5e67add 100644 --- a/src/utils/basemods.rs +++ b/src/utils/basemods.rs @@ -2,6 +2,7 @@ use crate::utils::bamannotations::*; use crate::utils::bio_io::*; use bio::alphabets::dna::revcomp; use lazy_static::lazy_static; +use molecular_annotation::{MolecularAnnotations, QualitySpec, Strand}; use regex::Regex; use rust_htslib::{ bam, @@ -11,6 +12,10 @@ use std::collections::HashMap; use std::convert::TryFrom; +/// Annotation type names emitted by `BaseMods::populate_ma`. +pub const M6A_TYPE: &str = "m6a"; +pub const CPG_TYPE: &str = "cpg"; + /// A group of base modification calls of one (base, strand, modification_type) /// triple — for example, "all m6A calls on adenines on the forward strand." /// @@ -304,6 +309,32 @@ impl BaseMods { Ranges::merge_ranges(ranges) } + /// Inject `m6a` and `cpg` annotation types into `annot` from the parsed + /// ML/MM data on this object. Coordinates are emitted in molecular + /// orientation (forward) and the per-base ML score is preserved as a + /// linear ("Q") quality. + /// + /// The MA tag layer in `ma_io` never reads or writes m6a/cpg — their + /// on-disk source of truth is ML/MM — so this is the only place the + /// `MolecularAnnotations` object gets these types attached. + pub fn populate_ma(&self, annot: &mut MolecularAnnotations) { + Self::add_basemod_type(annot, M6A_TYPE, &self.m6a()); + Self::add_basemod_type(annot, CPG_TYPE, &self.cpg()); + } + + fn add_basemod_type(annot: &mut MolecularAnnotations, type_name: &str, merged: &Ranges) { + if merged.annotations.is_empty() { + return; + } + let starts = merged.forward_starts(); + let quals = merged.get_forward_quals(); + let qspec = "Q".parse::().expect("Q parses"); + let t = annot.add_annotation_type(type_name, qspec); + for (s, q) in starts.iter().zip(quals.iter()) { + t.add(*s as u32, 1, Strand::Forward, vec![*q], None); + } + } + /// Example MM tag: MM:Z:C+m,11,6,10;A+a,0,0,0; /// Example ML tag: ML:B:C,157,30,2,164,118,255 pub fn add_mm_and_ml_tags(&self, record: &mut bam::Record) { diff --git a/src/utils/fire.rs b/src/utils/fire.rs index 81fe33ff..17bf4f3c 100644 --- a/src/utils/fire.rs +++ b/src/utils/fire.rs @@ -93,7 +93,7 @@ fn get_m6a_rle_data(rec: &FiberseqData, start: i64, end: i64) -> (f32, f32) { let mut _max_pos = 0; // if you are a position, on average you will be in an rle length of weighted_rle let mut weighted_rle = 0.0; - for (m6a_1, m6a_2) in rec.m6a.starts().iter().tuple_windows() { + for (m6a_1, m6a_2) in rec.m6a().starts().iter().tuple_windows() { // we only want m6a in the window if *m6a_1 < start || *m6a_1 > end || *m6a_2 < start || *m6a_2 > end { continue; @@ -203,7 +203,7 @@ impl<'a> FireFeats<'a> { } else { b'A' }; - for m6a_st in self.rec.m6a.starts().iter() { + for m6a_st in self.rec.m6a().starts().iter() { let m6a_bp = self.seq[*m6a_st as usize]; if m6a_bp != sequenced_bp { log::warn!( @@ -387,19 +387,15 @@ impl<'a> FireFeats<'a> { } pub fn get_fire_features(&mut self) { - let msp_data = self.rec.msp.into_iter().collect_vec(); + let msp_data: Vec<_> = self.rec.msp().into_iter().collect(); self.fire_feats = msp_data .into_iter() .map(|annotation| { - let s = annotation.start; - let e = annotation.end; - let (rs, re, _rl) = match ( - annotation.reference_start, - annotation.reference_end, - annotation.reference_length, - ) { - (Some(rs), Some(re), Some(rl)) => (rs, re, rl), - _ => (0, 0, 0), + let s = annotation.query_start as i64; + let e = annotation.query_end as i64; + let (rs, re) = match (annotation.ref_start, annotation.ref_end) { + (Some(rs), Some(re)) => (rs as i64, re as i64), + _ => (0, 0), }; (rs, re, self.msp_get_fire_features(s, e)) }) diff --git a/src/utils/input_bam.rs b/src/utils/input_bam.rs index b8afa8bb..90909425 100644 --- a/src/utils/input_bam.rs +++ b/src/utils/input_bam.rs @@ -356,6 +356,7 @@ mod tests { .collect(); FiberseqData { record: rust_htslib::bam::Record::new(), + annotations: molecular_annotation::MolecularAnnotations::new(1000), msp: FiberAnnotations::from_annotations(msp_anns, 1000, false), nuc: FiberAnnotations::from_annotations(vec![], 1000, false), m6a: FiberAnnotations::from_annotations(m6a_anns, 1000, false), From 2244e950a7231f63758ff534aaf75ded6d4a7cf9 Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Mon, 11 May 2026 22:18:35 -0600 Subject: [PATCH 07/24] chore: update ma library dep --- Cargo.lock | 1 + Cargo.toml | 2 +- src/subcommands/fire.rs | 12 ++++++++---- src/utils/bamannotations.rs | 7 +++---- src/utils/ma_io.rs | 6 +----- 5 files changed, 14 insertions(+), 14 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index 12771c0b..f887b946 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -4084,6 +4084,7 @@ checksum = "4e519fd9c6131c1c9a4a67f8bdc4f32eb4105b16c1468adea1b8e68c98c85ec4" [[package]] name = "molecular-annotation" version = "0.1.0" +source = "git+https://github.com/fiberseq/Molecular-annotation-spec?branch=main#7e052272a0b4ee45925bd78554c1d244a6761f53" dependencies = [ "bio 2.3.0", "lazy_static", diff --git a/Cargo.toml b/Cargo.toml index f93646de..0378c8e9 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -69,7 +69,7 @@ burn = { version = "0.18.0", optional = true, features = [ num = "0.4.3" rand = "0.8.5" noodles = { version = "0.100.0", features = ["fasta", "bed"] } -molecular-annotation = { path = "../Molecular-annotation-spec/rust", features = ["htslib"] } +molecular-annotation = { git = "https://github.com/fiberseq/Molecular-annotation-spec", branch = "main", features = ["htslib"] } [build-dependencies] burn-import = { version = "0.18.0", default-features = false, features = [ diff --git a/src/subcommands/fire.rs b/src/subcommands/fire.rs index 511c337f..7e7c3e23 100644 --- a/src/subcommands/fire.rs +++ b/src/subcommands/fire.rs @@ -27,7 +27,10 @@ pub fn add_fire_to_rec( let mut annot = match ma_io::read_annotations(&rec.record) { Ok(a) => a, - Err(e) => { log::warn!("FIRE: failed to read annotations: {e}"); return; } + Err(e) => { + log::warn!("FIRE: failed to read annotations: {e}"); + return; + } }; let Some(msp) = annot.get_type(ma_io::MSP_TYPE) else { @@ -37,17 +40,18 @@ pub fn add_fire_to_rec( if msp.annotations.len() != precisions.len() { log::warn!( "FIRE precision count ({}) does not match MSP count ({}); skipping", - precisions.len(), msp.annotations.len(), + precisions.len(), + msp.annotations.len(), ); return; } let starts: Vec = msp.annotations.iter().map(|a| a.start).collect(); - let lens: Vec = msp.annotations.iter().map(|a| a.length).collect(); + let lens: Vec = msp.annotations.iter().map(|a| a.length).collect(); ma_io::add_fire_annotations(&mut annot, &starts, &lens, &precisions); ma_io::write_annotations(&mut rec.record, &annot, legacy); - + log::trace!("precisions: {precisions:?}"); } diff --git a/src/utils/bamannotations.rs b/src/utils/bamannotations.rs index 0062fa6f..c81844ee 100644 --- a/src/utils/bamannotations.rs +++ b/src/utils/bamannotations.rs @@ -130,9 +130,9 @@ impl FiberAnnotations { // the legacy lift's exact source (the spec's `from_record` skips // records that report is_unmapped, which fibertig synthetic test // records can hit even with a valid CIGAR). - let pairs = record.aligned_block_pairs().map(|([qs, qe], [rs, re])| { - ([qs as u32, qe as u32], [rs as u32, re as u32]) - }); + let pairs = record + .aligned_block_pairs() + .map(|([qs, qe], [rs, re])| ([qs as u32, qe as u32], [rs as u32, re as u32])); let blocks = molecular_annotation::AlignedBlocks::from_pairs(pairs, seq_len as u32); let mut rs_vec: Vec> = Vec::with_capacity(starts.len()); let mut re_vec: Vec> = Vec::with_capacity(starts.len()); @@ -656,7 +656,6 @@ impl<'a> Iterator for FiberAnnotationsIterator<'a> { // Backward compatibility alias pub type RangesIterator<'a> = FiberAnnotationsIterator<'a>; - /// View over a specific annotation type, providing the column-oriented /// surface fibertools historically got from `FiberAnnotations` while /// delegating per-annotation iteration to the library's diff --git a/src/utils/ma_io.rs b/src/utils/ma_io.rs index fe292d73..e49ca48e 100644 --- a/src/utils/ma_io.rs +++ b/src/utils/ma_io.rs @@ -267,11 +267,7 @@ pub fn extract_nuc_msp_arrays( /// /// No-op if `starts` is empty. `starts` and `lens` must be the same length /// and paired positionally. -pub fn add_nuc_annotations( - annot: &mut MolecularAnnotations, - starts: &[u32], - lens: &[u32], -) { +pub fn add_nuc_annotations(annot: &mut MolecularAnnotations, starts: &[u32], lens: &[u32]) { if starts.is_empty() { return; } From 5b5e1434ca419aa6e051bb4a4513d661abd6d7be Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Tue, 12 May 2026 10:58:12 -0600 Subject: [PATCH 08/24] refactor: factor out primary_qual; debug-assert single-quality types MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Add `primary_qual(&[u8], &str) -> u8` and `AnnotationTypeView::qual_at(idx)` to make the single-quality assumption explicit. `qual()` now delegates to `qual_at(0)` with `debug_assert!(qualities.len() <= 1, …)`, so a future multi-quality annotation type can't silently lose qualities through `first().copied().unwrap_or(0)`. Migrates the existing single-quality call sites in ma_io (3 sites), footprint, and qc to the helper. Same byte-for-byte output; the assert fires only in debug builds if a multi-quality type appears. --- src/subcommands/footprint.rs | 5 +++- src/subcommands/qc.rs | 5 +++- src/utils/bamannotations.rs | 47 +++++++++++++++++++++++++++++++++++- src/utils/ma_io.rs | 10 +++++--- 4 files changed, 60 insertions(+), 7 deletions(-) diff --git a/src/subcommands/footprint.rs b/src/subcommands/footprint.rs index db7f32f1..fe521299 100644 --- a/src/subcommands/footprint.rs +++ b/src/subcommands/footprint.rs @@ -162,7 +162,10 @@ impl<'a> Footprint<'a> { if self.motif.spans(rs as i64, re as i64) { self.n_spanning_msps += 1; has_spanning_msp = true; - msp_qual = msp.qualities.first().copied().unwrap_or(0) as i16; + msp_qual = crate::utils::bamannotations::primary_qual( + msp.qualities, + msp.type_name, + ) as i16; break; } } diff --git a/src/subcommands/qc.rs b/src/subcommands/qc.rs index be38ebe8..c481dafc 100644 --- a/src/subcommands/qc.rs +++ b/src/subcommands/qc.rs @@ -246,7 +246,10 @@ impl<'a> QcStats<'a> { for annotation in &msp { let st = annotation.query_start as i64; let en = annotation.query_end as i64; - let qual = annotation.qualities.first().copied().unwrap_or(0); + let qual = crate::utils::bamannotations::primary_qual( + annotation.qualities, + annotation.type_name, + ); let is_fire = qual >= 230; let msp_size = en - st; let m6a_count = m6a_starts diff --git a/src/utils/bamannotations.rs b/src/utils/bamannotations.rs index c81844ee..9c9aa30d 100644 --- a/src/utils/bamannotations.rs +++ b/src/utils/bamannotations.rs @@ -2,6 +2,23 @@ use crate::utils::bamlift::*; use molecular_annotation::{AnnotationInfo, MolecularAnnotations}; use rust_htslib::bam; use rust_htslib::bam::ext::BamRecordExtensions; + +/// Extract the single per-annotation quality fibertools expects, returning +/// 0 when the annotation has none. Debug-asserts that the type carries at +/// most one quality — fibertools' current annotation types (`nuc`, `msp`, +/// `fire`, `m6a`, `cpg`) are all single-quality. If you add a multi-quality +/// type, pick the index explicitly at the call site instead of using this +/// helper. +#[inline] +pub fn primary_qual(qualities: &[u8], type_name: &str) -> u8 { + debug_assert!( + qualities.len() <= 1, + "primary_qual: type {:?} carries {} qualities; fibertools expects \u{2264} 1", + type_name, + qualities.len(), + ); + qualities.first().copied().unwrap_or(0) +} #[derive(Debug, Clone, PartialEq, Eq, Ord, PartialOrd)] pub struct FiberAnnotation { pub start: i64, @@ -738,10 +755,38 @@ impl<'a> AnnotationTypeView<'a> { .map(|a| (a.query_end - a.query_start) as i64) .collect() } + /// Convenience over [`Self::qual_at`] for the common case where the + /// annotation type carries at most one quality per annotation. Returns + /// 0 for annotations with no qualities. + /// + /// All fibertools-rs annotation types (`nuc`, `msp+` / `msp+Q`, + /// `fire+P`, `m6a+Q`, `cpg+Q`) are single-quality; this method debug- + /// asserts that invariant. If you add a multi-quality type, call + /// [`Self::qual_at`] with an explicit index instead — `qual()` + /// silently dropping quality columns would be a footgun. pub fn qual(&self) -> Vec { + self.qual_at(0) + } + + /// Per-annotation quality at the given index, BAM-orient ascending. + /// Returns 0 when the annotation has fewer than `idx + 1` qualities. + /// + /// `qual_at(0)` is the canonical single-quality accessor and + /// debug-asserts that the type has at most one quality. Other indices + /// skip the assertion — the caller is presumed to know the type's + /// `QualitySpec`. + pub fn qual_at(&self, idx: usize) -> Vec { self.bam_ordered() .into_iter() - .map(|a| a.qualities.first().copied().unwrap_or(0)) + .map(|a| { + debug_assert!( + idx > 0 || a.qualities.len() <= 1, + "AnnotationTypeView::qual() called on multi-quality type {:?} ({} qualities); use qual_at(idx)", + self.type_name, + a.qualities.len(), + ); + a.qualities.get(idx).copied().unwrap_or(0) + }) .collect() } pub fn reference_starts(&self) -> Vec> { diff --git a/src/utils/ma_io.rs b/src/utils/ma_io.rs index e49ca48e..89a4e3e7 100644 --- a/src/utils/ma_io.rs +++ b/src/utils/ma_io.rs @@ -179,7 +179,9 @@ fn write_legacy_nuc_msp(record: &mut bam::Record, annot: &MolecularAnnotations) Some( fire.annotations .iter() - .map(|a| a.qualities.first().copied().unwrap_or(0)) + .map(|a| { + crate::utils::bamannotations::primary_qual(&a.qualities, FIRE_TYPE) + }) .collect(), ) } else { @@ -189,7 +191,7 @@ fn write_legacy_nuc_msp(record: &mut bam::Record, annot: &MolecularAnnotations) Some( msp.annotations .iter() - .map(|a| a.qualities.first().copied().unwrap_or(0)) + .map(|a| crate::utils::bamannotations::primary_qual(&a.qualities, MSP_TYPE)) .collect(), ) } else { @@ -252,7 +254,7 @@ pub fn extract_nuc_msp_arrays( let qs: Vec = if t.quality_spec.has_quality() { t.annotations .iter() - .map(|a| a.qualities.first().copied().unwrap_or(0)) + .map(|a| crate::utils::bamannotations::primary_qual(&a.qualities, MSP_TYPE)) .collect() } else { Vec::new() @@ -369,7 +371,7 @@ pub fn extract_fire_arrays(record: &bam::Record) -> Result<(Vec, Vec, let phred = t .annotations .iter() - .map(|a| a.qualities.first().copied().unwrap_or(0)) + .map(|a| crate::utils::bamannotations::primary_qual(&a.qualities, FIRE_TYPE)) .collect(); (starts, lens, phred) }) From d4f56431154f305cbe5518031dc02868897a5005 Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Tue, 12 May 2026 10:59:24 -0600 Subject: [PATCH 09/24] refactor: move centering onto MA spec project_query/project_reference CenteredFiberData no longer mutates a cloned FiberseqData. Instead it stashes both offsets and projects on-demand via the spec library's project_query / project_reference (which return ProjectedAnnotation with the centered coords already computed). grab_data collapses to a single helper per type. validate_msp_m6a_alignment moved onto CenteredFiberData, also using project_query. FiberseqData drops msp/nuc/m6a/cpg Ranges fields; read sites already go through the AnnotationTypeView accessors over self.annotations. apply_filter_fsd switched to MolecularAnnotations::retain. Call sites in pileup, add_nucleosomes, fiber_hmm, qc, fire, input_bam adjusted to the new field-less FiberseqData; non-regression test files (extract_test, m6a_prediction_test) also migrated. Dead code left for a follow-up: FiberAnnotations::apply_offset / apply_offset_helper, and bamlift.rs (still used by Ranges::new 1bp path and CenteredFiberData::find_offset). --- src/fiber.rs | 75 +--------------- src/subcommands/add_nucleosomes.rs | 8 +- src/subcommands/center.rs | 129 +++++++++++++++++++++------ src/subcommands/fiber_hmm.rs | 8 +- src/subcommands/pileup.rs | 138 ++++++++++++----------------- src/subcommands/qc.rs | 2 +- src/utils/fire.rs | 4 +- src/utils/ftexpression.rs | 33 ++++--- src/utils/input_bam.rs | 61 +++++-------- tests/extract_test.rs | 10 +-- tests/m6a_prediction_test.rs | 12 ++- 11 files changed, 230 insertions(+), 250 deletions(-) diff --git a/src/fiber.rs b/src/fiber.rs index fd3ca53e..09ac75c1 100644 --- a/src/fiber.rs +++ b/src/fiber.rs @@ -1,5 +1,4 @@ use super::subcommands::center::CenterPosition; -use super::subcommands::center::CenteredFiberData; use super::utils::input_bam::FiberFilters; use super::*; use crate::utils::bamannotations::*; @@ -18,10 +17,6 @@ use std::fmt::Write; pub struct FiberseqData { pub record: bam::Record, pub annotations: MolecularAnnotations, - pub msp: Ranges, - pub nuc: Ranges, - pub m6a: Ranges, - pub cpg: Ranges, pub base_mods: BaseMods, pub ec: f32, pub target_name: String, @@ -43,16 +38,6 @@ impl FiberseqData { log::warn!("Failed to read annotations: {e}"); MolecularAnnotations::from_record(&record) }); - let (nuc_starts, nuc_length, msp_starts, msp_length, msp_qual) = - crate::utils::ma_io::extract_nuc_msp_arrays(&record).unwrap_or_else(|e| { - log::warn!("Failed to read annotations: {e}"); - Default::default() - }); - let nuc = Ranges::new(&record, nuc_starts, None, Some(nuc_length)); - let mut msp = Ranges::new(&record, msp_starts, None, Some(msp_length)); - if !msp_qual.is_empty() { - msp.set_qual(msp_qual); - } // get the number of passes let ec = if let Ok(Aux::Float(f)) = record.aux(b"ec") { @@ -67,23 +52,15 @@ impl FiberseqData { None => ".".to_string(), }; - // get fiberseq basemods + // get fiberseq basemods (also injects m6a/cpg into `annotations`) let mut base_mods = BaseMods::new(&record, filters.min_ml_score); base_mods.filter_at_read_ends(filters.strip_starting_basemods); base_mods.populate_ma(&mut annotations); - //let (m6a, cpg) = FiberMods::new(&base_mods); - let m6a = base_mods.m6a(); - let cpg = base_mods.cpg(); - let mut fsd = FiberseqData { record, annotations, - msp, - nuc, - m6a, base_mods, - cpg, ec, target_name, rg, @@ -179,56 +156,6 @@ impl FiberseqData { } } - /// Center all coordinates on the read using the offset attribute. - pub fn center(&self, center_position: &CenterPosition) -> Option { - // setup new fiberseq data object to return - let mut new = self.clone(); - let (ref_offset, mol_offset) = - CenteredFiberData::find_offsets(&self.record, center_position); - - // Apply offsets to all annotations using the new methods - new.m6a - .apply_offset(mol_offset, ref_offset, center_position.strand); - new.cpg - .apply_offset(mol_offset, ref_offset, center_position.strand); - new.msp - .apply_offset(mol_offset, ref_offset, center_position.strand); - new.nuc - .apply_offset(mol_offset, ref_offset, center_position.strand); - - // Validate that MSPs still start and end on m6A marks after centering - new.validate_msp_m6a_alignment(); - - Some(new) - } - - /// Validate that all MSP boundaries align with m6A positions after centering - fn validate_msp_m6a_alignment(&self) { - // Legacy fields are used here because centering only mutates the - // legacy Ranges (Branch 2 will move centering onto the MA spec). - let m6a_positions = self.m6a.starts(); - let msp_boundaries: Vec = self - .msp - .starts() - .into_iter() - .chain(self.msp.ends().into_iter().map(|x| x - 1)) - .collect(); - - if m6a_positions.is_empty() || msp_boundaries.is_empty() { - return; // Skip validation if no data - } - - for msp_pos in &msp_boundaries { - if !m6a_positions.contains(msp_pos) { - log::warn!( - "MSP boundary at position {} does not align with m6A mark after centering in read {}", - msp_pos, - String::from_utf8_lossy(self.record.qname()) - ); - } - } - } - // // WRITE BED12 FUNCTIONS // diff --git a/src/subcommands/add_nucleosomes.rs b/src/subcommands/add_nucleosomes.rs index 5219bdec..6347fb0a 100644 --- a/src/subcommands/add_nucleosomes.rs +++ b/src/subcommands/add_nucleosomes.rs @@ -20,8 +20,12 @@ pub fn add_nucleosomes_to_bam(nuc_opts: &mut AddNucleosomeOptions) { .par_iter_mut() .map(|record| { let fd = FiberseqData::new(record.clone(), None, &nuc_opts.input.filters); - //let m6a = fd.base_mods.forward_m6a(); - let m6a = fd.m6a.forward_starts(); + // m6a positions in molecular (forward) orientation + let m6a: Vec = fd + .annotations + .get_forward_coords("m6a") + .map(|v| v.into_iter().map(|(s, _)| s as i64).collect()) + .unwrap_or_default(); add_nucleosomes_to_record(record, &m6a, &nuc_opts.nuc, nuc_opts.legacy_tags); record }) diff --git a/src/subcommands/center.rs b/src/subcommands/center.rs index 98cdd96a..bb30aec0 100644 --- a/src/subcommands/center.rs +++ b/src/subcommands/center.rs @@ -1,5 +1,6 @@ use crate::cli::CenterOptions; use crate::fiber::FiberseqData; +use crate::utils::bamannotations::primary_qual; use crate::utils::bamlift::*; use crate::utils::bio_io; use crate::*; @@ -22,6 +23,8 @@ pub struct CenteredFiberData { pub dist: Option, center_position: CenterPosition, pub offset: i64, + mol_offset: i64, + ref_offset: i64, pub reference: bool, pub simplify: bool, } @@ -38,16 +41,102 @@ impl CenteredFiberData { CenteredFiberData::find_offsets(&fiber.record, ¢er_position); let offset = if reference { ref_offset } else { mol_offset }; - let fiber = fiber.center(¢er_position)?; - - Some(CenteredFiberData { + let cfd = CenteredFiberData { fiber, dist, center_position, offset, + mol_offset, + ref_offset, reference, simplify, - }) + }; + cfd.validate_msp_m6a_alignment(); + Some(cfd) + } + + /// Project this fiber's annotations of `type_name` into the active + /// frame (query when `!self.reference`, reference when `self.reference`) + /// via the spec library's `project_query` / `project_reference`. Returns + /// (centered_starts, centered_ends, quals) in lockstep. + /// + /// In query frame every annotation yields a row. In reference frame + /// annotations that don't lift are dropped (the spec's + /// `project_reference` filters them out); this matches the legacy + /// output which skipped `None` ref coords in `write_long`. + /// + /// Output is reversed when `flip != is_reverse_aligned` so the centered + /// coords come out ascending — matching the legacy `apply_offset` which + /// reversed the annotations vec for minus-strand centers. + fn centered_for_type(&self, type_name: &str) -> (Vec>, Vec>, Vec) { + let flip = self.center_position.strand == '-'; + let mut starts = Vec::new(); + let mut ends = Vec::new(); + let mut quals = Vec::new(); + if self.reference { + for p in self + .fiber + .annotations + .project_reference(self.ref_offset, flip) + { + if p.type_name != type_name { + continue; + } + starts.push(Some(p.start)); + ends.push(Some(p.end)); + quals.push(primary_qual(p.qualities, p.type_name)); + } + } else { + for p in self.fiber.annotations.project_query(self.mol_offset, flip) { + if p.type_name != type_name { + continue; + } + starts.push(Some(p.start)); + ends.push(Some(p.end)); + quals.push(primary_qual(p.qualities, p.type_name)); + } + } + if flip != self.fiber.annotations.is_reverse_aligned() { + starts.reverse(); + ends.reverse(); + quals.reverse(); + } + (starts, ends, quals) + } + + /// Validate that all MSP boundaries align with m6A positions after + /// centering. Operates on the centered (query-frame) coordinates the + /// short-form writer would emit, so the warning catches the same + /// misalignments the legacy in-place mutation did. + fn validate_msp_m6a_alignment(&self) { + let flip = self.center_position.strand == '-'; + let m6a_positions: Vec = self + .fiber + .annotations + .project_query(self.mol_offset, flip) + .filter(|p| p.type_name == "m6a") + .map(|p| p.start) + .collect(); + let msp_boundaries: Vec = self + .fiber + .annotations + .project_query(self.mol_offset, flip) + .filter(|p| p.type_name == "msp") + .flat_map(|p| [p.start, p.end - 1]) + .collect(); + + if m6a_positions.is_empty() || msp_boundaries.is_empty() { + return; + } + for msp_pos in &msp_boundaries { + if !m6a_positions.contains(msp_pos) { + log::warn!( + "MSP boundary at position {} does not align with m6A mark after centering in read {}", + msp_pos, + String::from_utf8_lossy(self.fiber.record.qname()) + ); + } + } } /// find both the ref and mol offsets pub fn find_offsets(record: &bam::Record, center_position: &CenterPosition) -> (i64, i64) { @@ -167,31 +256,13 @@ impl CenteredFiberData { Vec>, Vec, ) { - if self.reference { - ( - self.fiber.m6a.reference_starts(), - self.fiber.m6a.qual(), - self.fiber.cpg.reference_starts(), - self.fiber.cpg.qual(), - self.fiber.nuc.reference_starts(), - self.fiber.nuc.reference_ends(), - self.fiber.msp.reference_starts(), - self.fiber.msp.reference_ends(), - self.fiber.msp.qual(), - ) - } else { - ( - self.fiber.m6a.option_starts(), - self.fiber.m6a.qual(), - self.fiber.cpg.option_starts(), - self.fiber.cpg.qual(), - self.fiber.nuc.option_starts(), - self.fiber.nuc.option_ends(), - self.fiber.msp.option_starts(), - self.fiber.msp.option_ends(), - self.fiber.msp.qual(), - ) - } + let (m6a, _, m6a_qual) = self.centered_for_type("m6a"); + let (cpg, _, cpg_qual) = self.centered_for_type("cpg"); + let (nuc_st, nuc_en, _) = self.centered_for_type("nuc"); + let (msp_st, msp_en, fire) = self.centered_for_type("msp"); + ( + m6a, m6a_qual, cpg, cpg_qual, nuc_st, nuc_en, msp_st, msp_en, fire, + ) } pub fn write(&self) -> String { diff --git a/src/subcommands/fiber_hmm.rs b/src/subcommands/fiber_hmm.rs index 4d103f7a..e06c306f 100644 --- a/src/subcommands/fiber_hmm.rs +++ b/src/subcommands/fiber_hmm.rs @@ -7,8 +7,12 @@ pub fn run_fiber_hmm(opts: &mut FiberHmmOptions) -> Result<(), Error> { let mut bam = opts.input.bam_reader(); let mut out = opts.input.bam_writer(&opts.out); for fiber in opts.input.fibers(&mut bam) { - // m6a positions on the forward strand - let _m6a = fiber.m6a.forward_starts(); + // m6a positions on the forward (molecular) strand + let _m6a: Vec = fiber + .annotations + .get_forward_coords("m6a") + .map(|v| v.into_iter().map(|(s, _)| s).collect()) + .unwrap_or_default(); // forward strand sequence let mut seq = fiber.record.seq().as_bytes(); if fiber.record.is_reverse() { diff --git a/src/subcommands/pileup.rs b/src/subcommands/pileup.rs index 598cd41e..01bcb144 100644 --- a/src/subcommands/pileup.rs +++ b/src/subcommands/pileup.rs @@ -291,17 +291,15 @@ impl<'a> FireTrack<'a> { //#[inline] fn add_range_set( array: &mut [i32], - ranges: &bamannotations::Ranges, + view: &bamannotations::AnnotationTypeView<'_>, cur_offset: i64, chrom_start: usize, ) { - for annotation in ranges { - match ( - annotation.reference_start, - annotation.reference_end, - annotation.reference_length, - ) { - (Some(rs), Some(re), Some(_)) => { + for info in view { + match (info.ref_start, info.ref_end) { + (Some(rs), Some(re)) => { + let rs = rs as i64; + let re = re as i64; let re = if rs == re { re + 1 } else { re }; for i in rs..re { let pos = i + cur_offset - chrom_start as i64; @@ -326,30 +324,16 @@ impl<'a> FireTrack<'a> { } let mut start = i64::MAX; let mut end = i64::MIN; - for annotation in &fiber.msp { - match ( - annotation.reference_start, - annotation.reference_end, - annotation.reference_length, - ) { - (Some(rs), Some(re), Some(_)) => { - start = std::cmp::min(start, rs); - end = std::cmp::max(end, re); - } - _ => continue, + for info in &fiber.msp() { + if let (Some(rs), Some(re)) = (info.ref_start, info.ref_end) { + start = std::cmp::min(start, rs as i64); + end = std::cmp::max(end, re as i64); } } - for annotation in &fiber.nuc { - match ( - annotation.reference_start, - annotation.reference_end, - annotation.reference_length, - ) { - (Some(rs), Some(re), Some(_)) => { - start = std::cmp::min(start, rs); - end = std::cmp::max(end, re); - } - _ => continue, + for info in &fiber.nuc() { + if let (Some(rs), Some(re)) = (info.ref_start, info.ref_end) { + start = std::cmp::min(start, rs as i64); + end = std::cmp::max(end, re as i64); } } if start == i64::MAX { @@ -417,72 +401,66 @@ impl<'a> FireTrack<'a> { } // calculate the fire coverage and fire score - for annotation in &fiber.msp { - match ( - annotation.reference_start, - annotation.reference_end, - annotation.reference_length, - ) { - (Some(rs), Some(re), Some(_)) => { - if annotation.qual < MIN_FIRE_QUAL { - continue; - } - // Cap quality at 253 to avoid log10(0) issues, and cap score at 100 - let capped_qual = annotation.qual.min(253) as f32; - let score_update = ((1.0 - capped_qual / 255.0).log10() * -50.0).min(100.0); - - // If tracking FIRE elements, create a FireElement for this MSP - let fire_element = if self.fire_track_opts.track_fire_elements { - let elem_start = rs + self.cur_offset; - let elem_end = re + self.cur_offset; - let fire_id = self.next_fire_id; - self.next_fire_id += 1; - Some(FireElement { - start: elem_start, - end: elem_end, - id: fire_id, - }) - } else { - None - }; + for info in &fiber.msp() { + let (rs, re) = match (info.ref_start, info.ref_end) { + (Some(rs), Some(re)) => (rs as i64, re as i64), + _ => continue, + }; + let qual = crate::utils::bamannotations::primary_qual(info.qualities, info.type_name); + if qual < MIN_FIRE_QUAL { + continue; + } + // Cap quality at 253 to avoid log10(0) issues, and cap score at 100 + let capped_qual = qual.min(253) as f32; + let score_update = ((1.0 - capped_qual / 255.0).log10() * -50.0).min(100.0); + + // If tracking FIRE elements, create a FireElement for this MSP + let fire_element = if self.fire_track_opts.track_fire_elements { + let elem_start = rs + self.cur_offset; + let elem_end = re + self.cur_offset; + let fire_id = self.next_fire_id; + self.next_fire_id += 1; + Some(FireElement { + start: elem_start, + end: elem_end, + id: fire_id, + }) + } else { + None + }; - for i in rs..re { - let pos = i + self.cur_offset - self.chrom_start as i64; - if pos < 0 || pos >= self.track_len as i64 { - continue; - } - self.fire_coverage[pos as usize] += 1; - self.raw_scores[pos as usize] += score_update; - - // Store the FIRE element at this position if tracking is enabled - if let (Some(fire_elements), Some(elem)) = - (&mut self.fire_elements, fire_element) - { - fire_elements[pos as usize].push(elem); - } - } + for i in rs..re { + let pos = i + self.cur_offset - self.chrom_start as i64; + if pos < 0 || pos >= self.track_len as i64 { + continue; + } + self.fire_coverage[pos as usize] += 1; + self.raw_scores[pos as usize] += score_update; + + // Store the FIRE element at this position if tracking is enabled + if let (Some(fire_elements), Some(elem)) = (&mut self.fire_elements, fire_element) { + fire_elements[pos as usize].push(elem); } - _ => continue, } } // add other sets of data to the FireTrack depending on CLI opts let mut pairs = vec![]; if !self.fire_track_opts.no_nuc { - pairs.push((&mut self.nuc_coverage, &fiber.nuc)); + pairs.push((&mut self.nuc_coverage, fiber.nuc())); } if !self.fire_track_opts.no_msp { - pairs.push((&mut self.msp_coverage, &fiber.msp)); + pairs.push((&mut self.msp_coverage, fiber.msp())); } if self.fire_track_opts.m6a { - pairs.push((&mut self.m6a_coverage, &fiber.m6a)); + pairs.push((&mut self.m6a_coverage, fiber.m6a())); } if self.fire_track_opts.cpg { - pairs.push((&mut self.cpg_coverage, &fiber.cpg)); + pairs.push((&mut self.cpg_coverage, fiber.cpg())); } - for (array, ranges) in pairs { - Self::add_range_set(array, ranges, self.cur_offset, self.chrom_start); + for (array, view) in pairs { + Self::add_range_set(array, &view, self.cur_offset, self.chrom_start); } } diff --git a/src/subcommands/qc.rs b/src/subcommands/qc.rs index c481dafc..e76fb0d2 100644 --- a/src/subcommands/qc.rs +++ b/src/subcommands/qc.rs @@ -112,7 +112,7 @@ impl<'a> QcStats<'a> { /// converts the m6A calls into a boolean vector for the ACF calculation fn add_m6a_starts_for_acf(&mut self, fiber: &fiber::FiberseqData) { // skip conditions - if !self.qc_opts.acf || fiber.m6a.annotations.len() < self.qc_opts.acf_min_m6a { + if !self.qc_opts.acf || fiber.m6a().len() < self.qc_opts.acf_min_m6a { return; } diff --git a/src/utils/fire.rs b/src/utils/fire.rs index 17bf4f3c..38c8dc1f 100644 --- a/src/utils/fire.rs +++ b/src/utils/fire.rs @@ -226,7 +226,7 @@ impl<'a> FireFeats<'a> { fn get_5mc_count(&self, start: i64, end: i64) -> usize { self.rec - .cpg + .cpg() .starts() .iter() .filter(|&&pos| pos >= start && pos < end) @@ -236,7 +236,7 @@ impl<'a> FireFeats<'a> { fn get_m6a_count(&self, start: i64, end: i64) -> usize { let mut m6a_count = self .rec - .m6a + .m6a() .starts() .iter() .filter(|&&pos| pos >= start && pos < end) diff --git a/src/utils/ftexpression.rs b/src/utils/ftexpression.rs index 46e52533..4eb0faf3 100644 --- a/src/utils/ftexpression.rs +++ b/src/utils/ftexpression.rs @@ -178,19 +178,26 @@ pub fn apply_filter_to_range( pub fn apply_filter_fsd(fsd: &mut FiberseqData, filt: &FiberFilters) -> Result<(), anyhow::Error> { if let Some(s) = filt.filter_expression.as_ref() { if !s.is_empty() { - let parsers = parse_filter_all(s.as_str()); - for parser in parsers.iter() { - match parser.feat_name.as_str() { - "msp" => apply_filter_to_range(parser, &mut fsd.msp)?, - "nuc" => apply_filter_to_range(parser, &mut fsd.nuc)?, - "m6a" => apply_filter_to_range(parser, &mut fsd.m6a)?, - "5mC" => apply_filter_to_range(parser, &mut fsd.cpg)?, - _ => { - return Err(anyhow::anyhow!( - "Unknown feature name: {}", - parser.feat_name - )); - } + for parser in parse_filter_all(s.as_str()) { + let type_name = match parser.feat_name.as_str() { + "msp" => "msp", + "nuc" => "nuc", + "m6a" => "m6a", + "5mC" => "cpg", + other => anyhow::bail!("Unknown feature name: {}", other), + }; + match parser.fn_name.as_str() { + "len" => fsd.annotations.retain(type_name, |a| { + len(a.length as i64, &parser.op, &parser.threshold) + }), + "qual" => fsd.annotations.retain(type_name, |a| { + qual( + crate::utils::bamannotations::primary_qual(&a.qualities, type_name), + &parser.op, + &parser.threshold, + ) + }), + other => anyhow::bail!("Invalid function name: {}", other), } } } diff --git a/src/utils/input_bam.rs b/src/utils/input_bam.rs index 90909425..b33d1ce2 100644 --- a/src/utils/input_bam.rs +++ b/src/utils/input_bam.rs @@ -147,17 +147,18 @@ impl FiberFilters { if !self.fire_filter_active() { return true; } - let n_msps = rec.msp.annotations.len(); + let msp = rec.msp(); + let n_msps = msp.len(); if n_msps == 0 { return false; } - if self.resolved_skip_no_m6a() && rec.m6a.annotations.is_empty() { + if self.resolved_skip_no_m6a() && rec.m6a().is_empty() { return false; } if n_msps < self.resolved_min_msp() { return false; } - let ave_msp_size = rec.msp.lengths().iter().sum::() / n_msps as i64; + let ave_msp_size = msp.lengths().iter().sum::() / n_msps as i64; if ave_msp_size < self.resolved_min_ave_msp_size() { return false; } @@ -320,47 +321,31 @@ impl std::default::Default for InputBam { mod tests { use super::*; use crate::fiber::FiberseqData; - use crate::utils::bamannotations::{FiberAnnotation, FiberAnnotations}; use crate::utils::basemods::BaseMods; + use molecular_annotation::{MolecularAnnotations, QualitySpec, Strand}; /// Build a minimal `FiberseqData` shaped only for `passes_fire_filter`. - /// `msp_lengths` populates `rec.msp.annotations` (each entry contributes - /// to count and average size). `m6a_count` controls whether `m6a` - /// annotations are empty or present (only emptiness matters for the - /// filter). + /// `msp_lengths` populates the `msp` annotation type (each entry + /// contributes to count and average size). `m6a_count` controls whether + /// the `m6a` annotation type is empty or present (only emptiness + /// matters for the filter). fn make_fsd(msp_lengths: &[i64], m6a_count: usize) -> FiberseqData { - let msp_anns: Vec = msp_lengths - .iter() - .map(|&len| FiberAnnotation { - start: 0, - end: len, - length: len, - qual: 0, - reference_start: None, - reference_end: None, - reference_length: None, - extra_columns: None, - }) - .collect(); - let m6a_anns: Vec = (0..m6a_count) - .map(|i| FiberAnnotation { - start: i as i64, - end: i as i64 + 1, - length: 1, - qual: 0, - reference_start: None, - reference_end: None, - reference_length: None, - extra_columns: None, - }) - .collect(); + let mut annotations = MolecularAnnotations::new(1000); + if !msp_lengths.is_empty() { + let t = annotations.add_annotation_type("msp", QualitySpec::none()); + for &len in msp_lengths { + t.add(0, len as u32, Strand::Forward, vec![], None); + } + } + if m6a_count > 0 { + let t = annotations.add_annotation_type("m6a", "Q".parse().expect("Q parses")); + for i in 0..m6a_count { + t.add(i as u32, 1, Strand::Forward, vec![0], None); + } + } FiberseqData { record: rust_htslib::bam::Record::new(), - annotations: molecular_annotation::MolecularAnnotations::new(1000), - msp: FiberAnnotations::from_annotations(msp_anns, 1000, false), - nuc: FiberAnnotations::from_annotations(vec![], 1000, false), - m6a: FiberAnnotations::from_annotations(m6a_anns, 1000, false), - cpg: FiberAnnotations::from_annotations(vec![], 1000, false), + annotations, base_mods: BaseMods { base_mods: vec![] }, ec: 0.0, target_name: ".".to_string(), diff --git a/tests/extract_test.rs b/tests/extract_test.rs index 6353d86e..8f23ae2d 100644 --- a/tests/extract_test.rs +++ b/tests/extract_test.rs @@ -26,7 +26,7 @@ fn test_msp_extract() -> Result<(), Box> { let fiber_records = get_fiber_data_from_test_bam("tests/data/msp_nuc.bam"); assert!(fiber_records.len() == 1); let fiber_data = &fiber_records[0]; - assert_eq!(fiber_data.msp.option_starts(), expected_msp_starts); + assert_eq!(fiber_data.msp().option_starts(), expected_msp_starts); Ok(()) } @@ -34,18 +34,18 @@ fn test_msp_extract() -> Result<(), Box> { fn test_many_msps() { let fiber_records = get_fiber_data_from_test_bam("tests/data/all.bam"); for fiber_data in fiber_records { - let m6a_starts = fiber_data.m6a.starts(); + let m6a_starts = fiber_data.m6a().starts(); let m6a = m6a_starts.iter().collect::>(); if m6a.is_empty() { continue; } - let msps = fiber_data - .msp + let msp_view = fiber_data.msp(); + let msps = msp_view .starts() .iter() .copied() - .chain(fiber_data.msp.ends().iter().map(|&x| x - 1)) + .chain(msp_view.ends().iter().map(|&x| x - 1)) .collect::>(); eprintln!("m6a: {m6a:?}"); eprintln!("msp: {msps:?}"); diff --git a/tests/m6a_prediction_test.rs b/tests/m6a_prediction_test.rs index ccdf4808..045e02f6 100644 --- a/tests/m6a_prediction_test.rs +++ b/tests/m6a_prediction_test.rs @@ -14,12 +14,16 @@ fn sum_qual(bam: &mut Reader) -> usize { let max_pos = (fiber.record.seq_len() - WINDOW / 2) as i64; let mut this_count = 0; let this_qual_sum = fiber - .m6a + .m6a() .into_iter() - .filter(|annotation| annotation.start >= min_pos && annotation.end < max_pos) - .map(|annotation| { + .filter(|info| { + let s = info.query_start as i64; + let e = info.query_end as i64; + s >= min_pos && e < max_pos + }) + .map(|info| { this_count += 1; - annotation.qual as usize + info.qualities.first().copied().unwrap_or(0) as usize }) .sum::(); sum += this_qual_sum; From 9fafbc7e786d4ff8b587684c70de75040132a14d Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Tue, 12 May 2026 11:10:59 -0600 Subject: [PATCH 10/24] =?UTF-8?q?refactor:=20migrate=20fibertig=20BED=20?= =?UTF-8?q?=E2=86=94=20BAM=20pipeline=20onto=20MA=20spec?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Adds `read_fibertig_tags` / `write_fibertig_tags` helpers and a `FIBERTIG_TYPE = "fibertig"` annotation type name. The fs/fl/fa BAM tag wire format is unchanged (positions in molecular orientation, fa as `|`-separated chunks with `;`-joined columns), so existing fibertig-annotated BAMs decode byte-for-byte identically. In memory the pipeline now uses MolecularAnnotations / Annotation throughout: - read_bed_annotations returns HashMap. - approximately_divide_annotations_by_window_size operates on MolecularAnnotations. - create_annotated_records_from_splits shifts coords record-relative and writes via write_fibertig_tags. - extract_to_bed reads via read_fibertig_tags and lifts ref coords through the record's aligned blocks. The Annotation.name field carries the BED column 4+ payload as a single semicolon-joined string, so each annotation owns its own extras — the historical fa-pairing concern around shared/overlapping peaks (and the `forward_extras` plumbing in FiberAnnotations) is structurally impossible now. Tests in tests/fibertig_test.rs updated to the new API. Storage is molecular ascending (matches fs input order), and iter_type yields BAM-orient query coords + lifted ref coords. Remaining users of FiberAnnotations: BaseMods (ML/MM-derived ranges held internally). `FiberAnnotations::from_bam_tags` / `write_to_bam_tags` on bamannotations.rs are now unused dead code; left in place for a followup that also migrates BaseMods and lets us delete FiberAnnotations + bamlift.rs entirely. --- src/utils/fibertig.rs | 377 ++++++++++++++++++++++++++--------------- tests/fibertig_test.rs | 300 ++++++++++++-------------------- 2 files changed, 348 insertions(+), 329 deletions(-) diff --git a/src/utils/fibertig.rs b/src/utils/fibertig.rs index 08a08890..be7eb4fc 100644 --- a/src/utils/fibertig.rs +++ b/src/utils/fibertig.rs @@ -1,13 +1,120 @@ use crate::cli::PgInjectOptions; use crate::subcommands::pg_pansn; -pub use crate::utils::bamannotations::{FiberAnnotation, FiberAnnotations}; use crate::utils::bio_io; use anyhow::{Context, Result}; +use molecular_annotation::{AlignedBlocks, MolecularAnnotations, QualitySpec, Strand}; use noodles::fasta; +use rust_htslib::bam::ext::BamRecordExtensions; use rust_htslib::bam::header::HeaderRecord; +use rust_htslib::bam::record::Aux; use rust_htslib::bam::{Header, HeaderView, Read, Record}; use std::collections::HashMap; +/// Annotation type name used by the fibertig BED ↔ BAM pipeline. +pub const FIBERTIG_TYPE: &str = "fibertig"; + +/// Read the fibertig fs/fl/fa BAM tags into a [`MolecularAnnotations`]. +/// +/// - `fs`: feature starts (`B:I`), one per peak, molecular orientation. +/// - `fl`: feature lengths (`B:I`), one per peak, same order. +/// - `fa`: pipe-separated extras (`Z`), one chunk per peak in the same +/// order; within a chunk, columns from the source BED are joined by +/// `;`. Missing/blank entries map to `name = None` on the annotation. +/// +/// The returned [`MolecularAnnotations`] has the record's aligned blocks +/// set so ref coords can be lifted via `iter_type` / `get_ref_coords`. +pub fn read_fibertig_tags(record: &Record) -> Result { + // Build AlignedBlocks directly from `aligned_block_pairs` rather than + // `from_record`, because the spec's `from_record` early-returns empty + // for records that report `is_unmapped()` — synthetic test records + // built with `Record::new()` can hit that path even when they have a + // valid CIGAR and tid. + let mut annot = MolecularAnnotations::new(record.seq_len() as u32); + let pairs = record + .aligned_block_pairs() + .map(|([qs, qe], [rs, re])| ([qs as u32, qe as u32], [rs as u32, re as u32])); + annot.set_aligned_blocks_raw( + AlignedBlocks::from_pairs(pairs, record.seq_len() as u32), + record.is_reverse(), + ); + let fs = match record.aux(b"fs") { + Ok(Aux::ArrayU32(arr)) => Some(arr.iter().collect::>()), + Ok(Aux::ArrayI32(arr)) => Some(arr.iter().map(|v| v as u32).collect()), + _ => None, + }; + let fl = match record.aux(b"fl") { + Ok(Aux::ArrayU32(arr)) => Some(arr.iter().collect::>()), + Ok(Aux::ArrayI32(arr)) => Some(arr.iter().map(|v| v as u32).collect()), + _ => None, + }; + let (Some(fs), Some(fl)) = (fs, fl) else { + return Ok(annot); + }; + if fs.len() != fl.len() { + anyhow::bail!("fs ({}) and fl ({}) length mismatch", fs.len(), fl.len()); + } + if fs.is_empty() { + return Ok(annot); + } + + let names: Option>> = match record.aux(b"fa") { + Ok(Aux::String(s)) => { + let parts: Vec> = s + .split('|') + .map(|p| if p.is_empty() { None } else { Some(p.to_string()) }) + .collect(); + if parts.len() != fs.len() { + anyhow::bail!( + "fa ({}) and fs ({}) length mismatch", + parts.len(), + fs.len() + ); + } + Some(parts) + } + _ => None, + }; + + let t = annot.add_annotation_type(FIBERTIG_TYPE, QualitySpec::none()); + for (i, (s, l)) in fs.iter().zip(fl.iter()).enumerate() { + let name = names.as_ref().and_then(|v| v[i].clone()); + t.add(*s, *l, Strand::Forward, vec![], name); + } + Ok(annot) +} + +/// Write the fibertig fs/fl/fa BAM tags from a [`MolecularAnnotations`]'s +/// [`FIBERTIG_TYPE`] annotations. No-op when the type is absent or empty. +/// `fa` is only emitted if at least one annotation has a non-empty name. +pub fn write_fibertig_tags(record: &mut Record, annot: &MolecularAnnotations) -> Result<()> { + let Some(t) = annot.get_type(FIBERTIG_TYPE) else { + return Ok(()); + }; + if t.annotations.is_empty() { + return Ok(()); + } + let fs: Vec = t.annotations.iter().map(|a| a.start).collect(); + let fl: Vec = t.annotations.iter().map(|a| a.length).collect(); + record + .push_aux(b"fs", Aux::ArrayU32((&fs).into())) + .context("Failed to add fs tag")?; + record + .push_aux(b"fl", Aux::ArrayU32((&fl).into())) + .context("Failed to add fl tag")?; + if t.annotations.iter().any(|a| a.name.is_some()) { + let fa: String = t + .annotations + .iter() + .map(|a| a.name.as_deref().unwrap_or("")) + .collect::>() + .join("|"); + record + .push_aux(b"fa", Aux::String(&fa)) + .context("Failed to add fa tag")?; + } + Ok(()) +} + pub struct FiberTig { pub header: Header, pub records: Vec, @@ -15,18 +122,28 @@ pub struct FiberTig { } impl FiberTig { - /// Read BED file and return a mapping from contig name to FiberAnnotations and the header line if present + /// Read a BED file and return per-contig [`MolecularAnnotations`] plus + /// the BED header line if present. Each BED row becomes one annotation + /// in the [`FIBERTIG_TYPE`] type; extra columns (4..N) are `;`-joined + /// into [`Annotation::name`] so they round-trip through the `fa` BAM + /// tag's `|`-separated layout. + /// + /// Annotations within each contig are sorted by molecular start, and + /// each [`MolecularAnnotations`]'s `read_length` is set to that + /// contig's length from the BAM header (no aligned blocks are needed + /// here — ref coords for identity-aligned records are derived later). pub fn read_bed_annotations( bed_path: &str, header_view: &HeaderView, - ) -> Result<(HashMap, Option)> { + ) -> Result<(HashMap, Option)> { use std::io::BufRead; let reader = bio_io::buffer_from(bed_path).context("Failed to open BED file")?; - let mut contig_annotations: HashMap> = HashMap::new(); + // Per-contig (start, length, name) tuples collected first so we can + // sort by start before pushing into MolecularAnnotations. + let mut contig_rows: HashMap)>> = HashMap::new(); let mut bed_header: Option = None; - // Parse BED file line by line (simple approach) for (line_num, line) in reader.lines().enumerate() { let line = line?; if line.starts_with('#') && line_num == 0 { @@ -34,70 +151,57 @@ impl FiberTig { continue; } if line.starts_with('#') || line.trim().is_empty() { - continue; // Skip comments and empty lines + continue; } let fields: Vec<&str> = line.split('\t').collect(); if fields.len() < 3 { - continue; // Skip malformed lines + continue; } let contig_name = fields[0].to_string(); - let start: i64 = fields[1] + let start: u32 = fields[1] .parse() .context("Failed to parse start position")?; - let end: i64 = fields[2].parse().context("Failed to parse end position")?; + let end: u32 = fields[2].parse().context("Failed to parse end position")?; let length = end - start; - // Capture extra columns if they exist (columns 4 and beyond) - let extra_columns = if fields.len() > 3 { - Some(fields[3..].iter().map(|s| s.to_string()).collect()) + // BED columns 4+ → fa tag chunk (joined with ';') + let name = if fields.len() > 3 { + Some(fields[3..].join(";")) } else { None }; - let annotation = FiberAnnotation { - start, - end, - length, - qual: 0, - reference_start: Some(start), - reference_end: Some(end), - reference_length: Some(length), - extra_columns, - }; - - contig_annotations + contig_rows .entry(contig_name) .or_default() - .push(annotation); + .push((start, length, name)); } - // Convert to FiberAnnotations for each contig - let mut fiber_annotations_map = HashMap::new(); - for (contig_name, mut annotations) in contig_annotations { - // Sort annotations by start position for this contig - annotations.sort_by_key(|a| a.start); + let mut out = HashMap::new(); + for (contig_name, mut rows) in contig_rows { + rows.sort_by_key(|(s, _, _)| *s); - // Get sequence length for this contig let tid = header_view .tid(contig_name.as_bytes()) .with_context(|| format!("Contig '{contig_name}' not found in BAM header"))?; let seq_len = header_view .target_len(tid) .with_context(|| format!("Failed to get length for contig '{contig_name}'"))? - as i64; + as u32; - let fiber_annotations = FiberAnnotations::from_annotations( - annotations, - seq_len, - false, // BED coordinates are always forward - ); - - fiber_annotations_map.insert(contig_name, fiber_annotations); + let mut annot = MolecularAnnotations::new(seq_len); + if !rows.is_empty() { + let t = annot.add_annotation_type(FIBERTIG_TYPE, QualitySpec::none()); + for (s, l, name) in rows { + t.add(s, l, Strand::Forward, vec![], name); + } + } + out.insert(contig_name, annot); } - Ok((fiber_annotations_map, bed_header)) + Ok((out, bed_header)) } pub fn read_fasta_into_vec(fasta_path: &str) -> Result> { @@ -170,76 +274,85 @@ impl FiberTig { record } - /// Determine split points based on BED annotations - /// For each sequence, find the first annotation that ends past split_size and use that as split point + /// Determine split points based on BED annotations. + /// For each sequence, find the first annotation that ends past + /// `split_size` and use that as the split boundary. The split bound + /// extends out past `split_size` if needed so no annotation is cut + /// in half. + /// + /// Returns `((window_start, window_end), per-window MolecularAnnotations)`. + /// Coordinates in the returned annotations are still contig-absolute; + /// `create_annotated_records_from_splits` shifts them record-relative + /// when building each record's `fs`/`fl` tags. pub fn approximately_divide_annotations_by_window_size( seq_len: i64, split_size: i64, - annotations: &FiberAnnotations, - ) -> Vec<((i64, i64), FiberAnnotations)> { - let mut split_to_annotations: Vec<((i64, i64), FiberAnnotations)> = Vec::new(); + annotations: &MolecularAnnotations, + ) -> Vec<((i64, i64), MolecularAnnotations)> { + let read_length = annotations.read_length; + let peaks: Vec<(u32, u32, Option)> = annotations + .get_type(FIBERTIG_TYPE) + .map(|t| { + t.annotations + .iter() + .map(|a| (a.start, a.length, a.name.clone())) + .collect() + }) + .unwrap_or_default(); if split_size >= seq_len { - split_to_annotations.push(((0, seq_len), annotations.clone())); - return split_to_annotations; + return vec![((0, seq_len), annotations.clone())]; } - let mut current_start = 0; - let mut current_target_end = std::cmp::min(split_size, seq_len); - let mut current_annotations = Vec::new(); - let mut anno_index = 0; - - while anno_index < annotations.annotations.len() { - let anno = &annotations.annotations[anno_index]; - // If the annotation starts after the current target end, we need to split - if anno.start >= current_target_end { - // Save the current split - split_to_annotations.push(( - (current_start, current_target_end), - FiberAnnotations::from_annotations( - current_annotations.clone(), - seq_len, - false, // BED coordinates are always forward - ), - )); - - // Move to the next split - current_start = anno.start; - current_target_end = std::cmp::min(current_start + split_size, seq_len); - current_annotations.clear(); + let mut out: Vec<((i64, i64), MolecularAnnotations)> = Vec::new(); + let mut current_start: i64 = 0; + let mut current_target_end: i64 = std::cmp::min(split_size, seq_len); + let mut current_peaks: Vec<(u32, u32, Option)> = Vec::new(); + + let mut push_window = |start: i64, end: i64, peaks: Vec<(u32, u32, Option)>| { + let mut annot = MolecularAnnotations::new(read_length); + if !peaks.is_empty() { + let t = annot.add_annotation_type(FIBERTIG_TYPE, QualitySpec::none()); + for (s, l, name) in peaks { + t.add(s, l, Strand::Forward, vec![], name); + } } + out.push(((start, end), annot)); + }; - // if the annotation ends after the current target end, we need to extend the target end - if anno.end > current_target_end { - current_target_end = anno.end; + for (s, l, name) in peaks { + let s_i = s as i64; + let e_i = (s + l) as i64; + if s_i >= current_target_end { + // close the current window before starting a new one + push_window( + current_start, + current_target_end, + std::mem::take(&mut current_peaks), + ); + current_start = s_i; + current_target_end = std::cmp::min(current_start + split_size, seq_len); } - // Add the annotation to the current annotations - current_annotations.push(anno.clone()); - anno_index += 1; + if e_i > current_target_end { + current_target_end = e_i; + } + current_peaks.push((s, l, name)); } - // If we have any remaining annotations after the last split, add them - if !current_annotations.is_empty() { - current_target_end = std::cmp::min(seq_len, current_target_end); - split_to_annotations.push(( - (current_start, current_target_end), - FiberAnnotations::from_annotations( - current_annotations, - seq_len, - false, // BED coordinates are always forward - ), - )); + if !current_peaks.is_empty() { + let end = std::cmp::min(seq_len, current_target_end); + push_window(current_start, end, current_peaks); } - split_to_annotations + out } - /// Create BAM records from split annotations and sequence - /// This combines record creation and annotation in one step + /// Create BAM records from split annotations and sequence. + /// Combines record creation and annotation in one step. pub fn create_annotated_records_from_splits( contig_name: &str, fasta_record: &fasta::record::Record, - split_annotations: &mut [((i64, i64), FiberAnnotations)], + split_annotations: &mut [((i64, i64), MolecularAnnotations)], header_view: &HeaderView, ) -> Result> { let mut records = Vec::new(); @@ -302,20 +415,17 @@ impl FiberTig { .push_aux(b"xe", rust_htslib::bam::record::Aux::U32(end_pos as u32)) .context("Failed to add xe tag")?; - // Apply annotations to this record - // Adjust annotation coordinates to be relative to record start - for annotation in annotations.annotations.iter_mut() { - annotation.start -= start_pos as i64; - annotation.end -= start_pos as i64; + // Apply annotations to this record. Coordinates in `annotations` + // are still contig-absolute (per + // `approximately_divide_annotations_by_window_size`), so shift + // them record-relative before writing the fs/fl tags. + if let Some(t) = annotations.get_type_mut(FIBERTIG_TYPE) { + for a in t.annotations.iter_mut() { + a.start = a.start.saturating_sub(start_pos as u32); + } } - // Write annotations to BAM tags - annotations.write_to_bam_tags( - &mut record, - b"fs", // feature starts - b"fl", // feature lengths - Some(b"fa"), // feature annotations (extra columns) - )?; + write_fibertig_tags(&mut record, annotations)?; records.push(record); } @@ -465,7 +575,7 @@ impl FiberTig { // Determine split points based on annotations let mut split_annotations = Self::approximately_divide_annotations_by_window_size( - annotations.seq_len, + annotations.read_length as i64, split_size as i64, annotations, ); @@ -531,65 +641,50 @@ impl FiberTig { // IO functions // - /// Extract BED annotations from an annotated BAM file using FiberAnnotations + /// Extract BED annotations from an annotated BAM file using the fs/fl/fa + /// tags and the record's aligned blocks (for ref coords). pub fn extract_to_bed(opts: &PgInjectOptions) -> Result<()> { use crate::utils::bio_io; use std::io::Write; - // Open the BAM file (using the reference field as the input BAM) let mut reader = bio_io::bam_reader(&opts.reference); let mut header = Header::from_template(reader.header()); pg_pansn::apply_pansn_transformations(&mut header, &opts.pansn)?; let header_view = HeaderView::from_header(&header); - // Open output file for BED data let mut writer = bio_io::writer(&opts.out)?; - // Extract and write BED header if present if let Some(bed_header) = Self::extract_bed_header_from_bam_header(&header) { writeln!(writer, "{}", bed_header)?; } - // Read through BAM records and extract annotations for result in reader.records() { let record = result?; - - // Skip unmapped reads if record.tid() < 0 { continue; } - - // Try to extract annotations using the standard fs/fl/fa tags - if let Some(fiber_annotations) = FiberAnnotations::from_bam_tags( - &record, - b"fs", // feature starts - b"fl", // feature lengths - Some(b"fa"), // feature annotations - )? { - // Get contig name from header - let contig_name = - std::str::from_utf8(header_view.tid2name(record.tid() as u32))?.to_string(); - - // Write each annotation as a BED line - for annotation in &fiber_annotations.annotations { - // Skip if reference coordinates are None - let (ref_start, ref_end) = - match (annotation.reference_start, annotation.reference_end) { - (Some(start), Some(end)) => (start, end), - _ => continue, // Skip this annotation if coordinates are missing - }; - - // Write basic BED format (chrom, start, end) - write!(writer, "{contig_name}\t{ref_start}\t{ref_end}")?; - - // Add extra columns if they exist - if let Some(ref extra_cols) = annotation.extra_columns { - for col in extra_cols { - write!(writer, "\t{col}")?; - } + let annot = read_fibertig_tags(&record)?; + if annot.get_type(FIBERTIG_TYPE).is_none() { + continue; + } + let contig_name = + std::str::from_utf8(header_view.tid2name(record.tid() as u32))?.to_string(); + + for info in annot + .iter_type(FIBERTIG_TYPE) + .into_iter() + .flatten() + { + let (Some(ref_start), Some(ref_end)) = (info.ref_start, info.ref_end) else { + continue; + }; + write!(writer, "{contig_name}\t{ref_start}\t{ref_end}")?; + if let Some(name) = info.name { + for col in name.split(';') { + write!(writer, "\t{col}")?; } - writeln!(writer)?; } + writeln!(writer)?; } } diff --git a/tests/fibertig_test.rs b/tests/fibertig_test.rs index e811a24c..89fc347d 100644 --- a/tests/fibertig_test.rs +++ b/tests/fibertig_test.rs @@ -1,10 +1,20 @@ use anyhow::Result; use fibertools_rs::cli::{GlobalOpts, PansnParameters, PgInjectOptions}; -use fibertools_rs::utils::fibertig::{FiberAnnotation, FiberAnnotations, FiberTig}; +use fibertools_rs::utils::fibertig::{read_fibertig_tags, FiberTig, FIBERTIG_TYPE}; +use molecular_annotation::{MolecularAnnotations, QualitySpec, Strand}; use rust_htslib::bam::HeaderView; use std::io::Write; use tempfile::NamedTempFile; +/// Convenience: borrow the `fibertig` annotation type out of a +/// MolecularAnnotations, panicking if it isn't present. +fn fibertig_anns(annot: &MolecularAnnotations) -> &[molecular_annotation::Annotation] { + &annot + .get_type(FIBERTIG_TYPE) + .expect("fibertig annotation type missing") + .annotations +} + #[test] fn test_from_fasta_simple() -> Result<()> { // Create a temporary FASTA file @@ -65,19 +75,20 @@ fn test_read_bed_annotations() -> Result<()> { // Verify annotations were parsed correctly assert_eq!(annotations.len(), 1); let chr1_annotations = annotations.get("chr1").unwrap(); - assert_eq!(chr1_annotations.annotations.len(), 2); - assert_eq!(chr1_annotations.seq_len, 20); + let anns = fibertig_anns(chr1_annotations); + assert_eq!(anns.len(), 2); + assert_eq!(chr1_annotations.read_length, 20); // Check first annotation - let first_ann = &chr1_annotations.annotations[0]; + let first_ann = &anns[0]; assert_eq!(first_ann.start, 5); - assert_eq!(first_ann.end, 10); + assert_eq!(first_ann.end(), 10); assert_eq!(first_ann.length, 5); // Check second annotation - let second_ann = &chr1_annotations.annotations[1]; + let second_ann = &anns[1]; assert_eq!(second_ann.start, 15); - assert_eq!(second_ann.end, 18); + assert_eq!(second_ann.end(), 18); assert_eq!(second_ann.length, 3); Ok(()) @@ -107,56 +118,28 @@ fn test_bed_annotations_sorted() -> Result<()> { FiberTig::read_bed_annotations(bed_file.path().to_str().unwrap(), &header_view)?; let chr1_annotations = annotations.get("chr1").unwrap(); - assert_eq!(chr1_annotations.annotations.len(), 2); + let anns = fibertig_anns(chr1_annotations); + assert_eq!(anns.len(), 2); // Should be sorted by start position - assert_eq!(chr1_annotations.annotations[0].start, 5); - assert_eq!(chr1_annotations.annotations[1].start, 15); + assert_eq!(anns[0].start, 5); + assert_eq!(anns[1].start, 15); Ok(()) } #[test] fn test_approximately_divide_annotations_by_window_size() -> Result<()> { - // Create test annotations - let annotations = vec![ - FiberAnnotation { - start: 5, - end: 15, - length: 10, - qual: 0, - reference_start: Some(5), - reference_end: Some(15), - reference_length: Some(10), - extra_columns: Some(vec!["feature1".to_string()]), - }, - FiberAnnotation { - start: 25, - end: 35, - length: 10, - qual: 0, - reference_start: Some(25), - reference_end: Some(35), - reference_length: Some(10), - extra_columns: Some(vec!["feature2".to_string()]), - }, - FiberAnnotation { - start: 45, - end: 55, - length: 10, - qual: 0, - reference_start: Some(45), - reference_end: Some(55), - reference_length: Some(10), - extra_columns: Some(vec!["feature3".to_string()]), - }, - ]; - - let fiber_annotations = FiberAnnotations::from_annotations(annotations, 100, false); + let mut annot = MolecularAnnotations::new(100); + { + let t = annot.add_annotation_type(FIBERTIG_TYPE, QualitySpec::none()); + t.add(5, 10, Strand::Forward, vec![], Some("feature1".into())); + t.add(25, 10, Strand::Forward, vec![], Some("feature2".into())); + t.add(45, 10, Strand::Forward, vec![], Some("feature3".into())); + } // Test with split size 30 - should create splits that respect annotation boundaries - let splits = - FiberTig::approximately_divide_annotations_by_window_size(100, 30, &fiber_annotations); + let splits = FiberTig::approximately_divide_annotations_by_window_size(100, 30, &annot); // Should have multiple splits assert!(splits.len() > 1); @@ -166,7 +149,10 @@ fn test_approximately_divide_annotations_by_window_size() -> Result<()> { for ((start, end), split_annotations) in &splits { assert!(*start < *end); assert!(*end <= 100); - total_annotations += split_annotations.annotations.len(); + total_annotations += split_annotations + .get_type(FIBERTIG_TYPE) + .map(|t| t.annotations.len()) + .unwrap_or(0); } // Should have all 3 annotations distributed across splits @@ -191,36 +177,18 @@ fn test_create_annotated_records_from_splits() -> Result<()> { let mut split_annotations = Vec::new(); // First split: 0-20 - let split1_anns = vec![FiberAnnotation { - start: 5, - end: 15, - length: 10, - qual: 0, - reference_start: Some(5), - reference_end: Some(15), - reference_length: Some(10), - extra_columns: Some(vec!["feature1".to_string()]), - }]; - split_annotations.push(( - (0, 20), - FiberAnnotations::from_annotations(split1_anns, 36, false), - )); + let mut split1 = MolecularAnnotations::new(36); + split1 + .add_annotation_type(FIBERTIG_TYPE, QualitySpec::none()) + .add(5, 10, Strand::Forward, vec![], Some("feature1".into())); + split_annotations.push(((0, 20), split1)); // Second split: 20-36 - let split2_anns = vec![FiberAnnotation { - start: 25, - end: 35, - length: 10, - qual: 0, - reference_start: Some(25), - reference_end: Some(35), - reference_length: Some(10), - extra_columns: Some(vec!["feature2".to_string()]), - }]; - split_annotations.push(( - (20, 36), - FiberAnnotations::from_annotations(split2_anns, 36, false), - )); + let mut split2 = MolecularAnnotations::new(36); + split2 + .add_annotation_type(FIBERTIG_TYPE, QualitySpec::none()) + .add(25, 10, Strand::Forward, vec![], Some("feature2".into())); + split_annotations.push(((20, 36), split2)); // Create records from splits let records = FiberTig::create_annotated_records_from_splits( @@ -488,158 +456,114 @@ fn build_tagged_record( } #[test] -fn test_from_bam_tags_fa_pairing_forward_strand() -> Result<()> { - // Forward-strand sanity: no flip happens, extras must pair with the same-index peaks. - // Four non-overlapping peaks with distinguishable sizes and distinguishable fa values. +fn test_read_fibertig_tags_forward_strand() -> Result<()> { + // Forward-strand sanity: storage order matches fs/fl input order; iter_type + // gives BAM-orient query coords that for a forward identity-aligned record + // equal molecular coords, and ref_start/ref_end equal query_start/query_end. let seq_len: u32 = 10_000; let fs: Vec = vec![100, 1_000, 3_000, 6_000]; let fl: Vec = vec![100, 300, 500, 700]; let fa = "peakA|peakB|peakC|peakD"; let record = build_tagged_record(seq_len, &fs, &fl, fa, false); + let annot = read_fibertig_tags(&record)?; + let anns = fibertig_anns(&annot); + assert_eq!(anns.len(), 4); + assert!(!annot.is_reverse_aligned()); - let anns = FiberAnnotations::from_bam_tags(&record, b"fs", b"fl", Some(b"fa"))? - .expect("tags should parse"); - - assert_eq!(anns.annotations.len(), 4); - assert!(!anns.reverse); - - // Pure-match CIGAR at pos 0, forward: ref coords == query coords == fs/fl + // Storage = molecular ascending = fs input order. let expected = [ - (100_i64, 200_i64, "peakA"), + (100_u32, 200_u32, "peakA"), (1_000, 1_300, "peakB"), (3_000, 3_500, "peakC"), (6_000, 6_700, "peakD"), ]; - for (ann, (exp_start, exp_end, exp_tag)) in anns.annotations.iter().zip(expected.iter()) { - assert_eq!(ann.reference_start, Some(*exp_start)); - assert_eq!(ann.reference_end, Some(*exp_end)); - assert_eq!( - ann.extra_columns.as_ref().map(|c| c.join(";")), - Some((*exp_tag).to_string()), - ); + let infos: Vec<_> = annot.iter_type(FIBERTIG_TYPE).unwrap().collect(); + for (info, (exp_start, exp_end, exp_name)) in infos.iter().zip(expected.iter()) { + assert_eq!(info.ref_start, Some(*exp_start)); + assert_eq!(info.ref_end, Some(*exp_end)); + assert_eq!(info.name, Some(*exp_name)); } Ok(()) } #[test] -fn test_from_bam_tags_fa_pairing_reverse_strand_multi_peak() -> Result<()> { - // Reverse-strand regression test for the fa-swap bug. Five peaks with distinguishable - // sizes ensures that any off-by-one pairing error (pairwise swap, full reversal, etc.) - // is caught. Last two peaks OVERLAP in forward/contig coords, matching the original - // reported symptom where adjacent overlapping peaks had extras swapped. +fn test_read_fibertig_tags_reverse_strand_multi_peak() -> Result<()> { + // Reverse-strand parsing: read_fibertig_tags stores molecular coords as + // given by fs/fl. iter_type then yields AnnotationInfo with BAM-orient + // query coords (= read_len - molecular_end / read_len - molecular_start), + // and ref_start/ref_end via the record's aligned blocks. Storage order + // stays molecular ascending (fs input order); each annotation keeps its + // own name slot, so pairing can't be scrambled by sorting. let seq_len: u32 = 10_000; let fs: Vec = vec![100, 1_000, 3_000, 6_000, 6_500]; let fl: Vec = vec![100, 300, 500, 700, 900]; let fa = "peakA|peakB|peakC|peakD|peakE"; let record = build_tagged_record(seq_len, &fs, &fl, fa, true); - - let anns = FiberAnnotations::from_bam_tags(&record, b"fs", b"fl", Some(b"fa"))? - .expect("tags should parse"); - - assert_eq!(anns.annotations.len(), 5); - assert!(anns.reverse); - - // On reverse-strand with pure-match CIGAR at pos 0: - // forward peak [s, s+l) --> ref peak [seq_len - (s+l), seq_len - s) - // Peaks in ascending ref-start order after flip: - // peakE forward [6500, 7400) -> ref [2600, 3500), len 900 - // peakD forward [6000, 6700) -> ref [3300, 4000), len 700 - // peakC forward [3000, 3500) -> ref [6500, 7000), len 500 - // peakB forward [1000, 1300) -> ref [8700, 9000), len 300 - // peakA forward [100, 200) -> ref [9800, 9900), len 100 + let annot = read_fibertig_tags(&record)?; + let anns = fibertig_anns(&annot); + assert_eq!(anns.len(), 5); + assert!(annot.is_reverse_aligned()); + + // BAM-orient: forward [s, s+l) maps to ref [seq_len - (s+l), seq_len - s). + // Storage order is molecular ascending, so iter_type yields: + // peakA forward [100, 200) -> ref [9800, 9900) + // peakB forward [1000, 1300) -> ref [8700, 9000) + // peakC forward [3000, 3500) -> ref [6500, 7000) + // peakD forward [6000, 6700) -> ref [3300, 4000) + // peakE forward [6500, 7400) -> ref [2600, 3500) let expected = [ - (2_600_i64, 3_500_i64, 900_i64, "peakE"), - (3_300, 4_000, 700, "peakD"), - (6_500, 7_000, 500, "peakC"), - (8_700, 9_000, 300, "peakB"), - (9_800, 9_900, 100, "peakA"), + (9_800_u32, 9_900_u32, "peakA"), + (8_700, 9_000, "peakB"), + (6_500, 7_000, "peakC"), + (3_300, 4_000, "peakD"), + (2_600, 3_500, "peakE"), ]; - for (i, (ann, (exp_start, exp_end, exp_len, exp_tag))) in - anns.annotations.iter().zip(expected.iter()).enumerate() + let infos: Vec<_> = annot.iter_type(FIBERTIG_TYPE).unwrap().collect(); + for (i, (info, (exp_start, exp_end, exp_name))) in infos.iter().zip(expected.iter()).enumerate() { - assert_eq!( - ann.reference_start, - Some(*exp_start), - "ref_start mismatch at index {i}" - ); - assert_eq!( - ann.reference_end, - Some(*exp_end), - "ref_end mismatch at index {i}" - ); - assert_eq!( - ann.reference_length, - Some(*exp_len), - "ref_length mismatch at index {i}" - ); - assert_eq!( - ann.extra_columns.as_ref().map(|c| c.join(";")), - Some((*exp_tag).to_string()), - "fa-extras pairing wrong at index {i} (size {exp_len}): got {:?}", - ann.extra_columns, - ); + assert_eq!(info.ref_start, Some(*exp_start), "ref_start mismatch at {i}"); + assert_eq!(info.ref_end, Some(*exp_end), "ref_end mismatch at {i}"); + assert_eq!(info.name, Some(*exp_name), "name mismatch at {i}"); } Ok(()) } #[test] -fn test_from_bam_tags_fa_pairing_reverse_strand_shared_start() -> Result<()> { - // Regression test for Anna's fibertig peak-length scrambling: two peaks share - // forward-strand start position 0 (fs=0), and all four peaks overlap heavily. - // After flipping to aligned coordinates the sort by aligned start is no longer - // equivalent to reversing the input order, so a naive `ann_vals.reverse()` - // breaks the extras pairing. The extras must be carried through the sort. +fn test_read_fibertig_tags_reverse_strand_shared_start() -> Result<()> { + // Regression test for fa-pairing scrambling under shared/overlapping + // start positions. With the MA-spec model each Annotation owns its own + // name, so there is no sort-induced pairing problem to begin with — + // storage order matches fs input order regardless of overlap. let seq_len: u32 = 1_000; let fs: Vec = vec![0, 0, 12, 159]; let fl: Vec = vec![263, 124, 209, 305]; let fa = "peakA|peakB|peakC|peakD"; let record = build_tagged_record(seq_len, &fs, &fl, fa, true); - - let anns = FiberAnnotations::from_bam_tags(&record, b"fs", b"fl", Some(b"fa"))? - .expect("tags should parse"); - - assert_eq!(anns.annotations.len(), 4); - assert!(anns.reverse); - - // forward peak [s, s+l) -> ref peak [seq_len - (s+l), seq_len - s) - // peakA forward [0, 263) -> ref [737, 1000), len 263 - // peakB forward [0, 124) -> ref [876, 1000), len 124 - // peakC forward [12, 221) -> ref [779, 988), len 209 - // peakD forward [159, 464) -> ref [536, 841), len 305 - // Ref-start ascending: D, A, C, B. + let annot = read_fibertig_tags(&record)?; + let anns = fibertig_anns(&annot); + assert_eq!(anns.len(), 4); + assert!(annot.is_reverse_aligned()); + + // Storage order = fs input order, ref coords lifted via flip_range for reverse. + // peakA forward [0, 263) -> ref [737, 1000) + // peakB forward [0, 124) -> ref [876, 1000) + // peakC forward [12, 221) -> ref [779, 988) + // peakD forward [159, 464) -> ref [536, 841) let expected = [ - (536_i64, 841_i64, 305_i64, "peakD"), - (737, 1_000, 263, "peakA"), - (779, 988, 209, "peakC"), - (876, 1_000, 124, "peakB"), + (737_u32, 1_000_u32, "peakA"), + (876, 1_000, "peakB"), + (779, 988, "peakC"), + (536, 841, "peakD"), ]; - for (i, (ann, (exp_start, exp_end, exp_len, exp_tag))) in - anns.annotations.iter().zip(expected.iter()).enumerate() + let infos: Vec<_> = annot.iter_type(FIBERTIG_TYPE).unwrap().collect(); + for (i, (info, (exp_start, exp_end, exp_name))) in infos.iter().zip(expected.iter()).enumerate() { - assert_eq!( - ann.reference_start, - Some(*exp_start), - "ref_start mismatch at index {i}" - ); - assert_eq!( - ann.reference_end, - Some(*exp_end), - "ref_end mismatch at index {i}" - ); - assert_eq!( - ann.reference_length, - Some(*exp_len), - "ref_length mismatch at index {i}" - ); - assert_eq!( - ann.extra_columns.as_ref().map(|c| c.join(";")), - Some((*exp_tag).to_string()), - "fa-extras pairing wrong at index {i} (size {exp_len}): got {:?}", - ann.extra_columns, - ); + assert_eq!(info.ref_start, Some(*exp_start), "ref_start mismatch at {i}"); + assert_eq!(info.ref_end, Some(*exp_end), "ref_end mismatch at {i}"); + assert_eq!(info.name, Some(*exp_name), "name mismatch at {i}"); } Ok(()) } From f19fa72a56b8cca6f3c3fcc8998183793d94ee85 Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Tue, 12 May 2026 15:23:15 -0600 Subject: [PATCH 11/24] refactor: collapse BaseMods onto MolecularAnnotations Delete the BaseMods / BaseMod / ModCall intermediate. MM/ML is now pure I/O on a MolecularAnnotations object: parse_mm_ml_into_ma fills it, write_mm_ml emits it. The legacy FiberAnnotation / FiberAnnotations / Ranges types and their iterators are deleted entirely. Behavior change - MM tag canonicalization Canonical fiberseq groups (mod_type 'a' -> m6a, 'm' -> cpg) have their per-group (base, strand_sign) reconstructed from the forward sequence on write. Non-canonical groups (e.g. C+h, T+f, ChEBI numeric IDs) are preserved verbatim under an annotation type named after the MM group header and round-trip unchanged. | Input MM tag | Output MM tag | Note | |-----------------------------|---------------------|--------------------------------------| | A+a,5;T-a,3;C+m,2; | A+a,5;C+m,2;T-a,3; | unchanged; emitted in sorted order | | N+a,3,2,1; (calls on A/T/G) | A+a,3;G+a,0;T-a,2; | regrouped from forward seq | | C+h,5;C+m,2; | C+h,5;C+m,2; | non-canonical group preserved | Positions and ML qualities round-trip exactly in every case. --- src/fiber.rs | 16 +- src/subcommands/ddda_to_m6a.rs | 54 +-- src/subcommands/predict_m6a.rs | 117 +++--- src/subcommands/strip_basemods.rs | 62 ++- src/utils/bamannotations.rs | 658 +----------------------------- src/utils/basemods.rs | 642 +++++++++++++---------------- src/utils/fibertig.rs | 20 +- src/utils/ftexpression.rs | 98 ----- src/utils/input_bam.rs | 2 - tests/basemods.rs | 95 ++++- tests/fibertig_test.rs | 12 +- 11 files changed, 527 insertions(+), 1249 deletions(-) diff --git a/src/fiber.rs b/src/fiber.rs index 09ac75c1..1937e6b5 100644 --- a/src/fiber.rs +++ b/src/fiber.rs @@ -2,7 +2,7 @@ use super::subcommands::center::CenterPosition; use super::utils::input_bam::FiberFilters; use super::*; use crate::utils::bamannotations::*; -use crate::utils::basemods::{BaseMods, CPG_TYPE, M6A_TYPE}; +use crate::utils::basemods::{parse_mm_ml_into_ma, CPG_TYPE, M6A_TYPE}; use crate::utils::bio_io::*; use crate::utils::ftexpression::apply_filter_fsd; use crate::utils::ma_io::{MSP_TYPE, NUC_TYPE}; @@ -17,7 +17,6 @@ use std::fmt::Write; pub struct FiberseqData { pub record: bam::Record, pub annotations: MolecularAnnotations, - pub base_mods: BaseMods, pub ec: f32, pub target_name: String, pub rg: String, @@ -52,15 +51,18 @@ impl FiberseqData { None => ".".to_string(), }; - // get fiberseq basemods (also injects m6a/cpg into `annotations`) - let mut base_mods = BaseMods::new(&record, filters.min_ml_score); - base_mods.filter_at_read_ends(filters.strip_starting_basemods); - base_mods.populate_ma(&mut annotations); + // Parse MM/ML directly into the spec object as m6a / cpg types. + // No intermediate BaseMods needed on the read side. + parse_mm_ml_into_ma( + &record, + &mut annotations, + filters.min_ml_score, + filters.strip_starting_basemods, + ); let mut fsd = FiberseqData { record, annotations, - base_mods, ec, target_name, rg, diff --git a/src/subcommands/ddda_to_m6a.rs b/src/subcommands/ddda_to_m6a.rs index b5e6ed25..f6da7602 100644 --- a/src/subcommands/ddda_to_m6a.rs +++ b/src/subcommands/ddda_to_m6a.rs @@ -1,9 +1,9 @@ use crate::cli::DddaToM6aOptions; use crate::utils::basemods; -use crate::utils::basemods::BaseMods; use crate::*; use anyhow::Error; use bio::alphabets::dna::revcomp; +use molecular_annotation::{MolecularAnnotations, QualitySpec, Strand}; use rayon::iter::ParallelIterator; use rayon::prelude::*; use rust_htslib::bam::Record; @@ -22,17 +22,17 @@ pub fn ddda_to_m6a_record(record: &mut Record, _opts: &DddaToM6aOptions) { } // get the bases that will be modified - let mut modified_bases_forward = vec![]; + let mut modified_bases_forward: Vec = vec![]; let mut y_count = 0; let mut r_count = 0; let mut new_forward_seq = vec![]; for (idx, bp) in forward_seq.iter().enumerate() { if bp == &b'Y' { - modified_bases_forward.push(idx as i64); + modified_bases_forward.push(idx as u32); y_count += 1; new_forward_seq.push(b'T'); } else if bp == &b'R' { - modified_bases_forward.push(idx as i64); + modified_bases_forward.push(idx as u32); r_count += 1; new_forward_seq.push(b'A'); } else { @@ -47,16 +47,6 @@ pub fn ddda_to_m6a_record(record: &mut Record, _opts: &DddaToM6aOptions) { return; } - // check if we should set the read to the top or bottom strand - let is_top_strand = y_count > 0; - - // set things up for the bottom strand - // let is_bottom_strand = !is_top_strand; - //if is_bottom_strand { - // flag |= 1 << 4; - // record.set_flags(flag); - // record.set_reverse(); - //} if was_reverse { // must reverse complement the new sequence if we are on the bottom strand new_forward_seq = revcomp(&new_forward_seq); @@ -65,31 +55,17 @@ pub fn ddda_to_m6a_record(record: &mut Record, _opts: &DddaToM6aOptions) { // set values for the new modified record record.set(&q_name, Some(&cigar), &new_forward_seq, &qual); - // set up the fake base mods - let (modified_base, strand) = if is_top_strand { - (b'T', '-') - } else { - (b'A', '+') - }; - let modification_type = 'a'; - let modified_probabilities_forward = vec![255; modified_bases_forward.len()]; - - let fake_base_mods = basemods::BaseMod::new( - record, - modified_base, - strand, - modification_type, - modified_bases_forward, - modified_probabilities_forward, - ); - - // add to the record - let mut base_mods = basemods::BaseMods::new(record, 0); - base_mods.base_mods.push(fake_base_mods); - base_mods.add_mm_and_ml_tags(record); - - // validates that the base mods were added correctly - let _ = BaseMods::new(record, 0); + // Load existing MM/ML into a MolecularAnnotations, append the + // synthesized m6a calls, write back. write_mm_ml reconstructs the + // canonical group (A+a vs T-a) from the now-replaced forward seq. + let mut annot = MolecularAnnotations::from_record(record); + basemods::parse_mm_ml_into_ma(record, &mut annot, 0, 0); + let qspec = "Q".parse::().expect("Q parses"); + let t = annot.add_annotation_type(basemods::M6A_TYPE, qspec); + for pos in modified_bases_forward { + t.add(pos, 1, Strand::Forward, vec![255], None); + } + basemods::write_mm_ml(record, &annot); } pub fn ddda_to_m6a(opts: &mut DddaToM6aOptions) -> Result<(), Error> { diff --git a/src/subcommands/predict_m6a.rs b/src/subcommands/predict_m6a.rs index aa63996b..91dd60b6 100644 --- a/src/subcommands/predict_m6a.rs +++ b/src/subcommands/predict_m6a.rs @@ -222,35 +222,54 @@ where assert_eq!(data.len(), records.len()); let mut cur_predict_st = 0; for (option_data, record) in data.iter().zip(records) { - // base mods in the exiting record - let mut cur_basemods = basemods::BaseMods::new(record, 0); - cur_basemods.drop_m6a(); - log::trace!("Number of base mod types {}", cur_basemods.base_mods.len()); + // Load existing MM/ML into a MolecularAnnotations, then drop any + // pre-existing m6a calls — we're about to replace them with the + // model's predictions. CpG / other annotation types are preserved. + let mut annot = molecular_annotation::MolecularAnnotations::from_record(record); + basemods::parse_mm_ml_into_ma(record, &mut annot, 0, 0); + annot + .annotation_types + .retain(|t| t.name != basemods::M6A_TYPE); + // check if there is any data let (a_data, t_data) = match option_data { Some((a_data, t_data)) => (a_data, t_data), None => continue, }; - // iterate over A and then T basemods + // Iterate over A and then T basemods, collecting their forward + // positions + ML qualities into a single sorted m6a list. + let mut m6a_calls: Vec<(u32, u8)> = Vec::new(); for data in &[a_data, t_data] { let cur_predict_en = cur_predict_st + data.count; let cur_predictions = &predictions[cur_predict_st..cur_predict_en]; - cur_predict_st += data.count; - cur_basemods.base_mods.push(opts.basemod_from_ml( - record, - cur_predictions, - &data.positions, - &data.base_mod, - )); + let (poss, quals) = + opts.basemod_from_ml(record, cur_predictions, &data.positions, &data.base_mod); + m6a_calls.extend(poss.into_iter().zip(quals)); + } + if !m6a_calls.is_empty() { + m6a_calls.sort_by_key(|&(p, _)| p); + let qspec = "Q" + .parse::() + .expect("Q parses"); + let t = annot.add_annotation_type(basemods::M6A_TYPE, qspec); + for (pos, qual) in &m6a_calls { + t.add( + *pos, + 1, + molecular_annotation::Strand::Forward, + vec![*qual], + None, + ); + } } - // write the ml and mm tags - cur_basemods.add_mm_and_ml_tags(record); - //let modified_bases_forward = cur_basemods.forward_m6a().0; - let modified_bases_forward = cur_basemods.m6a().forward_starts(); + // write the ml and mm tags + basemods::write_mm_ml(record, &annot); - // adding the nucleosomes + // adding the nucleosomes — uses the forward m6a positions we just placed. + let modified_bases_forward: Vec = + m6a_calls.iter().map(|&(p, _)| p as i64).collect(); nucleosome::add_nucleosomes_to_record( record, &modified_bases_forward, @@ -270,56 +289,48 @@ where data.iter().flatten().count() } - /// Create a basemod object form our predictions + /// Filter raw model predictions into (forward_position, ML_quality) + /// pairs suitable for adding to a `MolecularAnnotations` m6a + /// annotation type. Drops predictions below the ML threshold and + /// within the first/last `WINDOW/2` bases of the read. pub fn basemod_from_ml( &self, record: &mut bam::Record, predictions: &[f32], positions: &[usize], - base_mod: &str, - ) -> basemods::BaseMod { + _base_mod: &str, + ) -> (Vec, Vec) { // do not report predictions for the first and last 7 bases let min_pos = (WINDOW / 2) as i64; let max_pos = (record.seq_len() - WINDOW / 2) as i64; - let (modified_probabilities_forward, full_probabilities_forward, modified_bases_forward): ( - Vec, - Vec, - Vec, - ) = predictions - .iter() - .zip(positions.iter()) - .map(|(&x, &pos)| (self.float_to_u8(x), x, pos as i64)) - .filter(|(ml, _, pos)| *ml >= self.min_ml_value() && *pos >= min_pos && *pos < max_pos) - .multiunzip(); + + let mut poss: Vec = Vec::new(); + let mut quals: Vec = Vec::new(); + let mut low_nonzero = 0usize; + let mut zero = 0usize; + for (&pred, &pos) in predictions.iter().zip(positions.iter()) { + let ml = self.float_to_u8(pred); + let pos_i = pos as i64; + if pred > 0.0 && pred <= 1.0 / 255.0 { + low_nonzero += 1; + } + if pred <= 0.0 && pred > -0.00000001 { + zero += 1; + } + if ml >= self.min_ml_value() && pos_i >= min_pos && pos_i < max_pos { + poss.push(pos as u32); + quals.push(ml); + } + } log::debug!( "Low but non zero values: {:?}\tZero values: {:?}\tlength:{:?}", - full_probabilities_forward - .iter() - .filter(|&x| *x <= 1.0 / 255.0) - .filter(|&x| *x > 0.0) - .count(), - full_probabilities_forward - .iter() - .filter(|&x| *x <= 0.0) - .filter(|&x| *x > -0.00000001) - .count(), + low_nonzero, + zero, predictions.len() ); - let base_mod = base_mod.as_bytes(); - let modified_base = base_mod[0]; - let strand = base_mod[1] as char; - let modification_type = base_mod[2] as char; - - basemods::BaseMod::new( - record, - modified_base, - strand, - modification_type, - modified_bases_forward, - modified_probabilities_forward, - ) + (poss, quals) } pub fn apply_model(&self, windows: &[f32], count: usize) -> Vec { diff --git a/src/subcommands/strip_basemods.rs b/src/subcommands/strip_basemods.rs index 7138f564..d2e24607 100644 --- a/src/subcommands/strip_basemods.rs +++ b/src/subcommands/strip_basemods.rs @@ -1,6 +1,10 @@ use crate::cli::StripBasemodsOptions; +use crate::utils::bamannotations::primary_qual; use crate::utils::basemods; +use crate::utils::basemods::{CPG_TYPE, M6A_TYPE}; use crate::utils::bio_io::BamChunk; +use bio::alphabets::dna::revcomp; +use molecular_annotation::MolecularAnnotations; use rayon::iter::ParallelIterator; use rayon::prelude::IntoParallelRefMutIterator; use rust_htslib::bam::Read; @@ -19,30 +23,60 @@ pub fn strip_base_mods(opts: &mut StripBasemodsOptions) { // iterate over chunks for mut chunk in bam_chunk_iter { - // strip let records: Vec<&mut Record> = chunk .par_iter_mut() .map(|record| { - let mut data = basemods::BaseMods::new(record, 0); - if (filter_mod == "5mC") || (filter_mod == "CpG") { - data.drop_cpg(); - } else if (filter_mod == "6mA") || (filter_mod == "m6A") { - data.drop_m6a(); - } - if opts.drop_forward { - data.drop_forward(); + let mut annot = MolecularAnnotations::from_record(record); + basemods::parse_mm_ml_into_ma(record, &mut annot, 0, 0); + + // Drop whole annotation types. + if filter_mod == "5mC" || filter_mod == "CpG" { + annot.annotation_types.retain(|t| t.name != CPG_TYPE); + } else if filter_mod == "6mA" || filter_mod == "m6A" { + annot.annotation_types.retain(|t| t.name != M6A_TYPE); } - if opts.drop_reverse { - data.drop_reverse(); + + // Drop by canonical-base / strand. The "strand" the legacy + // BaseMods stored was the MM tag's strand sign (`+` or `-`). + // After S2a the per-call strand is determined at write + // time from the forward seq: m6a calls on A → `+`, on T → `-`; + // 5mC calls on C → `+`, on G → `+` (canonical fiberseq + // never emits `-` for 5mC). drop_forward removes calls + // whose write-time strand would be `+`; drop_reverse `-`. + if opts.drop_forward || opts.drop_reverse { + let forward_seq = if record.is_reverse() { + revcomp(record.seq().as_bytes()) + } else { + record.seq().as_bytes() + }; + if opts.drop_forward { + annot.retain(M6A_TYPE, |a| { + forward_seq.get(a.start as usize).copied() != Some(b'A') + }); + annot.retain(CPG_TYPE, |a| { + forward_seq.get(a.start as usize).copied() != Some(b'C') + }); + } + if opts.drop_reverse { + annot.retain(M6A_TYPE, |a| { + forward_seq.get(a.start as usize).copied() != Some(b'T') + }); + // canonical fiberseq doesn't emit `-` for 5mC; nothing to drop. + } } + if opts.ml_m6a > 0 { - data.filter_m6a(opts.ml_m6a); + annot.retain(M6A_TYPE, |a| { + primary_qual(&a.qualities, M6A_TYPE) >= opts.ml_m6a + }); } if opts.ml_5mc > 0 { - data.filter_5mc(opts.ml_5mc); + annot.retain(CPG_TYPE, |a| { + primary_qual(&a.qualities, CPG_TYPE) >= opts.ml_5mc + }); } - data.add_mm_and_ml_tags(record); + basemods::write_mm_ml(record, &annot); record }) .collect(); diff --git a/src/utils/bamannotations.rs b/src/utils/bamannotations.rs index 9c9aa30d..e9f08e3b 100644 --- a/src/utils/bamannotations.rs +++ b/src/utils/bamannotations.rs @@ -1,7 +1,4 @@ -use crate::utils::bamlift::*; use molecular_annotation::{AnnotationInfo, MolecularAnnotations}; -use rust_htslib::bam; -use rust_htslib::bam::ext::BamRecordExtensions; /// Extract the single per-annotation quality fibertools expects, returning /// 0 when the annotation has none. Debug-asserts that the type carries at @@ -19,659 +16,6 @@ pub fn primary_qual(qualities: &[u8], type_name: &str) -> u8 { ); qualities.first().copied().unwrap_or(0) } -#[derive(Debug, Clone, PartialEq, Eq, Ord, PartialOrd)] -pub struct FiberAnnotation { - pub start: i64, - pub end: i64, - pub length: i64, - pub qual: u8, - pub reference_start: Option, - pub reference_end: Option, - pub reference_length: Option, - pub extra_columns: Option>, -} - -#[derive(Debug, Clone, PartialEq, Eq, Ord, PartialOrd)] -pub struct FiberAnnotations { - pub annotations: Vec, - pub seq_len: i64, - pub reverse: bool, -} - -// Keep Ranges as an alias for backward compatibility -pub type Ranges = FiberAnnotations; - -impl FiberAnnotations { - /// Create FiberAnnotations from a vector of FiberAnnotation items - pub fn from_annotations( - mut annotations: Vec, - seq_len: i64, - reverse: bool, - ) -> Self { - // Sort annotations by start position to ensure they are always in order - annotations.sort_by_key(|a| a.start); - - Self { - annotations, - seq_len, - reverse, - } - } - - /// starts and ends are [) intervals. - pub fn new( - record: &bam::Record, - forward_starts: Vec, - forward_ends: Option>, - lengths: Option>, - ) -> Self { - Self::new_with_extras(record, forward_starts, forward_ends, lengths, None) - } - - /// Same as [`FiberAnnotations::new`], but also accepts forward-order - /// `extras` that get carried through the flip and sort so each - /// annotation keeps its original extra_columns. - pub fn new_with_extras( - record: &bam::Record, - mut forward_starts: Vec, - forward_ends: Option>, - mut lengths: Option>, - mut forward_extras: Option>>>, - ) -> Self { - let mut single_bp_liftover = false; - // assume ends == starts if not provided - if forward_ends.is_none() && lengths.is_none() { - lengths = Some(vec![1; forward_starts.len()]); - single_bp_liftover = true; - } - - // use ends or calculate them - let mut forward_ends_inclusive: Vec = match forward_ends { - Some(x) => x.into_iter().map(|x| x + 1).collect(), - None => forward_starts - .iter() - .zip(lengths.unwrap().iter()) - .map(|(&x, &y)| x + y - 1) - .collect(), - }; - - // bam features for finding aligned positions - let is_reverse = record.is_reverse(); - let seq_len = i64::try_from(record.seq_len()).unwrap(); - - // get positions and lengths in reference orientation - Self::positions_on_aligned_sequence(&mut forward_starts, is_reverse, seq_len); - Self::positions_on_aligned_sequence(&mut forward_ends_inclusive, is_reverse, seq_len); - // Mirror the array reversal that positions_on_aligned_sequence applied - // so extras stay paired with their original peak. - if is_reverse { - if let Some(ref mut e) = forward_extras { - e.reverse(); - } - } - let mut starts = forward_starts; - let mut ends = forward_ends_inclusive; - - // swaps starts and ends if we reverse complemented - if record.is_reverse() { - std::mem::swap(&mut starts, &mut ends); - } - - // swap back to non-inclusive ends - ends = ends.into_iter().map(|x| x + 1).collect(); - - // get lengths - let lengths = starts - .iter() - .zip(ends.iter()) - .map(|(&x, &y)| Some(y - x)) - .collect::>(); - - let (reference_starts, reference_ends, reference_lengths) = if single_bp_liftover { - lift_query_range_exact(record, &starts, &starts).unwrap_or_else(|e| { - log::error!( - "Failed lifting over annotations in BAM record: {} aligned from {} to {}.", - String::from_utf8_lossy(record.qname()), - record.reference_start() + 1, - record.reference_end() - ); - log::error!("Failed to lift query range: {}", e); - panic!("Failed to lift query range: {}", e); - }) - } else { - // MA spec inward semantics for multi-bp query-space ranges. - // Half-open block matching; endpoints in indel gaps snap inward - // toward the aligned region rather than to the nearer block edge. - // - // Build AlignedBlocks directly from aligned_block_pairs to match - // the legacy lift's exact source (the spec's `from_record` skips - // records that report is_unmapped, which fibertig synthetic test - // records can hit even with a valid CIGAR). - let pairs = record - .aligned_block_pairs() - .map(|([qs, qe], [rs, re])| ([qs as u32, qe as u32], [rs as u32, re as u32])); - let blocks = molecular_annotation::AlignedBlocks::from_pairs(pairs, seq_len as u32); - let mut rs_vec: Vec> = Vec::with_capacity(starts.len()); - let mut re_vec: Vec> = Vec::with_capacity(starts.len()); - let mut rl_vec: Vec> = Vec::with_capacity(starts.len()); - for (&s, &e) in starts.iter().zip(ends.iter()) { - let (rs, re) = blocks.lift_to_reference(s as u32, e as u32); - let rs = rs.map(|x| x as i64); - let re = re.map(|x| x as i64); - let rl = match (rs, re) { - (Some(s), Some(e)) => Some(e - s), - _ => None, - }; - rs_vec.push(rs); - re_vec.push(re); - rl_vec.push(rl); - } - (rs_vec, re_vec, rl_vec) - }; - - // Normalize extras into a Vec matching the other parallel vectors so - // it can be zipped in and move with the annotation through the sort. - let extras_iter: Vec>> = match forward_extras { - Some(e) => { - assert_eq!( - e.len(), - starts.len(), - "extras length ({}) must match annotation count ({})", - e.len(), - starts.len(), - ); - e - } - None => vec![None; starts.len()], - }; - - // create annotations from parallel vectors - let mut annotations: Vec = starts - .into_iter() - .zip(ends) - .zip(lengths) - .zip(reference_starts) - .zip(reference_ends) - .zip(reference_lengths) - .zip(extras_iter) - .map( - |((((((start, end), length), ref_start), ref_end), ref_length), extra)| { - FiberAnnotation { - start, - end, - length: length.unwrap_or(end - start), - qual: 0, - reference_start: ref_start, - reference_end: ref_end, - reference_length: ref_length, - extra_columns: extra, - } - }, - ) - .collect(); - - // Sort annotations by start position to ensure they are always in - // order. `sort_by_key` is stable, so extras stay paired with their - // annotation even when multiple peaks share a start. - annotations.sort_by_key(|a| a.start); - - // return object - FiberAnnotations { - annotations, - seq_len, - reverse: is_reverse, - } - } - - pub fn set_qual(&mut self, mut forward_qual: Vec) { - assert_eq!(forward_qual.len(), self.annotations.len()); - // flip if we are on the reverse strand - if self.reverse { - forward_qual.reverse(); - } - - for (annotation, &q) in self.annotations.iter_mut().zip(forward_qual.iter()) { - annotation.qual = q; - } - } - - pub fn len(&self) -> usize { - self.annotations.len() - } - - pub fn is_empty(&self) -> bool { - self.annotations.is_empty() - } - - // Backward compatibility methods - pub fn starts(&self) -> Vec { - self.annotations.iter().map(|a| a.start).collect() - } - - pub fn ends(&self) -> Vec { - self.annotations.iter().map(|a| a.end).collect() - } - - pub fn lengths(&self) -> Vec { - self.annotations.iter().map(|a| a.length).collect() - } - - // Option versions for consistency with reference methods - pub fn option_starts(&self) -> Vec> { - self.annotations.iter().map(|a| Some(a.start)).collect() - } - pub fn option_ends(&self) -> Vec> { - self.annotations.iter().map(|a| Some(a.end)).collect() - } - pub fn option_lengths(&self) -> Vec> { - self.annotations.iter().map(|a| Some(a.length)).collect() - } - - pub fn qual(&self) -> Vec { - self.annotations.iter().map(|a| a.qual).collect() - } - - pub fn reference_starts(&self) -> Vec> { - self.annotations.iter().map(|a| a.reference_start).collect() - } - - pub fn reference_ends(&self) -> Vec> { - self.annotations.iter().map(|a| a.reference_end).collect() - } - - pub fn reference_lengths(&self) -> Vec> { - self.annotations - .iter() - .map(|a| a.reference_length) - .collect() - } - - /// get positions on the complimented sequence in the cigar record - fn positions_on_aligned_sequence(input_positions: &mut [i64], is_reverse: bool, seq_len: i64) { - if !is_reverse { - return; - } - //need to correct for going from [) to (] if we are part of a range - for p in input_positions.iter_mut() { - *p = seq_len - *p - 1; - } - input_positions.reverse(); - } - - /// get the molecular coordinates of the ranges, taking into account - /// the alignment orientation - pub fn get_molecular(&self) -> Vec> { - self.annotations - .iter() - .map(|annotation| Some((annotation.start, annotation.end, annotation.length))) - .collect() - } - - pub fn forward_starts(&self) -> Vec { - if !self.reverse { - // For forward reads, just return the starts as-is - self.starts() - } else { - // For reverse reads, we need to convert back to forward coordinates - // The stored starts are in reverse-complement coordinates and in reverse order - // We need to undo both transformations to get back to original forward coordinates - - // First collect all transformations (reverse-complement back to forward) - let mut forward_starts: Vec = self - .annotations - .iter() - .map(|a| self.seq_len - a.start - 1) - .collect(); - - // Then reverse the order to undo the array reversal that was done during storage - forward_starts.reverse(); - forward_starts - } - } - - pub fn get_forward_quals(&self) -> Vec { - let mut forward: Vec = self.annotations.iter().map(|a| a.qual).collect(); - if self.reverse { - forward.reverse(); - } - forward - } - - // filter out ranges that are less than the passed quality score - pub fn filter_by_qual(&mut self, min_qual: u8) { - self.annotations - .retain(|annotation| annotation.qual >= min_qual); - } - - /// filter out ranges that are within the first or last X bp of the read - pub fn filter_starts_at_read_ends(&mut self, strip: i64) { - if strip == 0 { - return; - } - - let original_len = self.annotations.len(); - self.annotations.retain(|annotation| { - annotation.start >= strip && annotation.start <= self.seq_len - strip - }); - - if self.annotations.len() != original_len { - log::trace!( - "basemods stripped, {} basemods removed", - original_len - self.annotations.len() - ); - } - } - - pub fn to_strings(&self, reference: bool, skip_none: bool) -> Vec { - let (s, e, l, q) = if reference { - ( - self.reference_starts(), - self.reference_ends(), - self.reference_lengths(), - self.qual(), - ) - } else { - ( - self.option_starts(), - self.option_ends(), - self.option_lengths(), - self.qual(), - ) - }; - - let s = crate::join_by_str_option_can_skip(&s, ",", skip_none); - let e = crate::join_by_str_option_can_skip(&e, ",", skip_none); - let l = crate::join_by_str_option_can_skip(&l, ",", skip_none); - if reference { - vec![s, e, l] - } else { - let q = crate::join_by_str(&q, ","); - vec![s, e, l, q] - } - } - - /// get the reference coordinates of the ranges, taking into account - /// the alignment orientation - pub fn get_reference(&self) -> Vec> { - self.annotations - .iter() - .map(|annotation| { - if let (Some(s), Some(e), Some(l)) = ( - annotation.reference_start, - annotation.reference_end, - annotation.reference_length, - ) { - Some((s, e, l)) - } else { - None - } - }) - .collect() - } - - pub fn merge_ranges(multiple_ranges: Vec<&Self>) -> Self { - if multiple_ranges.is_empty() { - return Self::from_annotations(vec![], 0, false); - } - - // check properties that must be the same - let reverse = multiple_ranges[0].reverse; - let seq_len = multiple_ranges[0].seq_len; - for r in multiple_ranges.iter() { - assert_eq!(r.reverse, reverse); - assert_eq!(r.seq_len, seq_len); - } - - // collect all annotations - let annotations: Vec = multiple_ranges - .iter() - .flat_map(|r| r.annotations.clone()) - .collect(); - - // Use from_annotations to ensure proper sorting - Self::from_annotations(annotations, seq_len, reverse) - } - - fn apply_offset_helper(in_start: i64, in_end: i64, offset: i64, strand: char) -> (i64, i64) { - let mut start = in_start - offset; - let mut end = in_end - offset - 1; // make the end inclusive for - if strand == '-' { - start = -start; - end = -end; - - // Swap start and end if we reverse complemented - if start > end { - std::mem::swap(&mut start, &mut end); - } - } - // make the end exclusive again - end += 1; - (start, end) - } - - /// Apply offset to all molecular coordinates in the annotations - pub fn apply_offset(&mut self, offset: i64, ref_offset: i64, strand: char) { - for annotation in &mut self.annotations { - let (new_start, new_end) = - Self::apply_offset_helper(annotation.start, annotation.end, offset, strand); - annotation.start = new_start; - annotation.end = new_end; - assert!( - annotation.end - annotation.start == annotation.length, - "Annotation length mismatch after centering: {} != {} - {}", - annotation.length, - annotation.end, - annotation.start - ); - - // Apply offset to reference coordinates if they exist - if let (Some(ref_start), Some(ref_end)) = - (annotation.reference_start, annotation.reference_end) - { - let (new_ref_start, new_ref_end) = - Self::apply_offset_helper(ref_start, ref_end, ref_offset, strand); - annotation.reference_start = Some(new_ref_start); - annotation.reference_end = Some(new_ref_end); - annotation.reference_length = Some(new_ref_end - new_ref_start + 1); - } - } - // reverse the annotations if we are on the reverse strand - if strand == '-' { - self.annotations.reverse(); - } - } - - /// Create FiberAnnotations from BAM tags with configurable tag names - pub fn from_bam_tags( - record: &rust_htslib::bam::Record, - start_tag: &[u8; 2], - length_tag: &[u8; 2], - annotation_tag: Option<&[u8; 2]>, - ) -> anyhow::Result> { - // Check if record has the specified start and length tags - if let (Ok(start_aux), Ok(length_aux)) = (record.aux(start_tag), record.aux(length_tag)) { - if let ( - rust_htslib::bam::record::Aux::ArrayU32(start_array), - rust_htslib::bam::record::Aux::ArrayU32(length_array), - ) = (start_aux, length_aux) - { - let start_values: Vec = start_array.iter().collect(); - let length_values: Vec = length_array.iter().collect(); - - if start_values.len() != length_values.len() { - return Err(anyhow::anyhow!( - "Mismatched {} and {} array lengths", - String::from_utf8_lossy(start_tag), - String::from_utf8_lossy(length_tag) - )); - } - - // Convert to i64 vectors for FiberAnnotations::new - let forward_starts: Vec = start_values.iter().map(|&x| x as i64).collect(); - let lengths: Vec = length_values.iter().map(|&x| x as i64).collect(); - - // Get annotation tag for extra columns if specified. Convert - // directly to the forward-order shape `FiberAnnotations` expects - // so extras travel through the flip+sort paired with their peak. - let forward_extras: Option>>> = match annotation_tag { - Some(ann_tag) => match record.aux(ann_tag) { - Ok(rust_htslib::bam::record::Aux::String(ann_string)) => { - let parts: Vec>> = ann_string - .split('|') - .map(|s| { - if s.is_empty() { - None - } else { - Some(s.split(';').map(|t| t.to_string()).collect()) - } - }) - .collect(); - if parts.len() != forward_starts.len() { - return Err(anyhow::anyhow!( - "Mismatched {} ({}) and {} ({}) array lengths", - String::from_utf8_lossy(ann_tag), - parts.len(), - String::from_utf8_lossy(start_tag), - forward_starts.len(), - )); - } - Some(parts) - } - _ => None, - }, - None => None, - }; - - let fiber_annotations = FiberAnnotations::new_with_extras( - record, - forward_starts, - None, // no ends provided - Some(lengths), // use lengths from fl tag - forward_extras, - ); - - Ok(Some(fiber_annotations)) - } else { - Ok(None) // Tags exist but wrong type - } - } else { - Ok(None) // No annotation tags - } - } - - /// Create FiberAnnotations containing only annotations that overlap with the given range - pub fn overlapping_annotations(&self, range_start: i64, range_end: i64) -> Self { - let mut overlapping = Vec::new(); - - for annotation in &self.annotations { - // Check if annotation overlaps with range - if annotation.end > range_start && annotation.start < range_end { - overlapping.push(annotation.clone()); - } - } - - FiberAnnotations::from_annotations(overlapping, range_end - range_start, self.reverse) - } - - /// Write annotations to BAM record as auxiliary tags - pub fn write_to_bam_tags( - &self, - record: &mut rust_htslib::bam::Record, - start_tag: &[u8; 2], - length_tag: &[u8; 2], - annotation_tag: Option<&[u8; 2]>, - ) -> anyhow::Result<()> { - use anyhow::Context; - - if self.annotations.is_empty() { - return Ok(()); - } - - // Collect starts and lengths - let starts: Vec = self.annotations.iter().map(|a| a.start as u32).collect(); - - let lengths: Vec = self.annotations.iter().map(|a| a.length as u32).collect(); - - // Add start positions tag - record - .push_aux( - start_tag, - rust_htslib::bam::record::Aux::ArrayU32((&starts).into()), - ) - .with_context(|| format!("Failed to add {} tag", String::from_utf8_lossy(start_tag)))?; - - // Add lengths tag - record - .push_aux( - length_tag, - rust_htslib::bam::record::Aux::ArrayU32((&lengths).into()), - ) - .with_context(|| { - format!("Failed to add {} tag", String::from_utf8_lossy(length_tag)) - })?; - - // Add annotation tag if requested and any annotations have extra columns - if let Some(ann_tag) = annotation_tag { - let extra_strings: Vec = self - .annotations - .iter() - .map(|a| { - if let Some(ref extra_cols) = a.extra_columns { - extra_cols.join(";") - } else { - String::new() - } - }) - .collect(); - - // Only add the tag if there are non-empty extra columns - if extra_strings.iter().any(|s| !s.is_empty()) { - let joined_extra = extra_strings.join("|"); - record - .push_aux( - ann_tag, - rust_htslib::bam::record::Aux::String(&joined_extra), - ) - .with_context(|| { - format!("Failed to add {} tag", String::from_utf8_lossy(ann_tag)) - })?; - } - } - Ok(()) - } -} - -impl<'a> IntoIterator for &'a FiberAnnotations { - type Item = &'a FiberAnnotation; - type IntoIter = FiberAnnotationsIterator<'a>; - - fn into_iter(self) -> Self::IntoIter { - FiberAnnotationsIterator { - annotations: self, - index: 0, - } - } -} - -pub struct FiberAnnotationsIterator<'a> { - annotations: &'a FiberAnnotations, - index: usize, -} - -impl<'a> Iterator for FiberAnnotationsIterator<'a> { - type Item = &'a FiberAnnotation; - fn next(&mut self) -> Option { - if self.index >= self.annotations.annotations.len() { - return None; - } - let annotation = &self.annotations.annotations[self.index]; - self.index += 1; - Some(annotation) - } -} - -// Backward compatibility alias -pub type RangesIterator<'a> = FiberAnnotationsIterator<'a>; /// View over a specific annotation type, providing the column-oriented /// surface fibertools historically got from `FiberAnnotations` while @@ -755,6 +99,7 @@ impl<'a> AnnotationTypeView<'a> { .map(|a| (a.query_end - a.query_start) as i64) .collect() } + /// Convenience over [`Self::qual_at`] for the common case where the /// annotation type carries at most one quality per annotation. Returns /// 0 for annotations with no qualities. @@ -789,6 +134,7 @@ impl<'a> AnnotationTypeView<'a> { }) .collect() } + pub fn reference_starts(&self) -> Vec> { self.bam_ordered() .into_iter() diff --git a/src/utils/basemods.rs b/src/utils/basemods.rs index d5e67add..718aa1f4 100644 --- a/src/utils/basemods.rs +++ b/src/utils/basemods.rs @@ -1,397 +1,325 @@ -use crate::utils::bamannotations::*; +//! MM/ML BAM tag I/O for fiberseq base modifications. +//! +//! Read path: `parse_mm_ml_into_ma` parses a record's MM/ML tags directly +//! into a [`MolecularAnnotations`] as annotation types. No intermediate +//! `BaseMods` struct — the spec object is the sole in-memory +//! representation. +//! +//! Mod-type dispatch: +//! - mod_type `'a'` (any group, e.g. `A+a`, `T-a`, `N+a`) → `m6a` type. +//! - mod_type `'m'` (any group, e.g. `C+m`, `G+m`) → `cpg` type. +//! - any other group (`C+h`, `T+f`, ChEBI IDs, etc.) → its own annotation +//! type named verbatim after the MM group header (e.g. `"C+h"`). +//! Calls round-trip through `write_mm_ml` unchanged. +//! +//! Write path: `write_mm_ml` emits MM/ML from a [`MolecularAnnotations`]. +//! Canonical types (`m6a`, `cpg`) have their groups reconstructed from +//! the forward sequence (`A`→`A+a`, `T`→`T-a`, `C`→`C+m`, `G`→`G+m`). +//! Non-canonical types stored under a valid MM group name are emitted +//! verbatim under that header. + use crate::utils::bio_io::*; use bio::alphabets::dna::revcomp; use lazy_static::lazy_static; use molecular_annotation::{MolecularAnnotations, QualitySpec, Strand}; use regex::Regex; -use rust_htslib::{ - bam, - bam::record::{Aux, AuxArray}, -}; -use std::collections::HashMap; - -use std::convert::TryFrom; +use rust_htslib::bam; +use rust_htslib::bam::record::Aux; +use std::collections::BTreeMap; -/// Annotation type names emitted by `BaseMods::populate_ma`. +/// Annotation type names emitted by `parse_mm_ml_into_ma`. pub const M6A_TYPE: &str = "m6a"; pub const CPG_TYPE: &str = "cpg"; -/// A group of base modification calls of one (base, strand, modification_type) -/// triple — for example, "all m6A calls on adenines on the forward strand." -/// -/// Per-call positions and qualities live in `ranges`. This reuses the -/// `Ranges`/`FiberAnnotations` infrastructure (rather than a separate type) -/// to share the position-flipping, quality-filtering, and reference-liftover -/// logic. Each call is stored as a 1bp range; the `length` field is always 1. -#[derive(Eq, PartialEq, Debug, PartialOrd, Ord, Clone)] -pub struct BaseMod { - pub modified_base: u8, - pub strand: char, - pub modification_type: char, - pub ranges: Ranges, - pub record_is_reverse: bool, -} - -impl BaseMod { - pub fn new( - record: &bam::Record, - modified_base: u8, - strand: char, - modification_type: char, - modified_bases_forward: Vec, - modified_probabilities_forward: Vec, - ) -> Self { - let tmp = modified_bases_forward.clone(); - let mut ranges = Ranges::new(record, modified_bases_forward, None, None); - ranges.set_qual(modified_probabilities_forward); - let record_is_reverse = record.is_reverse(); - assert_eq!(tmp, ranges.forward_starts(), "forward starts not equal"); - Self { - modified_base, - strand, - modification_type, - ranges, - record_is_reverse, - } - } - - pub fn is_m6a(&self) -> bool { - self.modification_type == 'a' - } - - pub fn is_cpg(&self) -> bool { - self.modification_type == 'm' - } - - pub fn filter_at_read_ends(&mut self, n_strip: i64) { - if n_strip <= 0 { - return; - } - self.ranges.filter_starts_at_read_ends(n_strip); - } +lazy_static! { + // MM:Z:([ACGTUN][-+]([A-Za-z]+|[0-9]+)[.?]?(,[0-9]+)*;)* + static ref MM_RE: Regex = + Regex::new(r"((([ACGTUN])([-+])([A-Za-z]+|[0-9]+))[.?]?((,[0-9]+)*;)*)").unwrap(); } -#[derive(Eq, PartialEq, Debug, Clone)] -pub struct BaseMods { - pub base_mods: Vec, -} - -impl BaseMods { - pub fn new(record: &bam::Record, min_ml_score: u8) -> BaseMods { - // my basemod parser is ~25% faster than rust_htslib's - BaseMods::my_mm_ml_parser(record, min_ml_score) - } +/// Parse the MM/ML tags of `record` directly into `annot`. Positions are +/// stored in molecular (forward) orientation as 1bp annotations with a +/// single `Q` quality score per call. +/// +/// Per-call filtering: +/// - calls with ML quality < `min_ml_score` are dropped. +/// - calls within `strip_at_ends` bp of either end of the forward +/// sequence are dropped (no-op if `strip_at_ends <= 0`). +/// +/// Dispatch by MM mod_type: +/// - `'a'` → [`M6A_TYPE`] (collapses `A+a`, `T-a`, `N+a`, etc.) +/// - `'m'` → [`CPG_TYPE`] (collapses `C+m`, `G+m`, etc.) +/// - any other → annotation type named verbatim after the MM group +/// header (e.g. `"C+h"` for 5hmC). [`write_mm_ml`] emits these +/// unchanged. +/// +/// For canonical `m6a` / `cpg`, MM's per-group `(canonical_base, +/// strand_sign)` is reconstructed from the forward sequence at write +/// time, so input encodings like `N+a` are normalized to `A+a` / `T-a` +/// on output. +pub fn parse_mm_ml_into_ma( + record: &bam::Record, + annot: &mut MolecularAnnotations, + min_ml_score: u8, + strip_at_ends: i64, +) { + let ml_tag = get_u8_tag(record, b"ML"); + let Ok(Aux::String(mm_text)) = record.aux(b"MM") else { + log::trace!("No MM tag found"); + return; + }; + + let forward_bases = if record.is_reverse() { + convert_seq_uppercase(revcomp(record.seq().as_bytes())) + } else { + convert_seq_uppercase(record.seq().as_bytes()) + }; + let seq_len = forward_bases.len(); + let strip = strip_at_ends.max(0) as usize; + let upper = seq_len.saturating_sub(strip); + + let mut m6a_calls: Vec<(u32, u8)> = Vec::new(); + let mut cpg_calls: Vec<(u32, u8)> = Vec::new(); + // Non-canonical groups: keyed by their MM header string (e.g. "C+h"). + let mut other_calls: BTreeMap> = BTreeMap::new(); + let mut num_mods_seen = 0usize; + + for cap in MM_RE.captures_iter(mm_text) { + let mod_base = cap.get(3).map(|m| m.as_str().as_bytes()[0]).unwrap(); + let strand_sign = cap + .get(4) + .map_or("+", |m| m.as_str()) + .chars() + .next() + .unwrap_or('+'); + let mod_type_str = cap.get(5).map_or("", |m| m.as_str()).to_string(); + let modification_type = mod_type_str.chars().next().unwrap_or(' '); + let mod_dists_str = cap.get(6).map_or("", |m| m.as_str()); + let mod_dists: Vec = mod_dists_str + .trim_end_matches(';') + .split(',') + .map(|s| s.trim()) + .filter(|s| !s.is_empty()) + .map(|s| s.parse().unwrap()) + .collect(); - pub fn my_mm_ml_parser(record: &bam::Record, min_ml_score: u8) -> BaseMods { - // regex for matching the MM tag - lazy_static! { - // MM:Z:([ACGTUN][-+]([A-Za-z]+|[0-9]+)[.?]?(,[0-9]+)*;)* - static ref MM_RE: Regex = - Regex::new(r"((([ACGTUN])([-+])([A-Za-z]+|[0-9]+))[.?]?((,[0-9]+)*;)*)").unwrap(); + if mod_dists.is_empty() { + continue; } - // Array to store all the different modifications within the MM tag - let mut rtn = vec![]; - - let ml_tag = get_u8_tag(record, b"ML"); - - let mut num_mods_seen = 0; - // if there is an MM tag iterate over all the regex matches - if let Ok(Aux::String(mm_text)) = record.aux(b"MM") { - for cap in MM_RE.captures_iter(mm_text) { - let mod_base = cap.get(3).map(|m| m.as_str().as_bytes()[0]).unwrap(); - let mod_strand = cap.get(4).map_or("", |m| m.as_str()); - let modification_type = cap.get(5).map_or("", |m| m.as_str()); - let mod_dists_str = cap.get(6).map_or("", |m| m.as_str()); - // parse the string containing distances between modifications into a vector of i64 - let mod_dists: Vec = mod_dists_str - .trim_end_matches(';') - .split(',') - .map(|s| s.trim()) - .filter(|s| !s.is_empty()) - .map(|s| s.parse().unwrap()) - .collect(); - - // get forward sequence bases from the bam record - let forward_bases = if record.is_reverse() { - convert_seq_uppercase(revcomp(record.seq().as_bytes())) - } else { - convert_seq_uppercase(record.seq().as_bytes()) - }; - log::trace!( - "mod_base: {}, mod_strand: {}, modification_type: {}, mod_dists: {:?}", - mod_base as char, - mod_strand, - modification_type, - mod_dists - ); - // find real positions in the forward sequence - let mut cur_mod_idx = 0; - let mut cur_seq_idx = 0; - let mut dist_from_last_mod_base = 0; - let mut unfiltered_modified_positions: Vec = vec![0; mod_dists.len()]; - while cur_seq_idx < forward_bases.len() && cur_mod_idx < mod_dists.len() { - let cur_base = forward_bases[cur_seq_idx]; - if (cur_base == mod_base || mod_base == b'N') - && dist_from_last_mod_base == mod_dists[cur_mod_idx] - { - unfiltered_modified_positions[cur_mod_idx] = - i64::try_from(cur_seq_idx).unwrap(); - dist_from_last_mod_base = 0; - cur_mod_idx += 1; - } else if cur_base == mod_base { - dist_from_last_mod_base += 1 - } - cur_seq_idx += 1; - } - // assert that we extract the same number of modifications as we have distances - assert_eq!( - cur_mod_idx, - mod_dists.len(), - "{:?} {}", - String::from_utf8_lossy(record.qname()), - record.is_reverse() - ); - - // check for the probability of modification. - let num_mods_cur_end = num_mods_seen + unfiltered_modified_positions.len(); - let unfiltered_modified_probabilities = if num_mods_cur_end > ml_tag.len() { - let needed_num_of_zeros = num_mods_cur_end - ml_tag.len(); - let mut to_add = vec![0; needed_num_of_zeros]; - let mut has = ml_tag[num_mods_seen..ml_tag.len()].to_vec(); - has.append(&mut to_add); - log::warn!( - "ML tag is too short for the number of modifications found in the MM tag. Assuming an ML value of 0 after the first {num_mods_cur_end} modifications." - ); - has - } else { - ml_tag[num_mods_seen..num_mods_cur_end].to_vec() - }; - num_mods_seen = num_mods_cur_end; - - // must be true for filtering, and at this point - assert_eq!( - unfiltered_modified_positions.len(), - unfiltered_modified_probabilities.len() - ); - - // Filter mods based on probabilities - let (modified_probabilities, modified_positions): (Vec, Vec) = - unfiltered_modified_probabilities - .iter() - .zip(unfiltered_modified_positions.iter()) - .filter(|(&ml, &_mm)| ml >= min_ml_score) - .unzip(); - - // don't add empty basemods - if modified_positions.is_empty() { - continue; - } - // add to a struct - let mods = BaseMod::new( - record, - mod_base, - mod_strand.chars().next().unwrap(), - modification_type.chars().next().unwrap(), - modified_positions, - modified_probabilities, - ); - rtn.push(mods); + // Resolve positions in forward sequence via the MM distance + // encoding: each value is "how many of `mod_base` to skip + // before the next modified base." + let mut positions: Vec = vec![0; mod_dists.len()]; + let mut cur_mod_idx = 0; + let mut dist_from_last_mod_base = 0i64; + for (cur_seq_idx, cur_base) in forward_bases.iter().enumerate() { + if cur_mod_idx >= mod_dists.len() { + break; + } + if (*cur_base == mod_base || mod_base == b'N') + && dist_from_last_mod_base == mod_dists[cur_mod_idx] + { + positions[cur_mod_idx] = cur_seq_idx as u32; + dist_from_last_mod_base = 0; + cur_mod_idx += 1; + } else if *cur_base == mod_base { + dist_from_last_mod_base += 1; } - } else { - log::trace!("No MM tag found"); } + assert_eq!( + cur_mod_idx, + mod_dists.len(), + "MM/ML parser: {} (reverse={})", + String::from_utf8_lossy(record.qname()), + record.is_reverse(), + ); - if ml_tag.len() != num_mods_seen { + // Pair this group's calls with ML qualities. + let group_end = num_mods_seen + positions.len(); + let group_quals: Vec = if group_end > ml_tag.len() { + let needed = group_end - ml_tag.len(); + let mut existing = ml_tag[num_mods_seen..].to_vec(); + existing.extend(std::iter::repeat_n(0, needed)); log::warn!( - "ML tag ({}) different number than MM tag ({}).", - ml_tag.len(), - num_mods_seen + "ML tag is too short for the number of modifications found in the MM tag. Assuming an ML value of 0 after the first {group_end} modifications." ); - } - // needed so I can compare methods - rtn.sort(); - BaseMods { base_mods: rtn } - } - - pub fn hashmap_to_basemods( - map: HashMap<(i32, i32, i32), Vec<(i64, u8)>>, - record: &bam::Record, - ) -> BaseMods { - let mut rtn = vec![]; - for (mod_info, mods) in map { - let mod_base = mod_info.0 as u8; - let mod_type = mod_info.1 as u8 as char; - let mod_strand = if mod_info.2 == 0 { '+' } else { '-' }; - let (mut positions, mut qualities): (Vec, Vec) = mods.into_iter().unzip(); - if record.is_reverse() { - let length = record.seq_len() as i64; - positions = positions - .into_iter() - .rev() - .map(|p| length - p - 1) - .collect(); - qualities.reverse(); + existing + } else { + ml_tag[num_mods_seen..group_end].to_vec() + }; + num_mods_seen = group_end; + + // Filter + dispatch by mod_type. Non-canonical groups are + // stored under their verbatim MM header so they round-trip + // exactly through write_mm_ml. + let bucket: &mut Vec<(u32, u8)> = match modification_type { + 'a' => &mut m6a_calls, + 'm' => &mut cpg_calls, + _ => { + let key = format!("{}{}{}", mod_base as char, strand_sign, mod_type_str); + other_calls.entry(key).or_default() + } + }; + for (pos, qual) in positions.iter().copied().zip(group_quals) { + if qual < min_ml_score { + continue; + } + let p = pos as usize; + if strip > 0 && (p < strip || p >= upper) { + continue; } - let mods = BaseMod::new(record, mod_base, mod_strand, mod_type, positions, qualities); - rtn.push(mods); + bucket.push((pos, qual)); } - // needed so I can compare methods - rtn.sort(); - BaseMods { base_mods: rtn } - } - - /// remove m6a base mods from the struct - pub fn drop_m6a(&mut self) { - self.base_mods.retain(|bm| !bm.is_m6a()); - } - - /// remove cpg/5mc base mods from the struct - pub fn drop_cpg(&mut self) { - self.base_mods.retain(|bm| !bm.is_cpg()); } - /// drop the forward stand of basemod calls - pub fn drop_forward(&mut self) { - self.base_mods.retain(|bm| bm.strand == '-'); + if ml_tag.len() != num_mods_seen { + log::warn!( + "ML tag ({}) different number than MM tag ({}).", + ml_tag.len(), + num_mods_seen, + ); } - /// drop the reverse strand of basemod calls - pub fn drop_reverse(&mut self) { - self.base_mods.retain(|bm| bm.strand == '+'); + add_calls(annot, M6A_TYPE, &mut m6a_calls); + add_calls(annot, CPG_TYPE, &mut cpg_calls); + for (name, mut calls) in other_calls { + add_calls(annot, &name, &mut calls); } +} - /// drop m6A modifications with a qual less than the min_ml_score - pub fn filter_m6a(&mut self, min_ml_score: u8) { - self.base_mods - .iter_mut() - .filter(|bm| bm.is_m6a()) - .for_each(|bm| bm.ranges.filter_by_qual(min_ml_score)); +fn add_calls(annot: &mut MolecularAnnotations, name: &str, calls: &mut [(u32, u8)]) { + if calls.is_empty() { + return; } - - /// drop 5mC modifications with a qual less than the min_ml_score - pub fn filter_5mc(&mut self, min_ml_score: u8) { - self.base_mods - .iter_mut() - .filter(|bm| bm.is_cpg()) - .for_each(|bm| bm.ranges.filter_by_qual(min_ml_score)); + calls.sort_by_key(|(p, _)| *p); + let qspec = "Q".parse::().expect("Q parses"); + let t = annot.add_annotation_type(name, qspec); + for &(pos, qual) in calls.iter() { + t.add(pos, 1, Strand::Forward, vec![qual], None); } +} - /// filter the basemods at the read ends - pub fn filter_at_read_ends(&mut self, n_strip: i64) { - if n_strip <= 0 { - return; +/// Emit MM/ML tags from `annot` onto `record`. Existing `MM` and `ML` +/// aux are removed first. +/// +/// Sources: +/// - [`M6A_TYPE`] / [`CPG_TYPE`] — canonical fiberseq types. MM groups +/// reconstructed from the forward sequence (`A`→`A+a`, `T`→`T-a`, +/// `C`→`C+m`, `G`→`G+m`). Calls landing on an unexpected base are +/// emitted under that base with `+` strand and a warning. +/// - Any other annotation type whose name is a valid MM group header +/// (e.g. `"C+h"`, `"N+a"`, `"T+12"`) is emitted verbatim under that +/// header. Skip counts are computed against the named base (`N` +/// counts every position). +/// - All other annotation types (`msp`, `nuc`, `fire`, etc.) are +/// skipped — they are not base modifications. +/// +/// MM groups are emitted in deterministic (lexicographic header) order. +pub fn write_mm_ml(record: &mut bam::Record, annot: &MolecularAnnotations) { + let forward_seq = if record.is_reverse() { + revcomp(record.seq().as_bytes()) + } else { + record.seq().as_bytes() + }; + + // header (e.g. "A+a", "C+h") → Vec<(pos, qual)>. BTreeMap gives + // deterministic emission order. + let mut groups: BTreeMap> = BTreeMap::new(); + + // Canonical types: reconstruct (base, strand) per call from forward seq. + for (type_name, mod_type_char, canonical) in [ + (M6A_TYPE, 'a', &[(b'A', '+'), (b'T', '-')] as &[(u8, char)]), + (CPG_TYPE, 'm', &[(b'C', '+'), (b'G', '+')] as &[(u8, char)]), + ] { + let Some(t) = annot.get_type(type_name) else { + continue; + }; + for a in &t.annotations { + let seq_base = forward_seq.get(a.start as usize).copied().unwrap_or(b'N'); + let (group_base, group_strand) = canonical + .iter() + .find(|&&(b, _)| b == seq_base) + .copied() + .unwrap_or_else(|| { + log::warn!( + "{} call at pos {} on unexpected base {:?}; emitting as {}{}{}", + type_name, + a.start, + seq_base as char, + seq_base as char, + '+', + mod_type_char, + ); + (seq_base, '+') + }); + let header = format!("{}{}{}", group_base as char, group_strand, mod_type_char); + let qual = a.qualities.first().copied().unwrap_or(0); + groups.entry(header).or_default().push((a.start, qual)); } - self.base_mods - .iter_mut() - .for_each(|bm| bm.filter_at_read_ends(n_strip)); } - /// combine the forward and reverse m6a data - pub fn m6a(&self) -> Ranges { - let ranges = self - .base_mods - .iter() - .filter(|x| x.is_m6a()) - .map(|x| &x.ranges) - .collect(); - Ranges::merge_ranges(ranges) - } - - /// combine the forward and reverse cpd/5mc data - pub fn cpg(&self) -> Ranges { - let ranges = self - .base_mods - .iter() - .filter(|x| x.is_cpg()) - .map(|x| &x.ranges) - .collect(); - Ranges::merge_ranges(ranges) - } - - /// Inject `m6a` and `cpg` annotation types into `annot` from the parsed - /// ML/MM data on this object. Coordinates are emitted in molecular - /// orientation (forward) and the per-base ML score is preserved as a - /// linear ("Q") quality. - /// - /// The MA tag layer in `ma_io` never reads or writes m6a/cpg — their - /// on-disk source of truth is ML/MM — so this is the only place the - /// `MolecularAnnotations` object gets these types attached. - pub fn populate_ma(&self, annot: &mut MolecularAnnotations) { - Self::add_basemod_type(annot, M6A_TYPE, &self.m6a()); - Self::add_basemod_type(annot, CPG_TYPE, &self.cpg()); - } - - fn add_basemod_type(annot: &mut MolecularAnnotations, type_name: &str, merged: &Ranges) { - if merged.annotations.is_empty() { - return; + // Non-canonical types: name is the MM group header (e.g. "C+h"). + for t in annot.annotation_types.iter() { + if t.name == M6A_TYPE || t.name == CPG_TYPE { + continue; } - let starts = merged.forward_starts(); - let quals = merged.get_forward_quals(); - let qspec = "Q".parse::().expect("Q parses"); - let t = annot.add_annotation_type(type_name, qspec); - for (s, q) in starts.iter().zip(quals.iter()) { - t.add(*s as u32, 1, Strand::Forward, vec![*q], None); + if !is_valid_mm_header(&t.name) { + continue; + } + for a in &t.annotations { + let qual = a.qualities.first().copied().unwrap_or(0); + groups + .entry(t.name.clone()) + .or_default() + .push((a.start, qual)); } } - /// Example MM tag: MM:Z:C+m,11,6,10;A+a,0,0,0; - /// Example ML tag: ML:B:C,157,30,2,164,118,255 - pub fn add_mm_and_ml_tags(&self, record: &mut bam::Record) { - // init the mm and ml tag to be populated - let mut ml_tag: Vec = vec![]; - let mut mm_tag = "".to_string(); - // need the original sequence for distances between bases. - let mut seq = record.seq().as_bytes(); - if record.is_reverse() { - seq = revcomp(seq); + let mut mm_tag = String::new(); + let mut ml_tag: Vec = Vec::new(); + for (header, mut calls) in groups { + calls.sort_by_key(|(p, _)| *p); + ml_tag.extend(calls.iter().map(|&(_, q)| q)); + mm_tag.push_str(&header); + // First byte of the header is the skip base (`N` counts everything). + let skip_base = header.as_bytes()[0]; + let mut last_pos = 0usize; + for (pos, _) in &calls { + let p = *pos as usize; + let in_between = if last_pos < p { + forward_seq[last_pos..p] + .iter() + .filter(|&&b| skip_base == b'N' || b == skip_base) + .count() + } else { + 0 + }; + last_pos = p + 1; + mm_tag.push_str(&format!(",{in_between}")); } - // add to the ml and mm tag. - for basemod in self.base_mods.iter() { - // adding quality values (ML) - ml_tag.extend(basemod.ranges.get_forward_quals()); - // get MM tag values - let mut cur_mm = vec![]; - let positions = basemod.ranges.forward_starts(); - let mut last_pos = 0; - for pos in positions { - let u_pos = pos as usize; - let mut in_between = 0; - if last_pos < u_pos { - for base in seq[last_pos..u_pos].iter() { - if *base == basemod.modified_base { - in_between += 1; - } - } - } - last_pos = u_pos + 1; - cur_mm.push(in_between); - } - // Add to the MM string - mm_tag.push(basemod.modified_base as char); - mm_tag.push(basemod.strand); - mm_tag.push(basemod.modification_type); - for diff in cur_mm { - mm_tag.push_str(&format!(",{diff}")); - } - mm_tag.push(';') - // next basemod - } - log::trace!( - "{}\n{}\n{}\n", - record.is_reverse(), - mm_tag, - String::from_utf8_lossy(&seq) - ); - // clear out the old base mods - record.remove_aux(b"MM").unwrap_or(()); - record.remove_aux(b"ML").unwrap_or(()); - // Add MM - let aux_integer_field = Aux::String(&mm_tag); - record.push_aux(b"MM", aux_integer_field).unwrap(); - // Add ML - let aux_array: AuxArray = (&ml_tag).into(); - let aux_array_field = Aux::ArrayU8(aux_array); - record.push_aux(b"ML", aux_array_field).unwrap(); + mm_tag.push(';'); + } + + record.remove_aux(b"MM").ok(); + record.remove_aux(b"ML").ok(); + record + .push_aux(b"MM", Aux::String(&mm_tag)) + .expect("push MM tag"); + record + .push_aux(b"ML", Aux::ArrayU8((&ml_tag).into())) + .expect("push ML tag"); +} + +/// True if `name` looks like an MM group header: one canonical base +/// (`ACGTUN`), a strand sign, then a non-empty alphanumeric mod type. +fn is_valid_mm_header(name: &str) -> bool { + let bytes = name.as_bytes(); + if bytes.len() < 3 { + return false; } + let base_ok = matches!(bytes[0], b'A' | b'C' | b'G' | b'T' | b'U' | b'N'); + let strand_ok = bytes[1] == b'+' || bytes[1] == b'-'; + let mod_ok = bytes[2..].iter().all(|b| b.is_ascii_alphanumeric()); + base_ok && strand_ok && mod_ok } diff --git a/src/utils/fibertig.rs b/src/utils/fibertig.rs index be7eb4fc..6856c56e 100644 --- a/src/utils/fibertig.rs +++ b/src/utils/fibertig.rs @@ -61,14 +61,16 @@ pub fn read_fibertig_tags(record: &Record) -> Result { Ok(Aux::String(s)) => { let parts: Vec> = s .split('|') - .map(|p| if p.is_empty() { None } else { Some(p.to_string()) }) + .map(|p| { + if p.is_empty() { + None + } else { + Some(p.to_string()) + } + }) .collect(); if parts.len() != fs.len() { - anyhow::bail!( - "fa ({}) and fs ({}) length mismatch", - parts.len(), - fs.len() - ); + anyhow::bail!("fa ({}) and fs ({}) length mismatch", parts.len(), fs.len()); } Some(parts) } @@ -670,11 +672,7 @@ impl FiberTig { let contig_name = std::str::from_utf8(header_view.tid2name(record.tid() as u32))?.to_string(); - for info in annot - .iter_type(FIBERTIG_TYPE) - .into_iter() - .flatten() - { + for info in annot.iter_type(FIBERTIG_TYPE).into_iter().flatten() { let (Some(ref_start), Some(ref_end)) = (info.ref_start, info.ref_end) else { continue; }; diff --git a/src/utils/ftexpression.rs b/src/utils/ftexpression.rs index 4eb0faf3..2d43e30d 100644 --- a/src/utils/ftexpression.rs +++ b/src/utils/ftexpression.rs @@ -1,5 +1,4 @@ use crate::fiber::FiberseqData; -use crate::utils::bamannotations; use crate::utils::input_bam::FiberFilters; #[derive(Debug)] @@ -138,43 +137,6 @@ pub fn parse_filter(filter_orig: &str) -> ParsedExpr { } } -pub fn apply_filter_to_range( - parsed: &ParsedExpr, - range: &mut bamannotations::Ranges, -) -> Result<(), anyhow::Error> { - let starting_len = range.annotations.len(); - - let to_keep: Vec = if parsed.fn_name == "len" { - range - .annotations - .iter() - .map(|annotation| len(annotation.length, &parsed.op, &parsed.threshold)) - .collect() - } else if parsed.fn_name == "qual" { - range - .annotations - .iter() - .map(|annotation| qual(annotation.qual, &parsed.op, &parsed.threshold)) - .collect() - } else { - anyhow::bail!("Invalid function name: {}", &parsed.fn_name); - }; - - // Filter annotations based on the to_keep boolean vector - range.annotations = range - .annotations - .iter() - .zip(to_keep.iter()) - .filter_map(|(annotation, &keep)| if keep { Some(annotation.clone()) } else { None }) - .collect(); - - // check we dropped the right number of values - let n_dropped = to_keep.iter().filter(|&x| !x).count(); - assert_eq!(starting_len, range.annotations.len() + n_dropped); - - Ok(()) -} - pub fn apply_filter_fsd(fsd: &mut FiberseqData, filt: &FiberFilters) -> Result<(), anyhow::Error> { if let Some(s) = filt.filter_expression.as_ref() { if !s.is_empty() { @@ -204,63 +166,3 @@ pub fn apply_filter_fsd(fsd: &mut FiberseqData, filt: &FiberFilters) -> Result<( } Ok(()) } - -/// tests -#[cfg(test)] -mod test { - use super::*; - use crate::utils::bamannotations; - - fn make_fake_range() -> bamannotations::Ranges { - use bamannotations::{FiberAnnotation, FiberAnnotations}; - - let annotations = vec![ - FiberAnnotation { - start: 0, - end: 5, - length: 5, - qual: 0, - reference_start: Some(0), - reference_end: Some(5), - reference_length: Some(5), - extra_columns: None, - }, - FiberAnnotation { - start: 10, - end: 15, - length: 5, - qual: 255, - reference_start: Some(10), - reference_end: Some(15), - reference_length: Some(5), - extra_columns: None, - }, - FiberAnnotation { - start: 17, - end: 20, - length: 3, - qual: 181, - reference_start: Some(17), - reference_end: Some(20), - reference_length: Some(3), - extra_columns: None, - }, - ]; - - FiberAnnotations { - annotations, - seq_len: 100, - reverse: false, - } - } - - #[test] - fn test_this_one() { - let filter = "len(msp)=50:100"; - let mut range = make_fake_range(); - let parser = parse_filter(filter); - eprintln!("{:?}", range.annotations.len()); - apply_filter_to_range(&parser, &mut range).unwrap(); - eprintln!("{:?}", range.annotations.len()); - } -} diff --git a/src/utils/input_bam.rs b/src/utils/input_bam.rs index b33d1ce2..4e384a2a 100644 --- a/src/utils/input_bam.rs +++ b/src/utils/input_bam.rs @@ -321,7 +321,6 @@ impl std::default::Default for InputBam { mod tests { use super::*; use crate::fiber::FiberseqData; - use crate::utils::basemods::BaseMods; use molecular_annotation::{MolecularAnnotations, QualitySpec, Strand}; /// Build a minimal `FiberseqData` shaped only for `passes_fire_filter`. @@ -346,7 +345,6 @@ mod tests { FiberseqData { record: rust_htslib::bam::Record::new(), annotations, - base_mods: BaseMods { base_mods: vec![] }, ec: 0.0, target_name: ".".to_string(), rg: ".".to_string(), diff --git a/tests/basemods.rs b/tests/basemods.rs index 37e34959..acff79b7 100644 --- a/tests/basemods.rs +++ b/tests/basemods.rs @@ -1,21 +1,96 @@ use env_logger::{Builder, Target}; -use fibertools_rs::utils::basemods::*; +use fibertools_rs::utils::basemods::{parse_mm_ml_into_ma, write_mm_ml, CPG_TYPE, M6A_TYPE}; +use molecular_annotation::MolecularAnnotations; +use rust_htslib::bam::record::Aux; use rust_htslib::{bam, bam::Read}; #[test] -/// checks that we can read base mods into BaseMods and the write the BaseMods to a new bam -/// record, extract them again and they remain the same. -fn test_mods_do_not_change() { - Builder::new() +/// Round-trip MM/ML through the new MolecularAnnotations-based parser +/// and writer: load MM/ML into a MolecularAnnotations, write it back to +/// the record, re-parse, and assert the m6a/cpg annotation types are +/// equal. Positions and ML qualities round-trip exactly; the MM tag's +/// per-group encoding is normalized to canonical fiberseq form on +/// output (see basemods.rs module docs for the canonicalization table). +fn test_mods_round_trip() { + let _ = Builder::new() .target(Target::Stderr) .filter(None, log::LevelFilter::Debug) - .init(); + .try_init(); let mut bam = bam::Reader::from_path("tests/data/all.bam").unwrap(); for rec in bam.records() { let mut rec = rec.unwrap(); - let mods = BaseMods::new(&rec, 0); - mods.add_mm_and_ml_tags(&mut rec); - let mods_2 = BaseMods::new(&rec, 0); - assert_eq!(mods, mods_2); + let mut a = MolecularAnnotations::from_record(&rec); + parse_mm_ml_into_ma(&rec, &mut a, 0, 0); + write_mm_ml(&mut rec, &a); + let mut b = MolecularAnnotations::from_record(&rec); + parse_mm_ml_into_ma(&rec, &mut b, 0, 0); + assert_eq!(a.get_type(M6A_TYPE), b.get_type(M6A_TYPE)); + assert_eq!(a.get_type(CPG_TYPE), b.get_type(CPG_TYPE)); } } + +/// Non-canonical MM groups (e.g. `C+h`, 5hmC) must survive round-trip +/// through `parse_mm_ml_into_ma` and `write_mm_ml`. The legacy +/// `BaseMods` preserved arbitrary mod types; the new path stores them +/// as annotation types named after the MM group header. +#[test] +fn test_non_canonical_mod_round_trip() { + // Load any record to get a real sequence, then overwrite MM/ML with + // a synthetic non-canonical tag set. + let mut bam = bam::Reader::from_path("tests/data/all.bam").unwrap(); + let mut rec = bam.records().next().expect("all.bam has records").unwrap(); + + // Find the first three C positions in the forward sequence to place + // hypothetical 5hmC calls on. + let fwd = if rec.is_reverse() { + bio::alphabets::dna::revcomp(rec.seq().as_bytes()) + } else { + rec.seq().as_bytes() + }; + let c_positions: Vec = fwd + .iter() + .enumerate() + .filter(|(_, &b)| b == b'C' || b == b'c') + .take(3) + .map(|(i, _)| i) + .collect(); + assert!(c_positions.len() >= 3, "need at least 3 C bases"); + + // Build a `C+h,...;` MM tag pointing at those C positions and + // matching ML qualities. + let mut skips: Vec = Vec::with_capacity(3); + let mut c_count = 0usize; + let mut next_target = 0; + for (i, &b) in fwd.iter().enumerate() { + if next_target >= c_positions.len() { + break; + } + if i == c_positions[next_target] { + skips.push(c_count); + c_count = 0; + next_target += 1; + } else if b == b'C' || b == b'c' { + c_count += 1; + } + } + let mm = format!("C+h,{},{},{};", skips[0], skips[1], skips[2]); + let ml: Vec = vec![200, 150, 100]; + + rec.remove_aux(b"MM").ok(); + rec.remove_aux(b"ML").ok(); + rec.push_aux(b"MM", Aux::String(&mm)).unwrap(); + rec.push_aux(b"ML", Aux::ArrayU8((&ml).into())).unwrap(); + + // Parse → write → re-parse, then assert C+h positions and qualities + // round-trip. + let mut a = MolecularAnnotations::from_record(&rec); + parse_mm_ml_into_ma(&rec, &mut a, 0, 0); + let a_ch = a.get_type("C+h").expect("C+h type present after parse"); + assert_eq!(a_ch.annotations.len(), 3); + + write_mm_ml(&mut rec, &a); + let mut b = MolecularAnnotations::from_record(&rec); + parse_mm_ml_into_ma(&rec, &mut b, 0, 0); + + assert_eq!(a.get_type("C+h"), b.get_type("C+h")); +} diff --git a/tests/fibertig_test.rs b/tests/fibertig_test.rs index 89fc347d..8c65f36c 100644 --- a/tests/fibertig_test.rs +++ b/tests/fibertig_test.rs @@ -523,7 +523,11 @@ fn test_read_fibertig_tags_reverse_strand_multi_peak() -> Result<()> { let infos: Vec<_> = annot.iter_type(FIBERTIG_TYPE).unwrap().collect(); for (i, (info, (exp_start, exp_end, exp_name))) in infos.iter().zip(expected.iter()).enumerate() { - assert_eq!(info.ref_start, Some(*exp_start), "ref_start mismatch at {i}"); + assert_eq!( + info.ref_start, + Some(*exp_start), + "ref_start mismatch at {i}" + ); assert_eq!(info.ref_end, Some(*exp_end), "ref_end mismatch at {i}"); assert_eq!(info.name, Some(*exp_name), "name mismatch at {i}"); } @@ -561,7 +565,11 @@ fn test_read_fibertig_tags_reverse_strand_shared_start() -> Result<()> { let infos: Vec<_> = annot.iter_type(FIBERTIG_TYPE).unwrap().collect(); for (i, (info, (exp_start, exp_end, exp_name))) in infos.iter().zip(expected.iter()).enumerate() { - assert_eq!(info.ref_start, Some(*exp_start), "ref_start mismatch at {i}"); + assert_eq!( + info.ref_start, + Some(*exp_start), + "ref_start mismatch at {i}" + ); assert_eq!(info.ref_end, Some(*exp_end), "ref_end mismatch at {i}"); assert_eq!(info.name, Some(*exp_name), "name mismatch at {i}"); } From 80f2e0923200f1cac29f9a77be46a2a62b10e4a5 Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Tue, 12 May 2026 15:23:22 -0600 Subject: [PATCH 12/24] chore: delete bamlift, migrate coord tests to spec liftover bamlift's lift_query_range / lift_reference_positions are gone - the spec library's AlignedBlocks::{lift_to_reference, lift_to_query} is the single liftover path. center::find_offset is rewired onto lift_to_query. The boundary-bug regression (#90) and coordinate-lift test are kept and migrated, not deleted. Both now exercise AlignedBlocks. The spec's inward-snap semantics natively fix #90: an MSP that ends exactly on a block boundary now lifts to the end of the current block, not the start of the next one. --- src/subcommands/center.rs | 32 +-- src/utils.rs | 1 - src/utils/bamlift.rs | 381 ---------------------------------- tests/boundary_bug_test.rs | 99 +++++---- tests/coordinate_lift_test.rs | 78 ++----- 5 files changed, 85 insertions(+), 506 deletions(-) delete mode 100644 src/utils/bamlift.rs diff --git a/src/subcommands/center.rs b/src/subcommands/center.rs index bb30aec0..aadbee13 100644 --- a/src/subcommands/center.rs +++ b/src/subcommands/center.rs @@ -1,11 +1,11 @@ use crate::cli::CenterOptions; use crate::fiber::FiberseqData; use crate::utils::bamannotations::primary_qual; -use crate::utils::bamlift::*; use crate::utils::bio_io; use crate::*; use bio::alphabets::dna::revcomp; use indicatif::{style, ProgressBar}; +use molecular_annotation::AlignedBlocks; use rayon::prelude::*; use rust_htslib::bam::Read; use rust_htslib::{bam, bam::ext::BamRecordExtensions}; @@ -146,25 +146,31 @@ impl CenteredFiberData { (ref_offset, mol_offset) } - /// find the query position that corresponds to the central reference position + /// find the query position that corresponds to the central reference position. + /// + /// Uses the spec library's exact-1bp `lift_to_query`. Builds + /// `AlignedBlocks` from `aligned_block_pairs` directly so synthetic + /// records with `is_unmapped()`-leaning flag combinations still get + /// their CIGAR-derived blocks (same trick `read_fibertig_tags` uses). pub fn find_offset(record: &bam::Record, reference_position: i64) -> Option { - let read_center: Vec = lift_query_positions_exact(record, &[reference_position]) - .ok()? - .into_iter() - .flatten() - .collect(); + if reference_position < 0 { + return None; + } + let pairs = record + .aligned_block_pairs() + .map(|([qs, qe], [rs, re])| ([qs as u32, qe as u32], [rs as u32, re as u32])); + let blocks = AlignedBlocks::from_pairs(pairs, record.seq_len() as u32); + let (q_start, _) = + blocks.lift_to_query(reference_position as u32, reference_position as u32 + 1); + let qp = q_start.map(|x| x as i64); log::debug!( "{}, {}, {}, {:?}", reference_position, record.reference_start(), record.reference_end(), - read_center + qp ); - if read_center.is_empty() { - None - } else { - Some(read_center[0]) - } + qp } /// Get the sequence diff --git a/src/utils.rs b/src/utils.rs index 6f35b107..d4d33260 100644 --- a/src/utils.rs +++ b/src/utils.rs @@ -1,6 +1,5 @@ pub mod acf; pub mod bamannotations; -pub mod bamlift; pub mod basemods; pub mod bio_io; pub mod fibertig; diff --git a/src/utils/bamlift.rs b/src/utils/bamlift.rs deleted file mode 100644 index 620f3a0d..00000000 --- a/src/utils/bamlift.rs +++ /dev/null @@ -1,381 +0,0 @@ -use anyhow::Result; -use itertools::multiunzip; -use rust_htslib::{bam, bam::ext::BamRecordExtensions}; -use std::collections::HashMap; - -/// Merge two lists into a sorted list -/// Normal sort is supposed to be very fast on two sorted lists -/// -pub fn merge_two_lists(left: &[T], right: &[T]) -> Vec -where - T: Ord, - T: Clone, -{ - let mut x: Vec = left.iter().chain(right.iter()).cloned().collect(); - x.sort(); - x -} - -/// Merge two lists based on a key -/// Normal sort is supposed to be very fast on two sorted lists -/// -/// ``` -/// use fibertools_rs::utils::bamlift::*; -/// let x = vec![1,3]; -/// let x_q = vec!["a","b"]; -/// let y = vec![2,4]; -/// let y_q = vec!["c", "d"]; -/// let z = merge_two_lists_with_qual(&x, &x_q, &y, &y_q); -/// assert_eq!(z, vec![(1,"a"), (2,"c"), (3,"b"), (4, "d")]); -/// ``` -pub fn merge_two_lists_with_qual( - left: &[T], - left_q: &[U], - right: &[T], - right_q: &[U], -) -> Vec<(T, U)> -where - T: Ord, - T: Clone, - U: Clone, -{ - let l = left - .iter() - .zip(left_q.iter()) - .map(|(a, b)| (a.clone(), b.clone())); - - let r = right - .iter() - .zip(right_q.iter()) - .map(|(a, b)| (a.clone(), b.clone())); - - let mut x: Vec<(T, U)> = l.chain(r).collect(); - x.sort_by_key(|(a, _b)| a.clone()); - x -} - -#[inline(always)] -pub fn is_sorted(v: &[T]) -> bool -where - T: Ord, -{ - v.windows(2).all(|w| w[0] <= w[1]) -} - -// -// CLOSEST LIFTOVER FUNCTIONS -// - -/// this is a helper function for liftover_closest that should only be called from there -/// The exception for this is test cases, where it should be easier to test this function -/// directly. -#[allow(clippy::all)] -fn liftover_closest( - positions: &[i64], - aligned_block_pairs: &Vec<([i64; 2], [i64; 2])>, -) -> Result>> { - // skip empty - if positions.is_empty() { - return Ok(vec![]); - } - if aligned_block_pairs.is_empty() { - return Ok(positions.iter().map(|_x| None).collect()); - } - if !is_sorted(positions) { - return Err(anyhow::anyhow!( - "Positions must be sorted before calling liftover! Array length: {}, first 5: {:?}, last 5: {:?}", - positions.len(), - &positions[..std::cmp::min(5, positions.len())], - &positions[positions.len().saturating_sub(5)..] - )); - } - - // find the closest position for every position - let mut starting_block = 0; - let ending_block = aligned_block_pairs.len(); - let mut pos_mapping = HashMap::new(); - for cur_pos in positions { - pos_mapping.insert(cur_pos, (-1, i64::MAX)); - let mut current_block = 0; - for block_index in starting_block..ending_block { - // get the current alignment block - let ([q_st, q_en], [r_st, r_en]) = &aligned_block_pairs[block_index]; - // get the previous closest position - let (best_r_pos, best_diff) = pos_mapping.get_mut(cur_pos).unwrap(); - // exact match found (including exact end of block) - if cur_pos >= q_st && cur_pos <= q_en { - let dist_from_start = cur_pos - q_st; - *best_diff = 0; - *best_r_pos = r_st + dist_from_start; - break; - } - // we are before the start of the block - else if cur_pos < q_st { - let diff = (q_st - cur_pos).abs(); - if diff < *best_diff { - *best_diff = diff; - *best_r_pos = *r_st; - } - } - // we are past the end of the block - else if cur_pos > q_en { - let diff = (cur_pos - q_en).abs(); - if diff < *best_diff { - *best_diff = diff; - *best_r_pos = *r_en; - } - // we don't need to return to previous blocks since the input is sorted - starting_block = current_block; - } - current_block += 1; - } - } - let mut rtn = vec![]; - for q_pos in positions { - let (r_pos, diff) = pos_mapping.get(q_pos).unwrap(); - if *r_pos == -1 && *diff == i64::MAX { - rtn.push(None); - } else { - rtn.push(Some(*r_pos)); - } - } - assert_eq!(rtn.len(), positions.len()); - Ok(rtn) -} - -/// find the closest reference positions for a list of query positions -pub fn lift_reference_positions( - aligned_block_pairs: &Vec<([i64; 2], [i64; 2])>, - query_positions: &[i64], -) -> Result>> { - liftover_closest(query_positions, aligned_block_pairs) -} - -/// find the closest query positions for a list of reference positions -pub fn lift_query_positions( - aligned_block_pairs: &[([i64; 2], [i64; 2])], - reference_positions: &[i64], -) -> Result>> { - // if lifting to the query, we need to reverse the pairs - let aligned_block_pairs = aligned_block_pairs.iter().map(|(q, r)| (*r, *q)).collect(); - liftover_closest(reference_positions, &aligned_block_pairs) -} - -/// Helper function to lift positions that may or may not be sorted -fn lift_positions_with_sort_handling( - aligned_block_pairs: &Vec<([i64; 2], [i64; 2])>, - positions: &[i64], - lift_reference_to_query: bool, -) -> Result>> { - if is_sorted(positions) { - // Fast path: positions are sorted, lift normally - if !lift_reference_to_query { - lift_reference_positions(aligned_block_pairs, positions) - } else { - lift_query_positions(aligned_block_pairs, positions) - } - } else { - // Slow path: positions are unsorted, need to sort positions independently - let mut indices: Vec = (0..positions.len()).collect(); - indices.sort_by_key(|&i| positions[i]); - - let sorted_positions: Vec = indices.iter().map(|&i| positions[i]).collect(); - - // Lift sorted positions - let lifted_positions = if !lift_reference_to_query { - lift_reference_positions(aligned_block_pairs, &sorted_positions)? - } else { - lift_query_positions(aligned_block_pairs, &sorted_positions)? - }; - - // Restore original order - let mut original_positions = vec![None; positions.len()]; - for (sorted_idx, &original_idx) in indices.iter().enumerate() { - original_positions[original_idx] = lifted_positions[sorted_idx]; - } - - Ok(original_positions) - } -} - -#[allow(clippy::type_complexity)] -fn lift_range( - aligned_block_pairs: &Vec<([i64; 2], [i64; 2])>, - starts: &[i64], - ends: &[i64], - lift_reference_to_query: bool, -) -> Result<(Vec>, Vec>, Vec>)> { - assert_eq!(starts.len(), ends.len()); - - // Lift starts and ends using the helper function - let ref_starts = - lift_positions_with_sort_handling(aligned_block_pairs, starts, lift_reference_to_query)?; - let ref_ends = - lift_positions_with_sort_handling(aligned_block_pairs, ends, lift_reference_to_query)?; - - // Common logic for processing lifted positions - assert_eq!(ref_starts.len(), ref_ends.len()); - let rtn = ref_starts - .into_iter() - .zip(ref_ends) - .map(|(start, end)| match (start, end) { - (Some(start), Some(end)) => { - if start == end { - (None, None, None) - } else { - (Some(start), Some(end), Some(end - start)) - } - } - _ => (None, None, None), - }) - .collect::>(); - Ok(multiunzip(rtn)) -} - -/// Find the closest range but hopefully better -#[allow(clippy::type_complexity)] -pub fn lift_query_range( - record: &bam::Record, - starts: &[i64], - ends: &[i64], -) -> Result<(Vec>, Vec>, Vec>)> { - // get the aligned block pairs - let aligned_block_pairs: Vec<([i64; 2], [i64; 2])> = record.aligned_block_pairs().collect(); - lift_range(&aligned_block_pairs, starts, ends, false) -} - -// -// EXACT LIFTOVER FUNCTIONS -// - -/// liftover positions using the cigar string -fn liftover_exact( - aligned_block_pairs: &Vec<([i64; 2], [i64; 2])>, - positions: &[i64], - lift_reference_to_query: bool, -) -> Result>> { - if !is_sorted(positions) { - return Err(anyhow::anyhow!( - "Positions must be sorted before calling liftover!" - )); - } - - // find the shared positions in the reference - let mut return_positions = vec![]; - let mut cur_idx = 0; - // ends are not inclusive, I checked. - for ([q_st, q_en], [r_st, r_en]) in aligned_block_pairs { - let (st, en) = if !lift_reference_to_query { - (q_st, q_en) - } else { - (r_st, r_en) - }; - // check bounds - if cur_idx == positions.len() { - break; - } - let mut cur_pos = positions[cur_idx]; - // need to go to the next block - while cur_pos < *en { - if cur_pos >= *st { - let dist_from_start = cur_pos - st; - let rtn_pos = if !lift_reference_to_query { - r_st + dist_from_start - } else { - q_st + dist_from_start - }; - return_positions.push(Some(rtn_pos)); - } else { - return_positions.push(None); - } - // reset current position - cur_idx += 1; - if cur_idx == positions.len() { - break; - } - cur_pos = positions[cur_idx]; - } - } - - // add values for things that won't lift at the end - while positions.len() > return_positions.len() { - return_positions.push(None); - } - assert_eq!(positions.len(), return_positions.len()); - Ok(return_positions) -} - -pub fn lift_reference_positions_exact( - record: &bam::Record, - query_positions: &[i64], -) -> Result>> { - if record.is_unmapped() { - Ok(query_positions.iter().map(|_x| None).collect()) - } else { - let aligned_block_pairs: Vec<([i64; 2], [i64; 2])> = record.aligned_block_pairs().collect(); - liftover_exact(&aligned_block_pairs, query_positions, false) - } -} - -pub fn lift_query_positions_exact( - record: &bam::Record, - reference_positions: &[i64], -) -> Result>> { - if record.is_unmapped() { - Ok(reference_positions.iter().map(|_x| None).collect()) - } else { - let aligned_block_pairs: Vec<([i64; 2], [i64; 2])> = record.aligned_block_pairs().collect(); - liftover_exact(&aligned_block_pairs, reference_positions, true) - } -} - -#[allow(clippy::type_complexity)] -fn lift_range_exact( - record: &bam::Record, - starts: &[i64], - ends: &[i64], - lift_reference_to_query: bool, -) -> Result<(Vec>, Vec>, Vec>)> { - assert_eq!(starts.len(), ends.len()); - let (ref_starts, ref_ends) = if !lift_reference_to_query { - ( - lift_reference_positions_exact(record, starts)?, - lift_reference_positions_exact(record, ends)?, - ) - } else { - ( - lift_query_positions_exact(record, starts)?, - lift_query_positions_exact(record, ends)?, - ) - }; - assert_eq!(ref_starts.len(), ref_ends.len()); - let rtn = ref_starts - .into_iter() - .zip(ref_ends) - .map(|(start, end)| match (start, end) { - (Some(start), Some(end)) => (Some(start), Some(end), Some(end - start)), - _ => (None, None, None), - }) - .collect::>(); - Ok(multiunzip(rtn)) -} - -/// Find the exact range in the reference from a query range -#[allow(clippy::type_complexity)] -pub fn lift_query_range_exact( - record: &bam::Record, - starts: &[i64], - ends: &[i64], -) -> Result<(Vec>, Vec>, Vec>)> { - lift_range_exact(record, starts, ends, false) -} - -/// Find the exact range in the query from a reference range -#[allow(clippy::type_complexity)] -pub fn lift_reference_range_exact( - record: &bam::Record, - starts: &[i64], - ends: &[i64], -) -> Result<(Vec>, Vec>, Vec>)> { - lift_range_exact(record, starts, ends, true) -} diff --git a/tests/boundary_bug_test.rs b/tests/boundary_bug_test.rs index 11f5e5f1..6d1ffbcf 100644 --- a/tests/boundary_bug_test.rs +++ b/tests/boundary_bug_test.rs @@ -1,53 +1,50 @@ -use fibertools_rs::utils::bamlift::lift_reference_positions; - +use molecular_annotation::liftover::AlignedBlocks; + +/// Regression for GitHub issue #90. +/// +/// Setup: +/// 0 1 2 +/// 01234567890123456789012 +/// Read MSP: | MSP | +/// Read ===========-------===== +/// Genome ======================= +/// Genome MSP: | MSP | +/// +/// Aligned blocks: +/// Block 1: query [0, 11) -> ref [0, 11) +/// Block 2: query [11, 16) -> ref [18, 23) (5bp gap on ref between blocks) +/// +/// MSP query range to lift: [4, 11). The end coordinate sits exactly on +/// the boundary between block 1 and block 2. +/// +/// The old `lift_reference_positions` (closest-snap) mapped query +/// position 11 to ref 18 (start of block 2), yielding MSP length +/// 18 - 4 = 14 in reference space. +/// +/// The spec library's `AlignedBlocks::lift_to_reference` (inward-snap) +/// correctly maps [4, 11) to ref [4, 11) — the requested range is +/// entirely inside block 1, and the half-open end snaps to the last +/// included base + 1 within the block. #[test] -fn test_alignment_boundary_bug() { - // Create alignment blocks that reproduce the issue described in GitHub issue #90 - // Based on the illustration: - // 0 1 2 - // 01234567890123456789012 - // Read MSP: | MSP | - // Read ===========-------===== - // Genome ======================= - // Genome MSP: | MSP | - - // Alignment blocks: - // Block 1: query [0, 11) -> reference [0, 11) (positions 0-10 aligned) - // Block 2: query [11, 16) -> reference [18, 23) (positions 11-15 -> 18-22, gap 11-17) - let aligned_block_pairs = vec![ - ([0, 11], [0, 11]), // First aligned block - ([11, 16], [18, 23]), // Second aligned block (with gap) - ]; - - // MSP/nucleosome ends exactly at position 11 (end of first alignment block) - let query_positions = vec![4, 11]; // MSP from position 4 to 11 - - println!("Alignment blocks: {:?}", aligned_block_pairs); - println!("Query positions to lift: {:?}", query_positions); - - // Lift the positions - let result = lift_reference_positions(&aligned_block_pairs, &query_positions).unwrap(); - println!("Lifted reference positions: {:?}", result); - - // The bug: position 11 should map to reference position 11 (end of first block) - // but the current code maps it to position 18 (start of second block) - assert_eq!(result[0], Some(4)); // Start position should be correct - - // This is the problematic case - position 11 at block boundary - println!("Position 11 maps to reference: {:?}", result[1]); - - // According to the issue, this currently maps to 18 but should map to 11 - // The MSP length becomes 18-4=14 instead of 11-4=7 - if let Some(end_pos) = result[1] { - let msp_length = end_pos - result[0].unwrap(); - println!("MSP length in reference: {}", msp_length); - println!("Expected length: 7, actual length: {}", msp_length); - - // The bug manifests as the end position being mapped to the start of the next block - if end_pos == 18 { - println!("BUG CONFIRMED: End position {} mapped to start of next block instead of end of current block", end_pos); - } else if end_pos == 11 { - println!("FIXED: End position correctly mapped to {}", end_pos); - } - } +fn test_alignment_boundary_bug_fixed_by_inward_snap() { + let blocks = AlignedBlocks::new( + vec![([0, 11], [0, 11]), ([11, 16], [18, 23])], + 16, // query_len + ); + + let (ref_start, ref_end) = blocks.lift_to_reference(4, 11); + assert_eq!( + ref_start, + Some(4), + "start of MSP should lift to ref position 4" + ); + assert_eq!( + ref_end, + Some(11), + "end of MSP at block boundary should lift to ref 11 (end of block 1), \ + not ref 18 (start of block 2)" + ); + + let length = ref_end.unwrap() - ref_start.unwrap(); + assert_eq!(length, 7, "MSP length in reference space"); } diff --git a/tests/coordinate_lift_test.rs b/tests/coordinate_lift_test.rs index 248482f9..dc742cb4 100644 --- a/tests/coordinate_lift_test.rs +++ b/tests/coordinate_lift_test.rs @@ -1,73 +1,31 @@ +use molecular_annotation::liftover::AlignedBlocks; use rust_htslib::bam; -use rust_htslib::bam::ext::BamRecordExtensions; use rust_htslib::bam::Read; +/// Exercise `AlignedBlocks::lift_to_reference` against a real fiberseq +/// record. Forward query range 3525-3628 (a 103bp nucleosome) should +/// lift to a reference range of the same length when the range sits +/// entirely inside an aligned block. #[test] fn test_coordinate_lift() -> anyhow::Result<()> { let mut bam = bam::Reader::from_path("tests/data/nuc_example.bam")?; - if let Some(result) = bam.records().next() { - let record = result?; + let record = bam + .records() + .next() + .expect("nuc_example.bam should have at least one record")?; - // Print basic record info - println!("Read: {}", String::from_utf8_lossy(record.qname())); - println!( - "Reference: {}, Position: {}, End: {}", - record.tid(), - record.reference_start(), - record.reference_end() - ); - println!("Is reverse: {}", record.is_reverse()); - println!("Sequence length: {}", record.seq_len()); + let blocks = AlignedBlocks::from_record(&record); + let (ref_start, ref_end) = blocks.lift_to_reference(3525, 3628); - // Get aligned block pairs for understanding the alignment - let aligned_blocks: Vec<_> = record.aligned_block_pairs().collect(); - println!("Total aligned blocks: {}", aligned_blocks.len()); - println!( - "First 5 aligned blocks: {:?}", - &aligned_blocks[..std::cmp::min(5, aligned_blocks.len())] - ); + let ref_start = ref_start.expect("3525 should lift"); + let ref_end = ref_end.expect("3628 should lift"); + let ref_length = ref_end - ref_start; - // Look for alignment blocks around position 3525-3628 - println!("Looking for blocks around nucleosome position 3525-3628:"); - for (i, ([q_st, q_en], [r_st, r_en])) in aligned_blocks.iter().enumerate() { - if (*q_st <= 3628 && *q_en >= 3525) || (*q_st >= 3520 && *q_st <= 3630) { - println!( - " Block {}: query=[{}, {}) -> ref=[{}, {})", - i, q_st, q_en, r_st, r_en - ); - } - } - - // Test the problematic nucleosome coordinates - // Forward position 3525, length 103 -> ends at 3628 - let starts = vec![3525]; - let ends = vec![3628]; - - println!("\nTesting nucleosome at forward pos 3525-3628:"); - - // Use the lift_query_range function from bamlift - match fibertools_rs::utils::bamlift::lift_query_range(&record, &starts, &ends) { - Ok((ref_starts, ref_ends, ref_lengths)) => { - if let (Some(ref_start), Some(ref_end), Some(ref_length)) = - (ref_starts[0], ref_ends[0], ref_lengths[0]) - { - println!( - "Reference coordinates: {}-{} (length={})", - ref_start, ref_end, ref_length - ); - println!("Expected from issue: 3367501-3367604 (length=103)"); - println!( - "Current result: {}-{} (length={})", - ref_start, ref_end, ref_length - ); - } else { - println!("Failed to lift coordinates"); - } - } - Err(e) => println!("Error lifting coordinates: {}", e), - } - } + assert_eq!( + ref_length, 103, + "lift should preserve length when the range is inside an aligned block (got {ref_start}-{ref_end})" + ); Ok(()) } From 5c737e983d1e649087375d4a8a8bff004d2623b7 Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Tue, 12 May 2026 17:05:30 -0600 Subject: [PATCH 13/24] refactor: centralize MA I/O on FiberseqData Collapses MA reads/writes to one spot each, addressing collaborator feedback that nuc/fire were doing their own from_record + write round-trips: - Add FiberseqData::serialize_annotations(legacy) as the single write entry point for code paths that have a FiberseqData. Wraps ma_io::write_annotations. - nucleosome::add_nucleosomes_to_record -> add_nucleosomes_to_annotations: takes &mut MolecularAnnotations and mutates in place; caller serializes. - fire::add_fire_to_rec uses rec.annotations directly instead of re-reading the record; emits via serialize_annotations. - subcommands/add_nucleosomes.rs constructs FiberseqData once per record and calls serialize_annotations at the end. - mock_fire.rs keeps its direct ma_io::write_annotations call (no FiberseqData since records are synthesized from BED); commented. While here: ma_io::write_annotations now strips m6a / cpg before emission as a safety net. The module already documented that base-mod types live in MM/ML, never in the MA tag set, but the writer wasn't enforcing it. Without this guard the new centralized flow would double-emit m6a (once via MM/ML, once via MA). Read path unchanged: FiberseqData::new is still the only place that reads MA tags + MM/ML. --- src/fiber.rs | 8 ++++++ src/subcommands/add_nucleosomes.rs | 38 +++++++++++++-------------- src/subcommands/fire.rs | 41 ++++++++++++++---------------- src/subcommands/mock_fire.rs | 4 +++ src/subcommands/predict_m6a.rs | 12 ++++++--- src/utils/ma_io.rs | 14 +++++++--- src/utils/nucleosome.rs | 16 +++++++----- 7 files changed, 79 insertions(+), 54 deletions(-) diff --git a/src/fiber.rs b/src/fiber.rs index 1937e6b5..09c06085 100644 --- a/src/fiber.rs +++ b/src/fiber.rs @@ -134,6 +134,14 @@ impl FiberseqData { AnnotationTypeView::new(&self.annotations, CPG_TYPE) } + /// Flush `self.annotations` onto the underlying record's MA aux + /// tags. The single write path — every subcommand that mutates + /// annotations should call this and then hand the record to the + /// BAM writer. + pub fn serialize_annotations(&mut self, legacy: bool) { + crate::utils::ma_io::write_annotations(&mut self.record, &self.annotations, legacy); + } + pub fn get_qname(&self) -> String { String::from_utf8_lossy(self.record.qname()).to_string() } diff --git a/src/subcommands/add_nucleosomes.rs b/src/subcommands/add_nucleosomes.rs index 6347fb0a..eda912cc 100644 --- a/src/subcommands/add_nucleosomes.rs +++ b/src/subcommands/add_nucleosomes.rs @@ -4,7 +4,6 @@ use crate::utils::nucleosome::*; use crate::*; use rayon::iter::ParallelIterator; use rayon::prelude::*; -use rust_htslib::bam::Record; pub fn add_nucleosomes_to_bam(nuc_opts: &mut AddNucleosomeOptions) { let mut bam = nuc_opts.input.bam_reader(); @@ -14,25 +13,26 @@ pub fn add_nucleosomes_to_bam(nuc_opts: &mut AddNucleosomeOptions) { let bam_chunk_iter = BamChunk::new(bam.records(), None); // iterate over chunks - for mut chunk in bam_chunk_iter { - // add nuc calls - let records: Vec<&mut Record> = chunk - .par_iter_mut() - .map(|record| { - let fd = FiberseqData::new(record.clone(), None, &nuc_opts.input.filters); - // m6a positions in molecular (forward) orientation - let m6a: Vec = fd - .annotations - .get_forward_coords("m6a") - .map(|v| v.into_iter().map(|(s, _)| s as i64).collect()) - .unwrap_or_default(); - add_nucleosomes_to_record(record, &m6a, &nuc_opts.nuc, nuc_opts.legacy_tags); - record - }) + for chunk in bam_chunk_iter { + let mut fibers: Vec = chunk + .into_iter() + .map(|r| FiberseqData::new(r, None, &nuc_opts.input.filters)) .collect(); - records - .into_iter() - .for_each(|record| out.write(record).unwrap()); + fibers.par_iter_mut().for_each(|fd| { + // m6a positions in molecular (forward) orientation + let m6a: Vec = fd + .annotations + .get_forward_coords("m6a") + .map(|v| v.into_iter().map(|(s, _)| s as i64).collect()) + .unwrap_or_default(); + let record = fd.record.clone(); + add_nucleosomes_to_annotations(&record, &mut fd.annotations, &m6a, &nuc_opts.nuc); + fd.serialize_annotations(nuc_opts.legacy_tags); + }); + + for fd in &fibers { + out.write(&fd.record).unwrap(); + } } } diff --git a/src/subcommands/fire.rs b/src/subcommands/fire.rs index 7e7c3e23..d4c0b8fe 100644 --- a/src/subcommands/fire.rs +++ b/src/subcommands/fire.rs @@ -25,32 +25,29 @@ pub fn add_fire_to_rec( precisions.reverse(); } - let mut annot = match ma_io::read_annotations(&rec.record) { - Ok(a) => a, - Err(e) => { - log::warn!("FIRE: failed to read annotations: {e}"); + // Use the FiberseqData's already-loaded MA object; no record + // re-read. MSP coords come from rec.annotations directly. + let (starts, lens): (Vec, Vec) = { + let Some(msp) = rec.annotations.get_type(ma_io::MSP_TYPE) else { + log::warn!("FIRE: no msp annotations on record; skipping"); + return; + }; + if msp.annotations.len() != precisions.len() { + log::warn!( + "FIRE precision count ({}) does not match MSP count ({}); skipping", + precisions.len(), + msp.annotations.len(), + ); return; } + ( + msp.annotations.iter().map(|a| a.start).collect(), + msp.annotations.iter().map(|a| a.length).collect(), + ) }; + ma_io::add_fire_annotations(&mut rec.annotations, &starts, &lens, &precisions); - let Some(msp) = annot.get_type(ma_io::MSP_TYPE) else { - log::warn!("FIRE: no msp annotations on record; skipping"); - return; - }; - if msp.annotations.len() != precisions.len() { - log::warn!( - "FIRE precision count ({}) does not match MSP count ({}); skipping", - precisions.len(), - msp.annotations.len(), - ); - return; - } - - let starts: Vec = msp.annotations.iter().map(|a| a.start).collect(); - let lens: Vec = msp.annotations.iter().map(|a| a.length).collect(); - ma_io::add_fire_annotations(&mut annot, &starts, &lens, &precisions); - - ma_io::write_annotations(&mut rec.record, &annot, legacy); + rec.serialize_annotations(legacy); log::trace!("precisions: {precisions:?}"); } diff --git a/src/subcommands/mock_fire.rs b/src/subcommands/mock_fire.rs index 1ef9e099..6ec4bcd1 100644 --- a/src/subcommands/mock_fire.rs +++ b/src/subcommands/mock_fire.rs @@ -124,6 +124,10 @@ fn create_mock_fire_record( // Build MA-spec annotations and emit. Mock FIRE only produces MSPs with // the FIRE precision (Q-scaled) quality; no nucleosomes are populated. + // Direct `ma_io::write_annotations` (rather than the + // `FiberseqData::serialize_annotations` path used elsewhere) is intentional + // here — we're synthesizing a record from BED, so there's no + // `FiberseqData` to round-trip through. let mut annot = MolecularAnnotations::from_record(&record); ma_io::add_fire_annotations(&mut annot, &starts, &lengths, &quals); ma_io::write_annotations(&mut record, &annot, false); diff --git a/src/subcommands/predict_m6a.rs b/src/subcommands/predict_m6a.rs index 91dd60b6..c0003a2b 100644 --- a/src/subcommands/predict_m6a.rs +++ b/src/subcommands/predict_m6a.rs @@ -267,16 +267,22 @@ where // write the ml and mm tags basemods::write_mm_ml(record, &annot); - // adding the nucleosomes — uses the forward m6a positions we just placed. + // Compute nucleosomes + MSPs from the forward m6a positions + // and append them to the same MA object we just built up. let modified_bases_forward: Vec = m6a_calls.iter().map(|&(p, _)| p as i64).collect(); - nucleosome::add_nucleosomes_to_record( + nucleosome::add_nucleosomes_to_annotations( record, + &mut annot, &modified_bases_forward, &opts.nuc_opts, - opts.legacy_tags, ); + // Single MA write — m6a went out via MM/ML above; nuc/msp + // (and any pre-existing annotation types we preserved) go + // out here. + crate::utils::ma_io::write_annotations(record, &annot, opts.legacy_tags); + // clear the existing data if !opts.keep { record.remove_aux(b"fp").unwrap_or(()); diff --git a/src/utils/ma_io.rs b/src/utils/ma_io.rs index 89a4e3e7..177ef2ba 100644 --- a/src/utils/ma_io.rs +++ b/src/utils/ma_io.rs @@ -15,8 +15,9 @@ //! - `fire` (forward strand, `P` phred quality) //! //! `m6a` and `cpg` types may appear *in memory* on a [`MolecularAnnotations`] -//! populated by `BaseMods::populate_ma`, but are NEVER read or written here: -//! their on-disk source of truth is `MM`/`ML`. +//! populated by [`crate::utils::basemods::parse_mm_ml_into_ma`], but are +//! NEVER read or written here: their on-disk source of truth is `MM`/`ML`. +//! The writer below strips them before emission as a safety net. use anyhow::{bail, Result}; use molecular_annotation::{Annotation, MolecularAnnotations, QualitySpec, Strand}; @@ -148,7 +149,14 @@ pub fn write_annotations(record: &mut bam::Record, annot: &MolecularAnnotations, for tag in LEGACY_NUC_MSP_TAGS { record.remove_aux(tag).ok(); } - annot.to_record(record); + // Base modifications (`m6a`, `cpg`) belong in MM/ML — never in the + // MA tag set. Drop them before serialization. See the module docs + // for the on-disk source-of-truth split. + let mut for_ma = annot.clone(); + for_ma.annotation_types.retain(|t| { + t.name != crate::utils::basemods::M6A_TYPE && t.name != crate::utils::basemods::CPG_TYPE + }); + for_ma.to_record(record); if legacy { write_legacy_nuc_msp(record, annot); } diff --git a/src/utils/nucleosome.rs b/src/utils/nucleosome.rs index 9bbb92a6..05ef81f3 100644 --- a/src/utils/nucleosome.rs +++ b/src/utils/nucleosome.rs @@ -184,11 +184,15 @@ pub fn filter_for_end( .unzip() } -pub fn add_nucleosomes_to_record( - record: &mut bam::Record, +/// Compute nucleosomes + MSPs from `m6a` calls and append them to +/// `annot` in place. Writing the MA tags onto the record is the +/// caller's responsibility (typically via [`FiberseqData::serialize_annotations`] +/// or [`ma_io::write_annotations`]). +pub fn add_nucleosomes_to_annotations( + record: &bam::Record, + annot: &mut MolecularAnnotations, m6a: &[i64], options: &NucleosomeParameters, - legacy: bool, ) { let nucs = if options.allowed_m6a_skips < 0 { find_nucleosomes(m6a, options) @@ -199,10 +203,8 @@ pub fn add_nucleosomes_to_record( let (nuc_starts, nuc_lengths) = filter_for_end(record, &nucs, options.distance_from_end); let (msp_starts, msp_lengths) = filter_for_end(record, &msps, options.distance_from_end); - let mut annot = MolecularAnnotations::from_record(record); - ma_io::add_nuc_annotations(&mut annot, &nuc_starts, &nuc_lengths); - ma_io::add_msp_annotations(&mut annot, &msp_starts, &msp_lengths, None); - ma_io::write_annotations(record, &annot, legacy); + ma_io::add_nuc_annotations(annot, &nuc_starts, &nuc_lengths); + ma_io::add_msp_annotations(annot, &msp_starts, &msp_lengths, None); } #[cfg(test)] From 18bde018370b97428bc901309b45a421a065dbe0 Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Wed, 13 May 2026 14:08:08 -0600 Subject: [PATCH 14/24] refactor: emit fibertig annotations as MA-spec tags, drop fs/fl/fa MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Finishes the fibertig migration: the BED ↔ BAM pipeline now goes through ma_io::{read,write}_annotations on the `fibertig` type, so fibertig data lives on the MA/AL/AN tag set like every other fibertools annotation type. Deletes read_fibertig_tags / write_fibertig_tags and the fs/fl/fa wire format entirely - no fallback, no legacy flag. Percent-encode `,` in BED extras The MA-spec AN tag uses `,` as its separator with no escape mechanism defined, but BED column 4+ payload can legally contain commas. The fibertig BED reader percent-encodes `,` (-> %2C) and `%` (-> %25) into Annotation.name on the way in; extract_to_bed reverses it on the way out. AN on disk stays spec-compliant; round-trip is lossless for any ASCII input. This is a breaking change for any external tool that reads fs/fl/fa from fibertig-annotated BAMs. --- src/subcommands/center.rs | 2 +- src/utils/fibertig.rs | 152 ++++++++------------------------- tests/fibertig_test.rs | 174 +++++++++++++++++++++++++++++--------- 3 files changed, 172 insertions(+), 156 deletions(-) diff --git a/src/subcommands/center.rs b/src/subcommands/center.rs index aadbee13..2f286e55 100644 --- a/src/subcommands/center.rs +++ b/src/subcommands/center.rs @@ -151,7 +151,7 @@ impl CenteredFiberData { /// Uses the spec library's exact-1bp `lift_to_query`. Builds /// `AlignedBlocks` from `aligned_block_pairs` directly so synthetic /// records with `is_unmapped()`-leaning flag combinations still get - /// their CIGAR-derived blocks (same trick `read_fibertig_tags` uses). + /// their CIGAR-derived blocks. pub fn find_offset(record: &bam::Record, reference_position: i64) -> Option { if reference_position < 0 { return None; diff --git a/src/utils/fibertig.rs b/src/utils/fibertig.rs index 6856c56e..a5a654fd 100644 --- a/src/utils/fibertig.rs +++ b/src/utils/fibertig.rs @@ -2,119 +2,27 @@ use crate::cli::PgInjectOptions; use crate::subcommands::pg_pansn; use crate::utils::bio_io; use anyhow::{Context, Result}; -use molecular_annotation::{AlignedBlocks, MolecularAnnotations, QualitySpec, Strand}; +use molecular_annotation::{MolecularAnnotations, QualitySpec, Strand}; use noodles::fasta; -use rust_htslib::bam::ext::BamRecordExtensions; use rust_htslib::bam::header::HeaderRecord; -use rust_htslib::bam::record::Aux; use rust_htslib::bam::{Header, HeaderView, Read, Record}; use std::collections::HashMap; /// Annotation type name used by the fibertig BED ↔ BAM pipeline. pub const FIBERTIG_TYPE: &str = "fibertig"; -/// Read the fibertig fs/fl/fa BAM tags into a [`MolecularAnnotations`]. -/// -/// - `fs`: feature starts (`B:I`), one per peak, molecular orientation. -/// - `fl`: feature lengths (`B:I`), one per peak, same order. -/// - `fa`: pipe-separated extras (`Z`), one chunk per peak in the same -/// order; within a chunk, columns from the source BED are joined by -/// `;`. Missing/blank entries map to `name = None` on the annotation. -/// -/// The returned [`MolecularAnnotations`] has the record's aligned blocks -/// set so ref coords can be lifted via `iter_type` / `get_ref_coords`. -pub fn read_fibertig_tags(record: &Record) -> Result { - // Build AlignedBlocks directly from `aligned_block_pairs` rather than - // `from_record`, because the spec's `from_record` early-returns empty - // for records that report `is_unmapped()` — synthetic test records - // built with `Record::new()` can hit that path even when they have a - // valid CIGAR and tid. - let mut annot = MolecularAnnotations::new(record.seq_len() as u32); - let pairs = record - .aligned_block_pairs() - .map(|([qs, qe], [rs, re])| ([qs as u32, qe as u32], [rs as u32, re as u32])); - annot.set_aligned_blocks_raw( - AlignedBlocks::from_pairs(pairs, record.seq_len() as u32), - record.is_reverse(), - ); - let fs = match record.aux(b"fs") { - Ok(Aux::ArrayU32(arr)) => Some(arr.iter().collect::>()), - Ok(Aux::ArrayI32(arr)) => Some(arr.iter().map(|v| v as u32).collect()), - _ => None, - }; - let fl = match record.aux(b"fl") { - Ok(Aux::ArrayU32(arr)) => Some(arr.iter().collect::>()), - Ok(Aux::ArrayI32(arr)) => Some(arr.iter().map(|v| v as u32).collect()), - _ => None, - }; - let (Some(fs), Some(fl)) = (fs, fl) else { - return Ok(annot); - }; - if fs.len() != fl.len() { - anyhow::bail!("fs ({}) and fl ({}) length mismatch", fs.len(), fl.len()); - } - if fs.is_empty() { - return Ok(annot); - } - - let names: Option>> = match record.aux(b"fa") { - Ok(Aux::String(s)) => { - let parts: Vec> = s - .split('|') - .map(|p| { - if p.is_empty() { - None - } else { - Some(p.to_string()) - } - }) - .collect(); - if parts.len() != fs.len() { - anyhow::bail!("fa ({}) and fs ({}) length mismatch", parts.len(), fs.len()); - } - Some(parts) - } - _ => None, - }; - - let t = annot.add_annotation_type(FIBERTIG_TYPE, QualitySpec::none()); - for (i, (s, l)) in fs.iter().zip(fl.iter()).enumerate() { - let name = names.as_ref().and_then(|v| v[i].clone()); - t.add(*s, *l, Strand::Forward, vec![], name); - } - Ok(annot) +/// Percent-encode `,` (and `%` itself) on the way into `Annotation.name`, +/// so BED column 4+ values containing `,` survive the MA-spec `AN` tag's +/// non-escapable `,` separator. The `%` -> `%25` step has to happen first +/// so the encoding is round-trippable. +fn encode_name_field(field: &str) -> String { + field.replace('%', "%25").replace(',', "%2C") } -/// Write the fibertig fs/fl/fa BAM tags from a [`MolecularAnnotations`]'s -/// [`FIBERTIG_TYPE`] annotations. No-op when the type is absent or empty. -/// `fa` is only emitted if at least one annotation has a non-empty name. -pub fn write_fibertig_tags(record: &mut Record, annot: &MolecularAnnotations) -> Result<()> { - let Some(t) = annot.get_type(FIBERTIG_TYPE) else { - return Ok(()); - }; - if t.annotations.is_empty() { - return Ok(()); - } - let fs: Vec = t.annotations.iter().map(|a| a.start).collect(); - let fl: Vec = t.annotations.iter().map(|a| a.length).collect(); - record - .push_aux(b"fs", Aux::ArrayU32((&fs).into())) - .context("Failed to add fs tag")?; - record - .push_aux(b"fl", Aux::ArrayU32((&fl).into())) - .context("Failed to add fl tag")?; - if t.annotations.iter().any(|a| a.name.is_some()) { - let fa: String = t - .annotations - .iter() - .map(|a| a.name.as_deref().unwrap_or("")) - .collect::>() - .join("|"); - record - .push_aux(b"fa", Aux::String(&fa)) - .context("Failed to add fa tag")?; - } - Ok(()) +/// Reverse of [`encode_name_field`]. `%2C` decodes first so a literal +/// `%25%2C` round-trips to `%,` rather than being mis-bracketed. +fn decode_name_field(field: &str) -> String { + field.replace("%2C", ",").replace("%25", "%") } pub struct FiberTig { @@ -126,9 +34,13 @@ pub struct FiberTig { impl FiberTig { /// Read a BED file and return per-contig [`MolecularAnnotations`] plus /// the BED header line if present. Each BED row becomes one annotation - /// in the [`FIBERTIG_TYPE`] type; extra columns (4..N) are `;`-joined - /// into [`Annotation::name`] so they round-trip through the `fa` BAM - /// tag's `|`-separated layout. + /// in the [`FIBERTIG_TYPE`] type; extra columns (4..N) are percent- + /// encoded (only `,` -> `%2C` and `%` -> `%25`) and then `;`-joined + /// into [`Annotation::name`]. The encoding is necessary because the + /// MA-spec `AN` tag uses `,` as a non-escapable separator; without it, + /// a comma in a BED name would silently split into a second AN entry + /// and break the MA↔AN count balance on read-back. `extract_to_bed` + /// decodes the fields back before writing. /// /// Annotations within each contig are sorted by molecular start, and /// each [`MolecularAnnotations`]'s `read_length` is set to that @@ -168,9 +80,14 @@ impl FiberTig { let end: u32 = fields[2].parse().context("Failed to parse end position")?; let length = end - start; - // BED columns 4+ → fa tag chunk (joined with ';') + // BED columns 4+ → `Annotation.name`. Each field is percent- + // encoded so commas survive the MA-spec AN tag's hard ',' + // separator, then ';'-joined into a single name string. + // `extract_to_bed` reverses this on the way out. let name = if fields.len() > 3 { - Some(fields[3..].join(";")) + let encoded: Vec = + fields[3..].iter().map(|f| encode_name_field(f)).collect(); + Some(encoded.join(";")) } else { None }; @@ -269,6 +186,11 @@ impl FiberTig { record.set_tid(tid); record.set_pos(pos); record.set_mapq(60); // High mapping quality + // `Record::new()` starts with the unmapped flag set. These records + // have tid/pos/CIGAR — they are mapped — so clear it. Otherwise the + // MA-spec reader's `AlignedBlocks::from_record` early-returns and + // ref coords come back as `None` on the round-trip read. + record.unset_unmapped(); record.unset_paired(); // Unpaired read record.set_mtid(-1); // No mate ID for unpaired read record.set_mpos(-1); // No mate position @@ -285,7 +207,7 @@ impl FiberTig { /// Returns `((window_start, window_end), per-window MolecularAnnotations)`. /// Coordinates in the returned annotations are still contig-absolute; /// `create_annotated_records_from_splits` shifts them record-relative - /// when building each record's `fs`/`fl` tags. + /// when serializing the record's MA-spec tags. pub fn approximately_divide_annotations_by_window_size( seq_len: i64, split_size: i64, @@ -420,14 +342,14 @@ impl FiberTig { // Apply annotations to this record. Coordinates in `annotations` // are still contig-absolute (per // `approximately_divide_annotations_by_window_size`), so shift - // them record-relative before writing the fs/fl tags. + // them record-relative before serializing. if let Some(t) = annotations.get_type_mut(FIBERTIG_TYPE) { for a in t.annotations.iter_mut() { a.start = a.start.saturating_sub(start_pos as u32); } } - write_fibertig_tags(&mut record, annotations)?; + crate::utils::ma_io::write_annotations(&mut record, annotations, false); records.push(record); } @@ -643,8 +565,8 @@ impl FiberTig { // IO functions // - /// Extract BED annotations from an annotated BAM file using the fs/fl/fa - /// tags and the record's aligned blocks (for ref coords). + /// Extract BED annotations from an annotated BAM file using the + /// MA-spec tags and the record's aligned blocks (for ref coords). pub fn extract_to_bed(opts: &PgInjectOptions) -> Result<()> { use crate::utils::bio_io; use std::io::Write; @@ -665,7 +587,7 @@ impl FiberTig { if record.tid() < 0 { continue; } - let annot = read_fibertig_tags(&record)?; + let annot = crate::utils::ma_io::read_annotations(&record)?; if annot.get_type(FIBERTIG_TYPE).is_none() { continue; } @@ -679,7 +601,7 @@ impl FiberTig { write!(writer, "{contig_name}\t{ref_start}\t{ref_end}")?; if let Some(name) = info.name { for col in name.split(';') { - write!(writer, "\t{col}")?; + write!(writer, "\t{}", decode_name_field(col))?; } } writeln!(writer)?; diff --git a/tests/fibertig_test.rs b/tests/fibertig_test.rs index 8c65f36c..645128e7 100644 --- a/tests/fibertig_test.rs +++ b/tests/fibertig_test.rs @@ -1,7 +1,9 @@ use anyhow::Result; use fibertools_rs::cli::{GlobalOpts, PansnParameters, PgInjectOptions}; -use fibertools_rs::utils::fibertig::{read_fibertig_tags, FiberTig, FIBERTIG_TYPE}; -use molecular_annotation::{MolecularAnnotations, QualitySpec, Strand}; +use fibertools_rs::utils::fibertig::{FiberTig, FIBERTIG_TYPE}; +use fibertools_rs::utils::ma_io; +use molecular_annotation::{AlignedBlocks, MolecularAnnotations, QualitySpec, Strand}; +use rust_htslib::bam::ext::BamRecordExtensions; use rust_htslib::bam::HeaderView; use std::io::Write; use tempfile::NamedTempFile; @@ -230,14 +232,14 @@ fn test_create_annotated_records_from_splits() -> Result<()> { assert_eq!(second_record.pos(), 20); assert_eq!(second_record.seq_len(), 16); - // Verify both records have fs/fl/fa tags - assert!(first_record.aux(b"fs").is_ok()); - assert!(first_record.aux(b"fl").is_ok()); - assert!(first_record.aux(b"fa").is_ok()); + // Verify both records have MA-spec tags. MA is always emitted; AN + // tags along because the fixtures supply names. AL is only emitted + // under the Separate encoding, which isn't the spec default. + assert!(first_record.aux(b"MA").is_ok()); + assert!(first_record.aux(b"AN").is_ok()); - assert!(second_record.aux(b"fs").is_ok()); - assert!(second_record.aux(b"fl").is_ok()); - assert!(second_record.aux(b"fa").is_ok()); + assert!(second_record.aux(b"MA").is_ok()); + assert!(second_record.aux(b"AN").is_ok()); Ok(()) } @@ -275,13 +277,12 @@ fn test_inject_with_bed_annotations() -> Result<()> { // Should have created records based on bed annotations assert!(!fiber_tig.records.is_empty()); - // Verify records have annotations + // Verify records have MA-spec annotation tags. Records that carry any + // fibertig annotations must have MA; AN tags along because the BED + // supplies feature names. for record in &fiber_tig.records { - // All records should have fs/fl/fa tags since we have annotations - if record.aux(b"fs").is_ok() { - // If fs tag exists, fl and fa should also exist - assert!(record.aux(b"fl").is_ok(), "fl tag missing when fs exists"); - assert!(record.aux(b"fa").is_ok(), "fa tag missing when fs exists"); + if record.aux(b"MA").is_ok() { + assert!(record.aux(b"AN").is_ok(), "AN tag missing when MA exists"); } } @@ -313,6 +314,72 @@ fn test_bed_annotations_with_unknown_contig() { assert!(error_msg.contains("Contig 'unknown_chr' not found in BAM header")); } +#[test] +fn test_bed_annotations_comma_in_extra_columns_roundtrips() -> Result<()> { + // BED column 4+ values containing the MA-spec AN separator (',') — + // and the percent-escape character itself — must round-trip through + // inject → extract unchanged. The percent encoding is applied at the + // BED↔in-memory boundary; on disk the AN tag is plain ASCII with + // commas escaped as %2C. + use fibertools_rs::cli::{GlobalOpts, PansnParameters}; + use std::io::BufRead; + + let mut fasta_file = NamedTempFile::new()?; + writeln!(fasta_file, ">chr1")?; + writeln!(fasta_file, "ATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG")?; // 40bp + fasta_file.flush()?; + + // Two BED rows with commas (and one with a literal `%`) in column 4+. + let mut bed_file = NamedTempFile::new()?; + writeln!(bed_file, "chr1\t5\t15\tfoo,bar\t100")?; + writeln!(bed_file, "chr1\t20\t30\t50%complete\tx,y,z")?; + bed_file.flush()?; + + let temp_bam = NamedTempFile::new()?; + let inject_opts = PgInjectOptions { + global: GlobalOpts::default(), + reference: fasta_file.path().to_str().unwrap().to_string(), + out: temp_bam.path().to_str().unwrap().to_string(), + bed: Some(bed_file.path().to_str().unwrap().to_string()), + split_size: 100_000, + uncompressed: false, + extract: false, + header_out: None, + pansn: PansnParameters::default(), + }; + let fiber_tig = FiberTig::from_inject_opts(&inject_opts)?; + fiber_tig.write_to_bam(&inject_opts)?; + + let temp_bed_output = NamedTempFile::new()?; + let extract_opts = PgInjectOptions { + global: GlobalOpts::default(), + reference: temp_bam.path().to_str().unwrap().to_string(), + out: temp_bed_output.path().to_str().unwrap().to_string(), + bed: None, + split_size: 100_000, + uncompressed: false, + extract: true, + header_out: None, + pansn: PansnParameters::default(), + }; + FiberTig::extract_to_bed(&extract_opts)?; + + let lines: Vec = + fibertools_rs::utils::bio_io::buffer_from(temp_bed_output.path().to_str().unwrap())? + .lines() + .collect::>>()?; + + let body: Vec<&String> = lines + .iter() + .filter(|l| !l.starts_with('#') && !l.trim().is_empty()) + .collect(); + assert_eq!(body.len(), 2, "expected two BED rows, got: {lines:?}"); + assert_eq!(body[0], "chr1\t5\t15\tfoo,bar\t100"); + assert_eq!(body[1], "chr1\t20\t30\t50%complete\tx,y,z"); + + Ok(()) +} + #[test] fn test_strip_pansn_from_contig_name() -> Result<()> { use fibertools_rs::subcommands::pg_pansn::strip_pansn_from_contig_name; @@ -419,8 +486,10 @@ fn test_extract_to_bed_with_pansn_strip() -> Result<()> { Ok(()) } -// Build a minimal mapped record with fs/fl/fa tags in forward/contig order, -// then optionally flip it to reverse-strand to simulate what an aligner would emit. +// Build a minimal mapped record with MA-spec annotation tags in +// forward/molecular order, then optionally flip it to reverse-strand to +// simulate what an aligner would emit. Names are taken pairwise from `fa` +// (`|`-separated); use the empty string for an unnamed annotation. fn build_tagged_record( seq_len: u32, fs: &[u32], @@ -428,7 +497,7 @@ fn build_tagged_record( fa: &str, reverse: bool, ) -> rust_htslib::bam::Record { - use rust_htslib::bam::record::{Aux, Cigar, CigarString}; + use rust_htslib::bam::record::{Cigar, CigarString}; use rust_htslib::bam::Record; let seq: Vec = vec![b'A'; seq_len as usize]; @@ -440,24 +509,49 @@ fn build_tagged_record( record.set_tid(0); record.set_pos(0); record.set_mapq(60); + // `Record::new()` starts in the unmapped state; clear it so + // `AlignedBlocks::from_record` (used by `ma_io::read_annotations`) + // actually lifts the CIGAR-derived blocks instead of bailing early. + record.unset_unmapped(); if reverse { record.set_reverse(); } - record - .push_aux(b"fs", Aux::ArrayU32((&fs.to_vec()).into())) - .unwrap(); - record - .push_aux(b"fl", Aux::ArrayU32((&fl.to_vec()).into())) - .unwrap(); - record.push_aux(b"fa", Aux::String(fa)).unwrap(); + assert_eq!(fs.len(), fl.len(), "fs/fl length mismatch in fixture"); + let names: Vec> = fa + .split('|') + .map(|p| { + if p.is_empty() { + None + } else { + Some(p.to_string()) + } + }) + .collect(); + assert_eq!(names.len(), fs.len(), "fa/fs length mismatch in fixture"); + + let mut annot = MolecularAnnotations::new(seq_len); + let pairs = record + .aligned_block_pairs() + .map(|([qs, qe], [rs, re])| ([qs as u32, qe as u32], [rs as u32, re as u32])); + annot.set_aligned_blocks_raw( + AlignedBlocks::from_pairs(pairs, seq_len), + record.is_reverse(), + ); + { + let t = annot.add_annotation_type(FIBERTIG_TYPE, QualitySpec::none()); + for ((s, l), name) in fs.iter().zip(fl.iter()).zip(names.into_iter()) { + t.add(*s, *l, Strand::Forward, vec![], name); + } + } + ma_io::write_annotations(&mut record, &annot, false); record } #[test] -fn test_read_fibertig_tags_forward_strand() -> Result<()> { - // Forward-strand sanity: storage order matches fs/fl input order; iter_type +fn test_read_fibertig_forward_strand() -> Result<()> { + // Forward-strand sanity: storage order matches input order; iter_type // gives BAM-orient query coords that for a forward identity-aligned record // equal molecular coords, and ref_start/ref_end equal query_start/query_end. let seq_len: u32 = 10_000; @@ -466,7 +560,7 @@ fn test_read_fibertig_tags_forward_strand() -> Result<()> { let fa = "peakA|peakB|peakC|peakD"; let record = build_tagged_record(seq_len, &fs, &fl, fa, false); - let annot = read_fibertig_tags(&record)?; + let annot = ma_io::read_annotations(&record)?; let anns = fibertig_anns(&annot); assert_eq!(anns.len(), 4); assert!(!annot.is_reverse_aligned()); @@ -488,20 +582,20 @@ fn test_read_fibertig_tags_forward_strand() -> Result<()> { } #[test] -fn test_read_fibertig_tags_reverse_strand_multi_peak() -> Result<()> { - // Reverse-strand parsing: read_fibertig_tags stores molecular coords as - // given by fs/fl. iter_type then yields AnnotationInfo with BAM-orient - // query coords (= read_len - molecular_end / read_len - molecular_start), - // and ref_start/ref_end via the record's aligned blocks. Storage order - // stays molecular ascending (fs input order); each annotation keeps its - // own name slot, so pairing can't be scrambled by sorting. +fn test_read_fibertig_reverse_strand_multi_peak() -> Result<()> { + // Reverse-strand parsing: storage holds molecular coords as written. + // iter_type then yields AnnotationInfo with BAM-orient query coords + // (= read_len - molecular_end / read_len - molecular_start), and + // ref_start/ref_end via the record's aligned blocks. Storage order + // stays molecular ascending; each annotation keeps its own name slot, + // so pairing can't be scrambled by sorting. let seq_len: u32 = 10_000; let fs: Vec = vec![100, 1_000, 3_000, 6_000, 6_500]; let fl: Vec = vec![100, 300, 500, 700, 900]; let fa = "peakA|peakB|peakC|peakD|peakE"; let record = build_tagged_record(seq_len, &fs, &fl, fa, true); - let annot = read_fibertig_tags(&record)?; + let annot = ma_io::read_annotations(&record)?; let anns = fibertig_anns(&annot); assert_eq!(anns.len(), 5); assert!(annot.is_reverse_aligned()); @@ -535,18 +629,18 @@ fn test_read_fibertig_tags_reverse_strand_multi_peak() -> Result<()> { } #[test] -fn test_read_fibertig_tags_reverse_strand_shared_start() -> Result<()> { - // Regression test for fa-pairing scrambling under shared/overlapping +fn test_read_fibertig_reverse_strand_shared_start() -> Result<()> { + // Regression test for name-pairing scrambling under shared/overlapping // start positions. With the MA-spec model each Annotation owns its own // name, so there is no sort-induced pairing problem to begin with — - // storage order matches fs input order regardless of overlap. + // storage order matches input order regardless of overlap. let seq_len: u32 = 1_000; let fs: Vec = vec![0, 0, 12, 159]; let fl: Vec = vec![263, 124, 209, 305]; let fa = "peakA|peakB|peakC|peakD"; let record = build_tagged_record(seq_len, &fs, &fl, fa, true); - let annot = read_fibertig_tags(&record)?; + let annot = ma_io::read_annotations(&record)?; let anns = fibertig_anns(&annot); assert_eq!(anns.len(), 4); assert!(annot.is_reverse_aligned()); From 2f1003d61b6ae790ec3b2faecaea25f2aa6dc738 Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Wed, 13 May 2026 14:59:33 -0600 Subject: [PATCH 15/24] fix: read FIRE precision from `fire` type, not msp.qual() Post-MA-migration `add_fire_to_rec` writes FIRE precisions to a separate `fire+P` annotation type and leaves MSP with `QualitySpec::none()`. But several consumers still read `msp.qual()` expecting FIRE precision, the legacy convention from when fibertools stored precisions on the MSP `aq` tag. --- src/fiber.rs | 40 ++++++++++++++- src/subcommands/decorator.rs | 2 +- src/subcommands/footprint.rs | 8 ++- src/subcommands/pileup.rs | 5 +- src/subcommands/validate.rs | 2 +- src/utils/ftexpression.rs | 49 ++++++++++++++++++ tests/molecular_annotation.rs | 94 +++++++++++++++++++++++++++++++++++ 7 files changed, 189 insertions(+), 11 deletions(-) diff --git a/src/fiber.rs b/src/fiber.rs index 09c06085..d762bd96 100644 --- a/src/fiber.rs +++ b/src/fiber.rs @@ -5,7 +5,7 @@ use crate::utils::bamannotations::*; use crate::utils::basemods::{parse_mm_ml_into_ma, CPG_TYPE, M6A_TYPE}; use crate::utils::bio_io::*; use crate::utils::ftexpression::apply_filter_fsd; -use crate::utils::ma_io::{MSP_TYPE, NUC_TYPE}; +use crate::utils::ma_io::{FIRE_TYPE, MSP_TYPE, NUC_TYPE}; use molecular_annotation::MolecularAnnotations; use rayon::prelude::*; use rust_htslib::bam::Read; @@ -134,6 +134,38 @@ impl FiberseqData { AnnotationTypeView::new(&self.annotations, CPG_TYPE) } + /// View over `fire` annotations derived from `self.annotations`. + pub fn fire(&self) -> AnnotationTypeView<'_> { + AnnotationTypeView::new(&self.annotations, FIRE_TYPE) + } + + /// Per-MSP FIRE precision in BAM-orient ascending order, aligned 1:1 + /// with [`Self::msp`] iteration. Returns `vec![0; msp_len]` when no + /// FIRE data is present. + /// + /// Resolves in two stages: + /// 1. If a `fire` annotation type exists with the same count as + /// `msp`, return its qualities (post-MA write path: FIRE precisions + /// live on `fire+P`). + /// 2. Otherwise fall back to `self.msp().qual()` — pre-MA fibertools + /// stored FIRE precisions on the MSP `aq` tag, so legacy BAMs land + /// them in `msp.qualities`. + pub fn fire_qual(&self) -> Vec { + let msp_len = self.msp().len(); + if msp_len == 0 { + return Vec::new(); + } + let fire = self.fire(); + if fire.len() == msp_len { + return fire.qual(); + } + let msp_q = self.msp().qual(); + if msp_q.len() == msp_len && msp_q.iter().any(|&q| q > 0) { + return msp_q; + } + vec![0; msp_len] + } + /// Flush `self.annotations` onto the underlying record's MA aux /// tags. The single write path — every subcommand that mutates /// annotations should call this and then hand the record to the @@ -386,7 +418,11 @@ impl FiberseqData { let m6a_qual = m6a.qual().iter().map(|a| Some(*a as i64)).collect(); let cpg_count = cpg.len(); let cpg_qual = cpg.qual().iter().map(|a| Some(*a as i64)).collect(); - let fire = msp.qual().iter().map(|a| Some(*a as i64)).collect(); + let fire: Vec> = self + .fire_qual() + .iter() + .map(|a| Some(*a as i64)) + .collect(); // write the features let mut rtn = String::with_capacity(0); diff --git a/src/subcommands/decorator.rs b/src/subcommands/decorator.rs index 9a580979..9d797c74 100644 --- a/src/subcommands/decorator.rs +++ b/src/subcommands/decorator.rs @@ -169,7 +169,7 @@ pub fn fire_decorators(fiber: &FiberseqData) -> Vec> { let msp = fiber.msp(); let ref_starts = msp.reference_starts(); let ref_lengths = msp.reference_lengths(); - let quals = msp.qual(); + let quals = fiber.fire_qual(); for ((pos, length), qual) in ref_starts.iter().zip(ref_lengths.iter()).zip(quals.iter()) { if let (Some(p), Some(l)) = (pos, length) { diff --git a/src/subcommands/footprint.rs b/src/subcommands/footprint.rs index fe521299..4a2fe414 100644 --- a/src/subcommands/footprint.rs +++ b/src/subcommands/footprint.rs @@ -155,17 +155,15 @@ impl<'a> Footprint<'a> { for fiber in self.fibers.iter() { let mut has_spanning_msp = false; let mut msp_qual = -1; - for msp in &fiber.msp() { + let fire_quals = fiber.fire_qual(); + for (idx, msp) in (&fiber.msp()).into_iter().enumerate() { // skip if there is no mapping of the msp match (msp.ref_start, msp.ref_end) { (Some(rs), Some(re)) => { if self.motif.spans(rs as i64, re as i64) { self.n_spanning_msps += 1; has_spanning_msp = true; - msp_qual = crate::utils::bamannotations::primary_qual( - msp.qualities, - msp.type_name, - ) as i16; + msp_qual = fire_quals.get(idx).copied().unwrap_or(0) as i16; break; } } diff --git a/src/subcommands/pileup.rs b/src/subcommands/pileup.rs index 01bcb144..d47f3ea2 100644 --- a/src/subcommands/pileup.rs +++ b/src/subcommands/pileup.rs @@ -401,12 +401,13 @@ impl<'a> FireTrack<'a> { } // calculate the fire coverage and fire score - for info in &fiber.msp() { + let fire_quals = fiber.fire_qual(); + for (idx, info) in (&fiber.msp()).into_iter().enumerate() { let (rs, re) = match (info.ref_start, info.ref_end) { (Some(rs), Some(re)) => (rs as i64, re as i64), _ => continue, }; - let qual = crate::utils::bamannotations::primary_qual(info.qualities, info.type_name); + let qual = fire_quals.get(idx).copied().unwrap_or(0); if qual < MIN_FIRE_QUAL { continue; } diff --git a/src/subcommands/validate.rs b/src/subcommands/validate.rs index 2d8fab47..050e9b01 100644 --- a/src/subcommands/validate.rs +++ b/src/subcommands/validate.rs @@ -35,7 +35,7 @@ pub fn validate_fiberseq_bam(opts: &mut ValidateOptions) -> Result<()> { for fiber in opts.bam.fibers(&mut bam) { let m6a_okay = !fiber.m6a().is_empty(); let nuc_okay = !fiber.nuc().is_empty(); - n_fire_calls += fiber.msp().qual().iter().filter(|q| **q > 0).count(); + n_fire_calls += fiber.fire_qual().iter().filter(|q| **q > 0).count(); n_aligned += !fiber.record.is_unmapped() as usize; n_phased += fiber.record.aux(b"HP").is_ok() as usize; diff --git a/src/utils/ftexpression.rs b/src/utils/ftexpression.rs index 2d43e30d..7872b6b9 100644 --- a/src/utils/ftexpression.rs +++ b/src/utils/ftexpression.rs @@ -152,6 +152,55 @@ pub fn apply_filter_fsd(fsd: &mut FiberseqData, filt: &FiberFilters) -> Result<( "len" => fsd.annotations.retain(type_name, |a| { len(a.length as i64, &parser.op, &parser.threshold) }), + "qual" if type_name == "msp" => { + // qual(msp) historically meant "filter MSPs by FIRE + // precision" (legacy fibertools wrote FIRE precisions + // onto the MSP `aq` tag). Post-MA, that quality lives + // on the `fire` annotation type instead. Collect + // per-MSP precisions in *molecular* order to align + // with retain's iteration, then drop msp and fire + // in lockstep. + let primary = crate::utils::bamannotations::primary_qual; + let mol_quals: Vec = if let Some(f) = fsd + .annotations + .get_type("fire") + .filter(|f| { + fsd.annotations + .get_type("msp") + .is_some_and(|m| m.annotations.len() == f.annotations.len()) + }) { + f.annotations + .iter() + .map(|a| primary(&a.qualities, "fire")) + .collect() + } else if let Some(m) = fsd.annotations.get_type("msp") { + m.annotations + .iter() + .map(|a| primary(&a.qualities, "msp")) + .collect() + } else { + Vec::new() + }; + let keep: Vec = mol_quals + .iter() + .map(|q| qual(*q, &parser.op, &parser.threshold)) + .collect(); + let has_fire = fsd.annotations.get_type("fire").is_some(); + let mut i = 0; + fsd.annotations.retain("msp", |_| { + let k = keep.get(i).copied().unwrap_or(false); + i += 1; + k + }); + if has_fire { + let mut i = 0; + fsd.annotations.retain("fire", |_| { + let k = keep.get(i).copied().unwrap_or(false); + i += 1; + k + }); + } + } "qual" => fsd.annotations.retain(type_name, |a| { qual( crate::utils::bamannotations::primary_qual(&a.qualities, type_name), diff --git a/tests/molecular_annotation.rs b/tests/molecular_annotation.rs index 650dd821..f90dcb58 100644 --- a/tests/molecular_annotation.rs +++ b/tests/molecular_annotation.rs @@ -234,6 +234,100 @@ fn missing_annotations_yield_empty_container() { assert_eq!(annot.read_length, blank.seq_len() as u32); } +#[test] +fn fire_qual_matches_legacy_and_ma_paths() { + // Pre-MA fibertools wrote FIRE precisions onto the MSP `aq` tag, so + // `msp.qual()` returned the FIRE precision. Post-MA, those precisions + // live on the separate `fire+P` annotation type and `msp.qual()` is + // empty. `FiberseqData::fire_qual()` must return the same per-MSP + // precision vector regardless of which on-disk format the BAM uses. + use fibertools_rs::fiber::FiberseqData; + use fibertools_rs::utils::input_bam::FiberFilters; + use fibertools_rs::utils::ma_io::{add_fire_annotations, add_msp_annotations, FIRE_TYPE}; + + let filters = FiberFilters::default(); + let mut legacy_count = 0; + for record in read_records("NAPA.bam") { + let legacy_aq = raw_u8(&record, b"aq"); + if legacy_aq.is_none() || legacy_aq.as_ref().unwrap().iter().all(|&q| q == 0) { + continue; + } + legacy_count += 1; + + // Legacy path: msp.qual() holds the precisions; no fire type yet. + let legacy_fsd = FiberseqData::new(record.clone(), None, &filters); + assert!( + legacy_fsd.fire().is_empty(), + "legacy fixture should not have a fire annotation type yet" + ); + let legacy_qual = legacy_fsd.fire_qual(); + assert_eq!( + legacy_qual, + legacy_fsd.msp().qual(), + "legacy fire_qual must equal msp.qual()" + ); + assert!( + legacy_qual.iter().any(|&q| q > 0), + "legacy fixture should expose nonzero FIRE precisions" + ); + + // Reshape to the post-FIRE MA layout (msp+ with no qualities, fire+P + // carrying the same precisions) — this is what `ft fire` produces + // post-migration. fire_qual() must yield the same vector. + let original = read_annotations(&record).unwrap(); + let mut reshaped = original.clone(); + // Drop the legacy msp+Q type and re-add msp+ without qualities. + reshaped.annotation_types.retain(|t| t.name != MSP_TYPE); + let msp_starts: Vec = original + .get_type(MSP_TYPE) + .unwrap() + .annotations + .iter() + .map(|a| a.start) + .collect(); + let msp_lens: Vec = original + .get_type(MSP_TYPE) + .unwrap() + .annotations + .iter() + .map(|a| a.length) + .collect(); + let msp_quals: Vec = original + .get_type(MSP_TYPE) + .unwrap() + .annotations + .iter() + .map(|a| a.qualities[0]) + .collect(); + add_msp_annotations(&mut reshaped, &msp_starts, &msp_lens, None); + add_fire_annotations(&mut reshaped, &msp_starts, &msp_lens, &msp_quals); + + let mut ma_only = record.clone(); + write_annotations(&mut ma_only, &reshaped, false); + let ma_fsd = FiberseqData::new(ma_only, None, &filters); + assert!( + !ma_fsd.fire().is_empty(), + "post-FIRE MA layout must expose a fire annotation type" + ); + assert_eq!( + ma_fsd.msp().qual().iter().filter(|q| **q > 0).count(), + 0, + "post-FIRE MA layout must not carry FIRE precisions on msp" + ); + assert_eq!( + ma_fsd.annotations.get_type(FIRE_TYPE).unwrap().annotations.len(), + ma_fsd.msp().len(), + "fire and msp must be 1:1" + ); + assert_eq!( + ma_fsd.fire_qual(), + legacy_qual, + "fire_qual must match across legacy and MA-only formats" + ); + } + assert!(legacy_count > 0, "expected at least one fixture with aq"); +} + #[test] fn mismatched_legacy_lengths_returns_error() { let mut record = read_records("nuc_example.bam").into_iter().next().unwrap(); From 1bb1d9565798f81dc7d41596ea2600a4fbbabf7e Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Wed, 13 May 2026 15:08:46 -0600 Subject: [PATCH 16/24] fix: clear stale annotations before re-adding on producer re-runs Three producers loaded the existing annotation set from the record and appended their fresh output without first dropping the type they were about to re-emit. Re-running the command on its own output silently doubled the annotation list (or, in the case of nuc+msp where the existing type had a different QualitySpec, panicked inside a par_iter_mut worker): - nucleosome::add_nucleosomes_to_annotations Now drops pre-existing nuc, msp, AND fire types before adding. fire is included because it's paired 1:1 with msp by index - leaving fire behind while replacing msp would strand fire precisions against unrelated MSPs. Affects `ft add-nucleosomes` and `ft predict-m6a` (which also runs nucleosome calling on its output). - fire::add_fire_to_rec Drops the pre-existing fire type before adding. Affects `ft fire` re-runs (e.g. re-running with a different model). - ddda_to_m6a::ddda_to_m6a_record Drops pre-existing m6a before appending the Y/R-derived calls. The old code would emit duplicate MM positions for any Y/R base that also had a prior m6a call. Tests: two new integration tests in tests/molecular_annotation.rs exercise re-run idempotency for nucleosomes (including the stale-fire case) and fire. Both fail without these fixes. --- src/subcommands/ddda_to_m6a.rs | 11 +++- src/subcommands/fire.rs | 5 ++ src/utils/nucleosome.rs | 7 ++ tests/molecular_annotation.rs | 113 +++++++++++++++++++++++++++++++++ 4 files changed, 133 insertions(+), 3 deletions(-) diff --git a/src/subcommands/ddda_to_m6a.rs b/src/subcommands/ddda_to_m6a.rs index f6da7602..3274d244 100644 --- a/src/subcommands/ddda_to_m6a.rs +++ b/src/subcommands/ddda_to_m6a.rs @@ -55,11 +55,16 @@ pub fn ddda_to_m6a_record(record: &mut Record, _opts: &DddaToM6aOptions) { // set values for the new modified record record.set(&q_name, Some(&cigar), &new_forward_seq, &qual); - // Load existing MM/ML into a MolecularAnnotations, append the - // synthesized m6a calls, write back. write_mm_ml reconstructs the - // canonical group (A+a vs T-a) from the now-replaced forward seq. + // Load existing MM/ML into a MolecularAnnotations, drop any + // pre-existing m6a (we're replacing it with the Y/R-derived calls), + // then append the synthesized m6a and write back. write_mm_ml + // reconstructs the canonical group (A+a vs T-a) from the now-replaced + // forward seq. let mut annot = MolecularAnnotations::from_record(record); basemods::parse_mm_ml_into_ma(record, &mut annot, 0, 0); + annot + .annotation_types + .retain(|t| t.name != basemods::M6A_TYPE); let qspec = "Q".parse::().expect("Q parses"); let t = annot.add_annotation_type(basemods::M6A_TYPE, qspec); for pos in modified_bases_forward { diff --git a/src/subcommands/fire.rs b/src/subcommands/fire.rs index d4c0b8fe..18107db7 100644 --- a/src/subcommands/fire.rs +++ b/src/subcommands/fire.rs @@ -45,6 +45,11 @@ pub fn add_fire_to_rec( msp.annotations.iter().map(|a| a.length).collect(), ) }; + // Drop any pre-existing fire annotations so a re-run replaces, rather + // than appends to, the previous call. + rec.annotations + .annotation_types + .retain(|t| t.name != ma_io::FIRE_TYPE); ma_io::add_fire_annotations(&mut rec.annotations, &starts, &lens, &precisions); rec.serialize_annotations(legacy); diff --git a/src/utils/nucleosome.rs b/src/utils/nucleosome.rs index 05ef81f3..8f50a011 100644 --- a/src/utils/nucleosome.rs +++ b/src/utils/nucleosome.rs @@ -203,6 +203,13 @@ pub fn add_nucleosomes_to_annotations( let (nuc_starts, nuc_lengths) = filter_for_end(record, &nucs, options.distance_from_end); let (msp_starts, msp_lengths) = filter_for_end(record, &msps, options.distance_from_end); + // Drop any pre-existing nuc/msp/fire annotations so a re-run replaces + // the previous call rather than appending. fire is paired 1:1 with msp + // by construction, so leaving fire behind while replacing msp would + // strand fire precisions against unrelated MSPs. + annot.annotation_types.retain(|t| { + t.name != ma_io::NUC_TYPE && t.name != ma_io::MSP_TYPE && t.name != ma_io::FIRE_TYPE + }); ma_io::add_nuc_annotations(annot, &nuc_starts, &nuc_lengths); ma_io::add_msp_annotations(annot, &msp_starts, &msp_lengths, None); } diff --git a/tests/molecular_annotation.rs b/tests/molecular_annotation.rs index f90dcb58..21c6cc0d 100644 --- a/tests/molecular_annotation.rs +++ b/tests/molecular_annotation.rs @@ -328,6 +328,119 @@ fn fire_qual_matches_legacy_and_ma_paths() { assert!(legacy_count > 0, "expected at least one fixture with aq"); } +#[test] +fn add_nucleosomes_is_idempotent_on_rerun() { + // Running `ft add-nucleosomes` (or `ft predict-m6a` with --nucleosomes) + // a second time on an already-annotated BAM must replace the previous + // nuc/msp/fire annotations, not append to them. Re-runs are common in + // the canonical pipeline (e.g. retuning nucleosome parameters). + use fibertools_rs::cli::NucleosomeParameters; + use fibertools_rs::fiber::FiberseqData; + use fibertools_rs::utils::input_bam::FiberFilters; + use fibertools_rs::utils::ma_io::FIRE_TYPE; + use fibertools_rs::utils::nucleosome::add_nucleosomes_to_annotations; + + let filters = FiberFilters::default(); + let nuc_opts = NucleosomeParameters::default(); + let mut covered = 0; + for record in read_records("NAPA.bam") { + let fsd = FiberseqData::new(record.clone(), None, &filters); + if fsd.m6a().is_empty() || fsd.msp().is_empty() { + continue; + } + covered += 1; + let m6a: Vec = fsd + .annotations + .get_forward_coords("m6a") + .map(|v| v.into_iter().map(|(s, _)| s as i64).collect()) + .unwrap_or_default(); + + // First pass. + let mut once = fsd.annotations.clone(); + add_nucleosomes_to_annotations(&record, &mut once, &m6a, &nuc_opts); + + // Second pass on already-annotated container — must equal first. + let mut twice = once.clone(); + add_nucleosomes_to_annotations(&record, &mut twice, &m6a, &nuc_opts); + + assert_eq!( + once.annotation_types, twice.annotation_types, + "add_nucleosomes_to_annotations must be idempotent on re-run" + ); + + // A pre-existing `fire` paired with the old MSPs must also be cleared + // on re-run, since fire/msp pairing is positional. + let mut with_fire = fsd.annotations.clone(); + let msp_len = with_fire.get_type(MSP_TYPE).unwrap().annotations.len(); + let starts: Vec = with_fire + .get_type(MSP_TYPE) + .unwrap() + .annotations + .iter() + .map(|a| a.start) + .collect(); + let lens: Vec = with_fire + .get_type(MSP_TYPE) + .unwrap() + .annotations + .iter() + .map(|a| a.length) + .collect(); + let precisions = vec![200u8; msp_len]; + fibertools_rs::utils::ma_io::add_fire_annotations( + &mut with_fire, + &starts, + &lens, + &precisions, + ); + assert!(with_fire.get_type(FIRE_TYPE).is_some()); + add_nucleosomes_to_annotations(&record, &mut with_fire, &m6a, &nuc_opts); + assert!( + with_fire.get_type(FIRE_TYPE).is_none(), + "re-run must drop stale `fire` annotations (paired with stale MSPs)" + ); + } + assert!(covered > 0, "expected NAPA.bam to have m6a+msp records"); +} + +#[test] +fn add_fire_is_idempotent_on_rerun() { + // Re-running `ft fire` on the same record must not double the fire + // annotation list. + use fibertools_rs::utils::ma_io::{add_fire_annotations, FIRE_TYPE, MSP_TYPE}; + + let record = read_records("NAPA.bam") + .into_iter() + .find(|r| raw_u32(r, b"as").is_some_and(|v| !v.is_empty())) + .expect("NAPA.bam should have an MSP-bearing record"); + let mut annot = read_annotations(&record).unwrap(); + let msp = annot.get_type(MSP_TYPE).unwrap(); + let starts: Vec = msp.annotations.iter().map(|a| a.start).collect(); + let lens: Vec = msp.annotations.iter().map(|a| a.length).collect(); + let precisions = vec![200u8; starts.len()]; + + // Mimic what `fire::add_fire_to_rec` does post-fix: retain off any + // pre-existing fire type, then add. The first call seeds the type; the + // second call demonstrates idempotency. + annot + .annotation_types + .retain(|t| t.name != FIRE_TYPE); + add_fire_annotations(&mut annot, &starts, &lens, &precisions); + let first_len = annot.get_type(FIRE_TYPE).unwrap().annotations.len(); + + annot + .annotation_types + .retain(|t| t.name != FIRE_TYPE); + add_fire_annotations(&mut annot, &starts, &lens, &precisions); + let second_len = annot.get_type(FIRE_TYPE).unwrap().annotations.len(); + + assert_eq!( + first_len, second_len, + "fire annotation count must not grow on re-run" + ); + assert_eq!(first_len, starts.len(), "fire must be 1:1 with msp"); +} + #[test] fn mismatched_legacy_lengths_returns_error() { let mut record = read_records("nuc_example.bam").into_iter().next().unwrap(); From 1e3e10ff6a0189cf32998f9a9ec6410a2cc0a125 Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Wed, 13 May 2026 15:21:10 -0600 Subject: [PATCH 17/24] fix: tighten MM/ML basemod dispatch and idempotency MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Two latent correctness bugs in `parse_mm_ml_into_ma`: 1. **Multi-char alpha mod types collided with canonical dispatch.** The bucket selector matched the first character of `mod_type_str` (`'a'`/`'m'`), so any non-canonical alpha code starting with one of those — `C+ac` (acetyl), hypothetical `A+myloride`, etc. — silently routed into the `m6a` / `cpg` bucket and was rewritten as fiberseq canonical on the next write. The SAM regex permits multi-char alpha mod codes (`[A-Za-z]+`), so the input is valid. Now matches the exact string `"a"` / `"m"`; everything else lands in the verbatim non-canonical bucket and round-trips unchanged. 2. **Pre-existing basemod types in `annot` silently merged.** `add_calls` ultimately calls `MolecularAnnotations::add_annotation_type`, which returns the existing type if the name+QualitySpec match, and then appends. Two paths could hit this: repeated calls to `parse_mm_ml_into_ma` on the same `annot`, or a third-party BAM that wrongly emits `m6a` into both the MA tag set AND MM/ML — `FiberseqData::new` runs `read_annotations` before `parse_mm_ml_into_ma`, so the latter would merge on top instead of overwriting. MM/ML is the on-disk source of truth for basemods; now the parser clears any m6a/cpg/non-canonical type off `annot` first, making the function idempotent and ensuring MM/ML always wins on conflict. Tests: - `test_multichar_alpha_modtype_not_treated_as_canonical` synthesizes a `C+ac` MM tag and asserts it lands in its own type, not m6a. - `test_parse_mm_ml_idempotent_on_rerun` confirms double-invocation is a no-op and stale pre-seeded m6a is replaced, not merged. Both tests fail without these fixes. --- src/utils/basemods.rs | 49 +++++++++++++------- tests/basemods.rs | 104 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 136 insertions(+), 17 deletions(-) diff --git a/src/utils/basemods.rs b/src/utils/basemods.rs index 718aa1f4..0f80e5a7 100644 --- a/src/utils/basemods.rs +++ b/src/utils/basemods.rs @@ -5,12 +5,12 @@ //! `BaseMods` struct — the spec object is the sole in-memory //! representation. //! -//! Mod-type dispatch: -//! - mod_type `'a'` (any group, e.g. `A+a`, `T-a`, `N+a`) → `m6a` type. -//! - mod_type `'m'` (any group, e.g. `C+m`, `G+m`) → `cpg` type. -//! - any other group (`C+h`, `T+f`, ChEBI IDs, etc.) → its own annotation -//! type named verbatim after the MM group header (e.g. `"C+h"`). -//! Calls round-trip through `write_mm_ml` unchanged. +//! Mod-type dispatch (exact match on the MM mod_type code): +//! - `"a"` (any group, e.g. `A+a`, `T-a`, `N+a`) → `m6a` type. +//! - `"m"` (any group, e.g. `C+m`, `G+m`) → `cpg` type. +//! - any other code (`C+h`, `T+f`, `C+ac`, ChEBI numeric IDs, etc.) → its +//! own annotation type named verbatim after the MM group header (e.g. +//! `"C+h"`). Calls round-trip through `write_mm_ml` unchanged. //! //! Write path: `write_mm_ml` emits MM/ML from a [`MolecularAnnotations`]. //! Canonical types (`m6a`, `cpg`) have their groups reconstructed from @@ -46,12 +46,18 @@ lazy_static! { /// - calls within `strip_at_ends` bp of either end of the forward /// sequence are dropped (no-op if `strip_at_ends <= 0`). /// -/// Dispatch by MM mod_type: -/// - `'a'` → [`M6A_TYPE`] (collapses `A+a`, `T-a`, `N+a`, etc.) -/// - `'m'` → [`CPG_TYPE`] (collapses `C+m`, `G+m`, etc.) +/// Dispatch by MM mod_type (exact-match): +/// - `"a"` → [`M6A_TYPE`] (collapses `A+a`, `T-a`, `N+a`, etc.) +/// - `"m"` → [`CPG_TYPE`] (collapses `C+m`, `G+m`, etc.) /// - any other → annotation type named verbatim after the MM group -/// header (e.g. `"C+h"` for 5hmC). [`write_mm_ml`] emits these -/// unchanged. +/// header (e.g. `"C+h"` for 5hmC, `"C+ac"` for acetyl). [`write_mm_ml`] +/// emits these unchanged. +/// +/// Idempotent: any pre-existing `m6a` / `cpg` / non-canonical basemod +/// types on `annot` are dropped first, so MM/ML always overwrites in- +/// memory state rather than appending. This guards against (a) repeated +/// calls on the same `annot`, and (b) malformed inputs that wrongly +/// emit `m6a` into the MA tag set in addition to MM/ML. /// /// For canonical `m6a` / `cpg`, MM's per-group `(canonical_base, /// strand_sign)` is reconstructed from the forward sequence at write @@ -63,6 +69,14 @@ pub fn parse_mm_ml_into_ma( min_ml_score: u8, strip_at_ends: i64, ) { + // MM/ML is the on-disk source of truth for base modifications; any + // basemod-shaped type that may already be in `annot` (from a prior + // pass, an MA-tag leak in a third-party producer, or repeated calls) + // is discarded so we don't silently append on top of stale data. + annot + .annotation_types + .retain(|t| t.name != M6A_TYPE && t.name != CPG_TYPE && !is_valid_mm_header(&t.name)); + let ml_tag = get_u8_tag(record, b"ML"); let Ok(Aux::String(mm_text)) = record.aux(b"MM") else { log::trace!("No MM tag found"); @@ -93,7 +107,6 @@ pub fn parse_mm_ml_into_ma( .next() .unwrap_or('+'); let mod_type_str = cap.get(5).map_or("", |m| m.as_str()).to_string(); - let modification_type = mod_type_str.chars().next().unwrap_or(' '); let mod_dists_str = cap.get(6).map_or("", |m| m.as_str()); let mod_dists: Vec = mod_dists_str .trim_end_matches(';') @@ -150,12 +163,14 @@ pub fn parse_mm_ml_into_ma( }; num_mods_seen = group_end; - // Filter + dispatch by mod_type. Non-canonical groups are - // stored under their verbatim MM header so they round-trip + // Filter + dispatch by mod_type. The canonical fiberseq codes are + // *exactly* "a" (m6A) and "m" (5mC) — any longer alpha mod type + // (`ac` acetyl, `pT` etc.) or ChEBI numeric ID is non-canonical + // and stored under its verbatim MM header so it round-trips // exactly through write_mm_ml. - let bucket: &mut Vec<(u32, u8)> = match modification_type { - 'a' => &mut m6a_calls, - 'm' => &mut cpg_calls, + let bucket: &mut Vec<(u32, u8)> = match mod_type_str.as_str() { + "a" => &mut m6a_calls, + "m" => &mut cpg_calls, _ => { let key = format!("{}{}{}", mod_base as char, strand_sign, mod_type_str); other_calls.entry(key).or_default() diff --git a/tests/basemods.rs b/tests/basemods.rs index acff79b7..b1acef14 100644 --- a/tests/basemods.rs +++ b/tests/basemods.rs @@ -94,3 +94,107 @@ fn test_non_canonical_mod_round_trip() { assert_eq!(a.get_type("C+h"), b.get_type("C+h")); } + +/// Canonical dispatch is on the exact mod-type code (`"a"` / `"m"`), +/// not the first character. A multi-char alpha mod type like `C+ac` +/// (acetylation) starts with `'a'` but must NOT route into `m6a`; it +/// must be preserved verbatim as a `"C+ac"` annotation type. +#[test] +fn test_multichar_alpha_modtype_not_treated_as_canonical() { + let mut bam = bam::Reader::from_path("tests/data/all.bam").unwrap(); + let mut rec = bam.records().next().expect("all.bam has records").unwrap(); + + let fwd = if rec.is_reverse() { + bio::alphabets::dna::revcomp(rec.seq().as_bytes()) + } else { + rec.seq().as_bytes() + }; + let c_positions: Vec = fwd + .iter() + .enumerate() + .filter(|(_, &b)| b == b'C' || b == b'c') + .take(2) + .map(|(i, _)| i) + .collect(); + assert!(c_positions.len() >= 2); + let mut skips: Vec = Vec::with_capacity(2); + let mut c_count = 0usize; + let mut next_target = 0; + for (i, &b) in fwd.iter().enumerate() { + if next_target >= c_positions.len() { + break; + } + if i == c_positions[next_target] { + skips.push(c_count); + c_count = 0; + next_target += 1; + } else if b == b'C' || b == b'c' { + c_count += 1; + } + } + let mm = format!("C+ac,{},{};", skips[0], skips[1]); + let ml: Vec = vec![180, 220]; + + rec.remove_aux(b"MM").ok(); + rec.remove_aux(b"ML").ok(); + rec.push_aux(b"MM", Aux::String(&mm)).unwrap(); + rec.push_aux(b"ML", Aux::ArrayU8((&ml).into())).unwrap(); + + let mut a = MolecularAnnotations::from_record(&rec); + parse_mm_ml_into_ma(&rec, &mut a, 0, 0); + + // Must land in its own type, not in m6a. + assert!( + a.get_type(M6A_TYPE).is_none(), + "C+ac must not be routed to m6a" + ); + let acetyl = a.get_type("C+ac").expect("C+ac type present after parse"); + assert_eq!(acetyl.annotations.len(), 2); + + // And round-trips through write_mm_ml unchanged. + write_mm_ml(&mut rec, &a); + let mut b = MolecularAnnotations::from_record(&rec); + parse_mm_ml_into_ma(&rec, &mut b, 0, 0); + assert_eq!(a.get_type("C+ac"), b.get_type("C+ac")); + assert!(b.get_type(M6A_TYPE).is_none()); +} + +/// `parse_mm_ml_into_ma` is idempotent: calling it twice on the same +/// `annot` (or once on an `annot` that already has a stale `m6a` type +/// from elsewhere) must overwrite, not append. +#[test] +fn test_parse_mm_ml_idempotent_on_rerun() { + let mut bam = bam::Reader::from_path("tests/data/all.bam").unwrap(); + let rec = bam + .records() + .filter_map(|r| r.ok()) + .find(|r| matches!(r.aux(b"MM"), Ok(Aux::String(_)))) + .expect("all.bam has at least one record with MM"); + + let mut once = MolecularAnnotations::from_record(&rec); + parse_mm_ml_into_ma(&rec, &mut once, 0, 0); + let once_m6a = once.get_type(M6A_TYPE).cloned(); + let once_cpg = once.get_type(CPG_TYPE).cloned(); + + // Second pass on the same annot must produce the same counts. + parse_mm_ml_into_ma(&rec, &mut once, 0, 0); + assert_eq!(once.get_type(M6A_TYPE).cloned(), once_m6a); + assert_eq!(once.get_type(CPG_TYPE).cloned(), once_cpg); + + // Pre-seeded stale m6a (as if leaked into the MA tag set by a bad + // producer) must be discarded, not merged. + let mut seeded = MolecularAnnotations::from_record(&rec); + let qspec = "Q" + .parse::() + .expect("Q parses"); + seeded + .add_annotation_type(M6A_TYPE, qspec) + .add(0, 1, molecular_annotation::Strand::Forward, vec![123], None) + .add(1, 1, molecular_annotation::Strand::Forward, vec![45], None); + parse_mm_ml_into_ma(&rec, &mut seeded, 0, 0); + assert_eq!( + seeded.get_type(M6A_TYPE).cloned(), + once_m6a, + "stale m6a must be replaced by MM/ML, not merged" + ); +} From 2e72ce07f10789b664ab2ffdd485d575e654fd2b Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Wed, 13 May 2026 15:23:07 -0600 Subject: [PATCH 18/24] fix: recover from malformed MM tags without panicking MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit `parse_mm_ml_into_ma` previously aborted on any MM group that claimed more `mod_base` positions than the forward sequence contained — the `assert_eq!` after the resolver loop panicked the whole worker thread. A single bad-actor BAM record could take down a `par_iter` chunk. Now warns and truncates the resolved positions. Critically, the ML offset arithmetic still advances by the *on-disk* slot count (`mod_dists.len()`), not the resolved count — otherwise the next group's ML qualities would be shifted by the truncated remainder and silently re-align with the wrong positions. Test: synthesizes a record whose first MM group `A+a` claims `total_a + 2` positions (impossible), followed by a legitimate `C+m` group with a sentinel quality. Asserts (a) no panic, (b) the m6a count is truncated to actual `A` count, (c) the C+m sentinel quality survives — proving the ML offset stayed correctly aligned. --- src/utils/basemods.rs | 34 ++++++++++++++++++-------- tests/basemods.rs | 55 +++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 79 insertions(+), 10 deletions(-) diff --git a/src/utils/basemods.rs b/src/utils/basemods.rs index 0f80e5a7..f3161130 100644 --- a/src/utils/basemods.rs +++ b/src/utils/basemods.rs @@ -140,16 +140,26 @@ pub fn parse_mm_ml_into_ma( dist_from_last_mod_base += 1; } } - assert_eq!( - cur_mod_idx, - mod_dists.len(), - "MM/ML parser: {} (reverse={})", - String::from_utf8_lossy(record.qname()), - record.is_reverse(), - ); + let resolved = cur_mod_idx; + if resolved != mod_dists.len() { + // MM tag claims more `mod_base` positions than the forward + // sequence actually has. Warn and emit only the calls we + // could resolve — the alternative was to panic the whole + // worker. ML offsets must still advance by the on-disk + // slot count (`mod_dists.len()`) so the next group reads + // from the correct ML section. + log::warn!( + "MM/ML parser: {} (reverse={}) — MM group ended {} positions short of the forward sequence; truncating", + String::from_utf8_lossy(record.qname()), + record.is_reverse(), + mod_dists.len() - resolved, + ); + } - // Pair this group's calls with ML qualities. - let group_end = num_mods_seen + positions.len(); + // Pair this group's calls with ML qualities. The on-disk ML + // section for this group has `mod_dists.len()` entries even if + // we could only resolve `resolved` of them. + let group_end = num_mods_seen + mod_dists.len(); let group_quals: Vec = if group_end > ml_tag.len() { let needed = group_end - ml_tag.len(); let mut existing = ml_tag[num_mods_seen..].to_vec(); @@ -162,6 +172,10 @@ pub fn parse_mm_ml_into_ma( ml_tag[num_mods_seen..group_end].to_vec() }; num_mods_seen = group_end; + // Drop ML qualities whose position couldn't be resolved, so the + // dispatch zip below pairs only the surviving calls. + positions.truncate(resolved); + let group_quals = &group_quals[..resolved]; // Filter + dispatch by mod_type. The canonical fiberseq codes are // *exactly* "a" (m6A) and "m" (5mC) — any longer alpha mod type @@ -176,7 +190,7 @@ pub fn parse_mm_ml_into_ma( other_calls.entry(key).or_default() } }; - for (pos, qual) in positions.iter().copied().zip(group_quals) { + for (pos, &qual) in positions.iter().copied().zip(group_quals) { if qual < min_ml_score { continue; } diff --git a/tests/basemods.rs b/tests/basemods.rs index b1acef14..d633e647 100644 --- a/tests/basemods.rs +++ b/tests/basemods.rs @@ -159,6 +159,61 @@ fn test_multichar_alpha_modtype_not_treated_as_canonical() { assert!(b.get_type(M6A_TYPE).is_none()); } +/// A malformed MM tag — claiming more `mod_base` positions than the +/// forward sequence actually contains — must warn and truncate, not +/// panic. The next group's ML qualities must still align with its +/// positions (ML offsets are based on on-disk slot count, not resolved +/// count). +#[test] +fn test_malformed_mm_truncates_without_panic() { + let mut bam = bam::Reader::from_path("tests/data/all.bam").unwrap(); + let mut rec = bam.records().next().expect("all.bam has records").unwrap(); + + let fwd = if rec.is_reverse() { + bio::alphabets::dna::revcomp(rec.seq().as_bytes()) + } else { + rec.seq().as_bytes() + }; + let total_a = fwd.iter().filter(|&&b| b == b'A' || b == b'a').count(); + let total_c = fwd.iter().filter(|&&b| b == b'C' || b == b'c').count(); + assert!(total_a >= 2 && total_c >= 1); + + // First group `A+a` claims `total_a + 2` positions — two more than + // the sequence has, forcing the resolver to truncate. Second group + // `C+m` claims one legitimate C. The ML tag has the on-disk slot + // count for both groups; if ML offsets advance correctly, the + // C+m quality is the LAST byte. + let bogus_a_count = total_a + 2; + let mut mm = String::from("A+a"); + for _ in 0..bogus_a_count { + mm.push_str(",0"); + } + mm.push(';'); + mm.push_str("C+m,0;"); + + let mut ml: Vec = vec![100; bogus_a_count]; + ml.push(222); // sentinel for the C+m call + + rec.remove_aux(b"MM").ok(); + rec.remove_aux(b"ML").ok(); + rec.push_aux(b"MM", Aux::String(&mm)).unwrap(); + rec.push_aux(b"ML", Aux::ArrayU8((&ml).into())).unwrap(); + + let mut a = MolecularAnnotations::from_record(&rec); + // Must not panic. + parse_mm_ml_into_ma(&rec, &mut a, 0, 0); + + // The resolved m6a count equals the number of A bases in the + // sequence (truncated from the claimed bogus count). + let m6a = a.get_type(M6A_TYPE).expect("m6a present"); + assert_eq!(m6a.annotations.len(), total_a); + // And the C+m quality survived intact — proving the ML offset + // didn't get shifted by the truncated A+a section. + let cpg = a.get_type(CPG_TYPE).expect("cpg present"); + assert_eq!(cpg.annotations.len(), 1); + assert_eq!(cpg.annotations[0].qualities, vec![222]); +} + /// `parse_mm_ml_into_ma` is idempotent: calling it twice on the same /// `annot` (or once on an `annot` that already has a stale `m6a` type /// from elsewhere) must overwrite, not append. From 7f69a6aedc1cdea17e1503f51a300a26f3318873 Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Thu, 14 May 2026 11:22:28 -0600 Subject: [PATCH 19/24] fix: correct FIRE quality spec; use strand::unknown for nuc/msp/fire --- src/utils/ma_io.rs | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/src/utils/ma_io.rs b/src/utils/ma_io.rs index 177ef2ba..9e628ce5 100644 --- a/src/utils/ma_io.rs +++ b/src/utils/ma_io.rs @@ -10,9 +10,9 @@ //! migration. With `legacy=false` any pre-existing legacy tags are stripped. //! //! Annotation type names produced by fibertools-rs: -//! - `nuc` (forward strand, no quality) -//! - `msp` (forward strand, no quality pre-FIRE; `Q` post-FIRE) -//! - `fire` (forward strand, `P` phred quality) +//! - `nuc` (no strand, no quality) +//! - `msp` (no strand, no quality pre-FIRE; `Q` post-FIRE) +//! - `fire` (no strand, `Q` linear precision 0–255) //! //! `m6a` and `cpg` types may appear *in memory* on a [`MolecularAnnotations`] //! populated by [`crate::utils::basemods::parse_mm_ml_into_ma`], but are @@ -91,7 +91,7 @@ fn read_legacy_nuc_msp(record: &bam::Record) -> Result { if !ns.is_empty() { let nuc = annot.add_annotation_type(NUC_TYPE, QualitySpec::none()); for (s, l) in ns.iter().zip(nl.iter()) { - nuc.add(*s, *l, Strand::Forward, vec![], None); + nuc.add(*s, *l, Strand::Unknown, vec![], None); } } } @@ -122,7 +122,7 @@ fn read_legacy_nuc_msp(record: &bam::Record) -> Result { let msp = annot.add_annotation_type(MSP_TYPE, q_spec); for (i, (s, l)) in starts.iter().zip(lens.iter()).enumerate() { let qualities = aq.as_ref().map(|q| vec![q[i]]).unwrap_or_default(); - msp.add(*s, *l, Strand::Forward, qualities, None); + msp.add(*s, *l, Strand::Unknown, qualities, None); } } } @@ -283,7 +283,7 @@ pub fn add_nuc_annotations(annot: &mut MolecularAnnotations, starts: &[u32], len } let t = annot.add_annotation_type(NUC_TYPE, QualitySpec::none()); for (s, l) in starts.iter().zip(lens.iter()) { - t.add(*s, *l, Strand::Forward, vec![], None); + t.add(*s, *l, Strand::Unknown, vec![], None); } } @@ -308,11 +308,11 @@ pub fn add_msp_annotations( let t = annot.add_annotation_type(MSP_TYPE, qspec); for (i, (s, l)) in starts.iter().zip(lens.iter()).enumerate() { let qv = qualities.map(|q| vec![q[i]]).unwrap_or_default(); - t.add(*s, *l, Strand::Forward, qv, None); + t.add(*s, *l, Strand::Unknown, qv, None); } } -/// Add `fire` annotations (forward strand, phred quality) to `annot`. +/// Add `fire` annotations (no strand, linear precision 0–255) to `annot`. /// /// No-op if `starts` is empty. All input slices must be the same length and /// paired positionally. @@ -320,14 +320,14 @@ pub fn add_fire_annotations( annot: &mut MolecularAnnotations, starts: &[u32], lens: &[u32], - phred: &[u8], + precisions: &[u8], ) { if starts.is_empty() { return; } - let t = annot.add_annotation_type(FIRE_TYPE, "P".parse::().expect("P parses")); + let t = annot.add_annotation_type(FIRE_TYPE, "Q".parse::().expect("Q parses")); for (i, (s, l)) in starts.iter().zip(lens.iter()).enumerate() { - t.add(*s, *l, Strand::Forward, vec![phred[i]], None); + t.add(*s, *l, Strand::Unknown, vec![precisions[i]], None); } } @@ -344,8 +344,8 @@ pub fn build_annotations( if let Some((starts, lens, q)) = msp { add_msp_annotations(&mut annot, starts, lens, q); } - if let Some((starts, lens, phred)) = fire { - add_fire_annotations(&mut annot, starts, lens, phred); + if let Some((starts, lens, precisions)) = fire { + add_fire_annotations(&mut annot, starts, lens, precisions); } annot } @@ -367,8 +367,8 @@ pub fn build_nuc_msp_annotations( } /// Convenience: read fire annotations as raw arrays in molecular orientation. -/// Returns `(starts, lengths, phred_qualities)`. All three are empty if the -/// record has no `fire` MA type. +/// Returns `(starts, lengths, precisions)`. All three are empty if the record +/// has no `fire` MA type. pub fn extract_fire_arrays(record: &bam::Record) -> Result<(Vec, Vec, Vec)> { let annot = read_annotations(record)?; Ok(annot @@ -376,12 +376,12 @@ pub fn extract_fire_arrays(record: &bam::Record) -> Result<(Vec, Vec, .map(|t| { let starts = t.annotations.iter().map(|a| a.start).collect(); let lens = t.annotations.iter().map(|a| a.length).collect(); - let phred = t + let precisions = t .annotations .iter() .map(|a| crate::utils::bamannotations::primary_qual(&a.qualities, FIRE_TYPE)) .collect(); - (starts, lens, phred) + (starts, lens, precisions) }) .unwrap_or_default()) } From 8964c3952b1cd343d07192d0967a76febd98cfc2 Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Thu, 14 May 2026 14:03:19 -0600 Subject: [PATCH 20/24] refactor: drop legacy tag emission across all writers --- src/cli/fire_opts.rs | 5 -- src/cli/nucleosome_opts.rs | 4 - src/cli/predict_opts.rs | 5 -- src/fiber.rs | 4 +- src/subcommands/add_nucleosomes.rs | 2 +- src/subcommands/fire.rs | 11 +-- src/subcommands/mock_fire.rs | 2 +- src/subcommands/predict_m6a.rs | 15 +--- src/utils/fibertig.rs | 2 +- src/utils/ma_io.rs | 117 ++++------------------------- 10 files changed, 24 insertions(+), 143 deletions(-) diff --git a/src/cli/fire_opts.rs b/src/cli/fire_opts.rs index cce04c98..63160359 100644 --- a/src/cli/fire_opts.rs +++ b/src/cli/fire_opts.rs @@ -56,10 +56,6 @@ pub struct FireOptions { /// Optional path to a FDR table #[clap(long, env)] pub fdr_table: Option, - /// Also emit legacy ns/nl/as/al/aq tags alongside the MA-spec tags - /// (`MA`/`AQ`/`AN`). Default: only MA-spec tags are written. - #[clap(long)] - pub legacy_tags: bool, } impl Default for FireOptions { @@ -80,7 +76,6 @@ impl Default for FireOptions { min_msp_length_for_positive_fire_call: 85, model: None, fdr_table: None, - legacy_tags: false, } } } diff --git a/src/cli/nucleosome_opts.rs b/src/cli/nucleosome_opts.rs index 9d342470..8cb9e2fc 100644 --- a/src/cli/nucleosome_opts.rs +++ b/src/cli/nucleosome_opts.rs @@ -48,8 +48,4 @@ pub struct AddNucleosomeOptions { pub out: String, #[clap(flatten)] pub nuc: NucleosomeParameters, - /// Also emit legacy ns/nl/as/al/aq tags alongside the MA-spec tags - /// (`MA`/`AQ`/`AN`). Default: only MA-spec tags are written. - #[clap(long)] - pub legacy_tags: bool, } diff --git a/src/cli/predict_opts.rs b/src/cli/predict_opts.rs index 81e52bec..eaf00683 100644 --- a/src/cli/predict_opts.rs +++ b/src/cli/predict_opts.rs @@ -29,10 +29,6 @@ pub struct PredictM6AOptions { /// Skip the actual prediction step to allow for testing the speed of other parts of the code #[clap(long, help_heading = "Developer-Options", hide = true)] pub fake: bool, - /// Also emit legacy ns/nl/as/al/aq tags alongside the MA-spec tags - /// (`MA`/`AQ`/`AN`). Default: only MA-spec tags are written. - #[clap(long)] - pub legacy_tags: bool, } impl std::default::Default for PredictM6AOptions { @@ -46,7 +42,6 @@ impl std::default::Default for PredictM6AOptions { all_calls: false, batch_size: 1, fake: false, - legacy_tags: false, } } } diff --git a/src/fiber.rs b/src/fiber.rs index d762bd96..3345d8ea 100644 --- a/src/fiber.rs +++ b/src/fiber.rs @@ -170,8 +170,8 @@ impl FiberseqData { /// tags. The single write path — every subcommand that mutates /// annotations should call this and then hand the record to the /// BAM writer. - pub fn serialize_annotations(&mut self, legacy: bool) { - crate::utils::ma_io::write_annotations(&mut self.record, &self.annotations, legacy); + pub fn serialize_annotations(&mut self) { + crate::utils::ma_io::write_annotations(&mut self.record, &self.annotations); } pub fn get_qname(&self) -> String { diff --git a/src/subcommands/add_nucleosomes.rs b/src/subcommands/add_nucleosomes.rs index eda912cc..013bf455 100644 --- a/src/subcommands/add_nucleosomes.rs +++ b/src/subcommands/add_nucleosomes.rs @@ -28,7 +28,7 @@ pub fn add_nucleosomes_to_bam(nuc_opts: &mut AddNucleosomeOptions) { .unwrap_or_default(); let record = fd.record.clone(); add_nucleosomes_to_annotations(&record, &mut fd.annotations, &m6a, &nuc_opts.nuc); - fd.serialize_annotations(nuc_opts.legacy_tags); + fd.serialize_annotations(); }); for fd in &fibers { diff --git a/src/subcommands/fire.rs b/src/subcommands/fire.rs index 18107db7..5cbf471e 100644 --- a/src/subcommands/fire.rs +++ b/src/subcommands/fire.rs @@ -14,7 +14,6 @@ pub fn add_fire_to_rec( fire_opts: &FireOptions, model: &GBDT, precision_table: &MapPrecisionValues, - legacy: bool, ) { let fire_feats = FireFeats::new(rec, fire_opts); let mut precisions = fire_feats.predict_with_xgb(model, precision_table); @@ -52,7 +51,7 @@ pub fn add_fire_to_rec( .retain(|t| t.name != ma_io::FIRE_TYPE); ma_io::add_fire_annotations(&mut rec.annotations, &starts, &lens, &precisions); - rec.serialize_annotations(legacy); + rec.serialize_annotations(); log::trace!("precisions: {precisions:?}"); } @@ -92,13 +91,7 @@ pub fn add_fire_to_bam(fire_opts: &mut FireOptions) -> Result<(), anyhow::Error> for recs in &fibers.chunks(2_000) { let mut recs: Vec = recs.collect(); recs.par_iter_mut().for_each(|r| { - add_fire_to_rec( - r, - fire_opts, - &model, - &precision_table, - fire_opts.legacy_tags, - ); + add_fire_to_rec(r, fire_opts, &model, &precision_table); }); for rec in recs { out.write(&rec.record)?; diff --git a/src/subcommands/mock_fire.rs b/src/subcommands/mock_fire.rs index 6ec4bcd1..f386cece 100644 --- a/src/subcommands/mock_fire.rs +++ b/src/subcommands/mock_fire.rs @@ -130,7 +130,7 @@ fn create_mock_fire_record( // `FiberseqData` to round-trip through. let mut annot = MolecularAnnotations::from_record(&record); ma_io::add_fire_annotations(&mut annot, &starts, &lengths, &quals); - ma_io::write_annotations(&mut record, &annot, false); + ma_io::write_annotations(&mut record, &annot); Ok(record) } diff --git a/src/subcommands/predict_m6a.rs b/src/subcommands/predict_m6a.rs index c0003a2b..27c7a98f 100644 --- a/src/subcommands/predict_m6a.rs +++ b/src/subcommands/predict_m6a.rs @@ -47,7 +47,6 @@ where pub nuc_opts: cli::NucleosomeParameters, pub burn_models: m6a_burn::BurnModels, pub fake: bool, - pub legacy_tags: bool, } impl PredictOptions @@ -64,7 +63,6 @@ where batch_size: usize, nuc_opts: cli::NucleosomeParameters, fake: bool, - legacy_tags: bool, ) -> Self { // set up a precision table let mut map = BTreeMap::new(); @@ -83,7 +81,6 @@ where nuc_opts, burn_models: m6a_burn::BurnModels::new(&polymerase), fake, - legacy_tags, }; options.add_model().expect("Error loading model"); options @@ -281,7 +278,7 @@ where // Single MA write — m6a went out via MM/ML above; nuc/msp // (and any pre-existing annotation types we preserved) go // out here. - crate::utils::ma_io::write_annotations(record, &annot, opts.legacy_tags); + crate::utils::ma_io::write_annotations(record, &annot); // clear the existing data if !opts.keep { @@ -543,7 +540,6 @@ pub fn read_bam_into_fiberdata(opts: &mut PredictM6AOptions) { opts.batch_size, opts.nuc.clone(), opts.fake, - opts.legacy_tags, ); // get default fire options let fire_opts = crate::cli::FireOptions::default(); @@ -568,7 +564,6 @@ pub fn read_bam_into_fiberdata(opts: &mut PredictM6AOptions) { predict_options.batch_size, predict_options.nuc_opts.clone(), predict_options.fake, - predict_options.legacy_tags, ); PredictOptions::predict_m6a_on_records(&thread_opts, records) }) @@ -583,13 +578,7 @@ pub fn read_bam_into_fiberdata(opts: &mut PredictM6AOptions) { let mut fd_recs = FiberseqData::from_records(chunk, &opts.input.header_view(), &opts.input.filters); fd_recs.par_iter_mut().for_each(|fd| { - crate::subcommands::fire::add_fire_to_rec( - fd, - &fire_opts, - &model, - &precision_table, - opts.legacy_tags, - ); + crate::subcommands::fire::add_fire_to_rec(fd, &fire_opts, &model, &precision_table); }); // write to output diff --git a/src/utils/fibertig.rs b/src/utils/fibertig.rs index a5a654fd..cf6fdd94 100644 --- a/src/utils/fibertig.rs +++ b/src/utils/fibertig.rs @@ -349,7 +349,7 @@ impl FiberTig { } } - crate::utils::ma_io::write_annotations(&mut record, annotations, false); + crate::utils::ma_io::write_annotations(&mut record, annotations); records.push(record); } diff --git a/src/utils/ma_io.rs b/src/utils/ma_io.rs index 9e628ce5..f623ce1c 100644 --- a/src/utils/ma_io.rs +++ b/src/utils/ma_io.rs @@ -4,14 +4,14 @@ //! MA tag is present. Returns a populated [`MolecularAnnotations`] (read //! length and aligned blocks set) even when no annotation tags exist. //! -//! Writing: always emits MA-spec tags. With `legacy=true` it additionally -//! emits legacy `ns/nl/as/al/aq` for `nuc` and `msp` types so pre-MA -//! consumers (older pyft, IGV decorators) keep working during the -//! migration. With `legacy=false` any pre-existing legacy tags are stripped. +//! Writing: emits MA-spec tags only. Legacy `ns/nl/as/al/aq` emission is +//! intentionally not supported — the new FIRE-as-subset semantics is +//! incompatible with the legacy dense `aq` layout. Pre-MA BAMs remain +//! readable; downstream consumers must migrate to the MA tag set. //! //! Annotation type names produced by fibertools-rs: //! - `nuc` (no strand, no quality) -//! - `msp` (no strand, no quality pre-FIRE; `Q` post-FIRE) +//! - `msp` (no strand, `Q` zero-valued — qualities live on `fire`) //! - `fire` (no strand, `Q` linear precision 0–255) //! //! `m6a` and `cpg` types may appear *in memory* on a [`MolecularAnnotations`] @@ -20,7 +20,7 @@ //! The writer below strips them before emission as a safety net. use anyhow::{bail, Result}; -use molecular_annotation::{Annotation, MolecularAnnotations, QualitySpec, Strand}; +use molecular_annotation::{MolecularAnnotations, QualitySpec, Strand}; use rust_htslib::bam::{self, record::Aux}; /// Annotation type names used by fibertools-rs. @@ -28,9 +28,9 @@ pub const NUC_TYPE: &str = "nuc"; pub const MSP_TYPE: &str = "msp"; pub const FIRE_TYPE: &str = "fire"; -/// Legacy fibertools-rs tags. Listed here so callers (and the writer below) -/// have one place to look up which tags this module produces/consumes. -pub const LEGACY_NUC_MSP_TAGS: &[&[u8]] = &[b"ns", b"nl", b"as", b"al", b"aq"]; +/// Legacy fibertools-rs tags consumed by the reader as a fallback when no +/// MA tag is present. These are never emitted; we only ingest them. +pub const LEGACY_READ_TAGS: &[&[u8]] = &[b"ns", b"nl", b"as", b"al", b"aq"]; /// Read annotations from a BAM record. /// @@ -132,23 +132,10 @@ fn read_legacy_nuc_msp(record: &bam::Record) -> Result { /// Write annotations to a BAM record. /// -/// Always emits the MA-spec tags. When `legacy` is set, also emits the -/// fibertools-rs legacy `ns`/`nl`/`as`/`al`/`aq` tags so pre-MA consumers -/// (older pyft, IGV decorators) keep working during the migration. -/// -/// The legacy mapping: -/// - `nuc` → `ns`/`nl` -/// - `msp` → `as`/`al` -/// - `fire` → `aq` (paired with the `as`/`al` from `msp`, since pre-MA -/// fibertools stored FIRE precisions as MSP qualities). When no `fire` -/// type is present, `aq` falls back to `msp`'s own quality if it has one. -/// -/// When `legacy` is not set, any pre-existing legacy tags are stripped so -/// the output is MA-only. -pub fn write_annotations(record: &mut bam::Record, annot: &MolecularAnnotations, legacy: bool) { - for tag in LEGACY_NUC_MSP_TAGS { - record.remove_aux(tag).ok(); - } +/// Emits MA-spec tags only. Base modifications (`m6a`, `cpg`) are stripped +/// before serialization — their on-disk source of truth is `MM`/`ML`, not +/// the MA tag set. +pub fn write_annotations(record: &mut bam::Record, annot: &MolecularAnnotations) { // Base modifications (`m6a`, `cpg`) belong in MM/ML — never in the // MA tag set. Drop them before serialization. See the module docs // for the on-disk source-of-truth split. @@ -157,80 +144,6 @@ pub fn write_annotations(record: &mut bam::Record, annot: &MolecularAnnotations, t.name != crate::utils::basemods::M6A_TYPE && t.name != crate::utils::basemods::CPG_TYPE }); for_ma.to_record(record); - if legacy { - write_legacy_nuc_msp(record, annot); - } -} - -fn write_legacy_nuc_msp(record: &mut bam::Record, annot: &MolecularAnnotations) { - if let Some(nuc) = annot.get_type(NUC_TYPE) { - push_starts_lens(record, b"ns", b"nl", &nuc.annotations); - } - - // Legacy convention: pre-MA fibertools wrote FIRE precisions onto the - // MSP `aq` tag — there was no separate FIRE tag. So legacy MSP output - // takes coords from MSP and quality from FIRE when FIRE is present; - // otherwise it falls back to MSP's own quality (when present), or no - // `aq` at all (pre-FIRE state). - if let Some(msp) = annot.get_type(MSP_TYPE) { - push_starts_lens(record, b"as", b"al", &msp.annotations); - - let aq: Option> = if let Some(fire) = annot.get_type(FIRE_TYPE) { - // Sanity: legacy convention assumes FIRE coords mirror MSP coords. - // If they don't, the `aq` array we emit won't align with `as`/`al`. - debug_assert_eq!( - fire.annotations.len(), - msp.annotations.len(), - "legacy aq emission requires fire and msp to have matching counts" - ); - if fire.annotations.len() == msp.annotations.len() { - Some( - fire.annotations - .iter() - .map(|a| { - crate::utils::bamannotations::primary_qual(&a.qualities, FIRE_TYPE) - }) - .collect(), - ) - } else { - None - } - } else if msp.quality_spec.num_qualities() == 1 && msp.quality_spec.has_quality() { - Some( - msp.annotations - .iter() - .map(|a| crate::utils::bamannotations::primary_qual(&a.qualities, MSP_TYPE)) - .collect(), - ) - } else { - None - }; - - if let Some(aq) = aq { - if !aq.is_empty() { - record.push_aux(b"aq", Aux::ArrayU8((&aq).into())).ok(); - } - } - } -} - -fn push_starts_lens( - record: &mut bam::Record, - starts_tag: &[u8], - lens_tag: &[u8], - items: &[Annotation], -) { - if items.is_empty() { - return; - } - let starts: Vec = items.iter().map(|a| a.start).collect(); - let lens: Vec = items.iter().map(|a| a.length).collect(); - record - .push_aux(starts_tag, Aux::ArrayU32((&starts).into())) - .ok(); - record - .push_aux(lens_tag, Aux::ArrayU32((&lens).into())) - .ok(); } /// Convenience for callers that still operate on raw `i64` arrays of @@ -273,7 +186,7 @@ pub fn extract_nuc_msp_arrays( Ok((nuc_starts, nuc_lengths, msp_starts, msp_lengths, msp_qual)) } -/// Add `nuc` annotations (forward strand, no quality) to `annot`. +/// Add `nuc` annotations (unknown strand, no quality) to `annot`. /// /// No-op if `starts` is empty. `starts` and `lens` must be the same length /// and paired positionally. @@ -287,7 +200,7 @@ pub fn add_nuc_annotations(annot: &mut MolecularAnnotations, starts: &[u32], len } } -/// Add `msp` annotations (forward strand) to `annot`. +/// Add `msp` annotations (unknown strand) to `annot`. /// /// With `qualities` present, the type uses `msp+Q`; without, `msp+` (no /// quality). No-op if `starts` is empty. All input slices must be the same From 0b13982ed77efea48d02c19911d593d0a6cd5b14 Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Thu, 14 May 2026 16:09:27 -0600 Subject: [PATCH 21/24] refactor: treat MSP and FIRE as independent annotation types MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit FIRE is now the filtered subset of MSPs with non-zero XGB precision — its own coords and qualities, not a sidecar to MSP. Consumers that previously asked "what's the FIRE qual for this MSP" via the legacy 1:1 model are rewritten to iterate fiber.fire() directly. * add_fire_to_rec filters precisions to p > 0 before building fire+Q * fire_qual() helper deleted — its semantics conflated MSP iteration with FIRE quality lookup * pileup, validate, decorator/fire_decorators iterate fiber.fire() * footprint splits the conflated msp_fire_scores into independent has_spanning_msp + fire_quals tracked over fiber.fire() spanning * BED12 (fibertools extract --all) and centered TSV writers emit FIRE as its own coord group (starts/lengths/qual/ref_starts/ ref_lengths) parallel to nuc/m6a/cpg, not wedged into MSP columns Obsolete tests removed: legacy_write_emits_both_tag_sets, legacy_write_inverse_roundtrip, fire_qual_matches_legacy_and_ma_paths. extract_all_napa snapshot regenerated to reflect new column shape. --- src/fiber.rs | 51 +-- src/subcommands/center.rs | 49 ++- src/subcommands/decorator.rs | 10 +- src/subcommands/fire.rs | 25 +- src/subcommands/footprint.rs | 56 ++-- src/subcommands/pileup.rs | 9 +- src/subcommands/validate.rs | 2 +- tests/fibertig_test.rs | 2 +- tests/molecular_annotation.rs | 163 +-------- tests/regression/extract.rs | 4 +- ...regression__extract__extract_all_napa.snap | 313 +++++++++--------- 11 files changed, 284 insertions(+), 400 deletions(-) diff --git a/src/fiber.rs b/src/fiber.rs index 3345d8ea..1e4ac272 100644 --- a/src/fiber.rs +++ b/src/fiber.rs @@ -139,33 +139,6 @@ impl FiberseqData { AnnotationTypeView::new(&self.annotations, FIRE_TYPE) } - /// Per-MSP FIRE precision in BAM-orient ascending order, aligned 1:1 - /// with [`Self::msp`] iteration. Returns `vec![0; msp_len]` when no - /// FIRE data is present. - /// - /// Resolves in two stages: - /// 1. If a `fire` annotation type exists with the same count as - /// `msp`, return its qualities (post-MA write path: FIRE precisions - /// live on `fire+P`). - /// 2. Otherwise fall back to `self.msp().qual()` — pre-MA fibertools - /// stored FIRE precisions on the MSP `aq` tag, so legacy BAMs land - /// them in `msp.qualities`. - pub fn fire_qual(&self) -> Vec { - let msp_len = self.msp().len(); - if msp_len == 0 { - return Vec::new(); - } - let fire = self.fire(); - if fire.len() == msp_len { - return fire.qual(); - } - let msp_q = self.msp().qual(); - if msp_q.len() == msp_len && msp_q.iter().any(|&q| q > 0) { - return msp_q; - } - vec![0; msp_len] - } - /// Flush `self.annotations` onto the underlying record's MA aux /// tags. The single write path — every subcommand that mutates /// annotations should call this and then hand the record to the @@ -346,7 +319,7 @@ impl FiberseqData { x.push_str("fiber_qual\t") } x.push_str(&format!( - "{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n", + "{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n", "ec", "rq", "total_AT_bp", @@ -360,9 +333,13 @@ impl FiberseqData { "ref_nuc_lengths", "msp_starts", "msp_lengths", - "fire", "ref_msp_starts", "ref_msp_lengths", + "fire_starts", + "fire_lengths", + "fire_qual", + "ref_fire_starts", + "ref_fire_lengths", "m6a", "ref_m6a", "m6a_qual", @@ -414,15 +391,12 @@ impl FiberseqData { let cpg = self.cpg(); let msp = self.msp(); let nuc = self.nuc(); + let fire = self.fire(); let m6a_count = m6a.len(); let m6a_qual = m6a.qual().iter().map(|a| Some(*a as i64)).collect(); let cpg_count = cpg.len(); let cpg_qual = cpg.qual().iter().map(|a| Some(*a as i64)).collect(); - let fire: Vec> = self - .fire_qual() - .iter() - .map(|a| Some(*a as i64)) - .collect(); + let fire_qual: Vec> = fire.qual().iter().map(|a| Some(*a as i64)).collect(); // write the features let mut rtn = String::with_capacity(0); @@ -463,7 +437,8 @@ impl FiberseqData { self.ec, rq, at_count, m6a_count, total_nuc_bp, total_msp_bp, cpg_count )) .unwrap(); - // add fiber features + // add fiber features. FIRE is its own coord group (parallel to + // nuc/m6a/cpg) — not wedged into the MSP columns. let vecs = [ nuc.option_starts(), nuc.option_lengths(), @@ -471,9 +446,13 @@ impl FiberseqData { nuc.reference_lengths(), msp.option_starts(), msp.option_lengths(), - fire, msp.reference_starts(), msp.reference_lengths(), + fire.option_starts(), + fire.option_lengths(), + fire_qual, + fire.reference_starts(), + fire.reference_lengths(), m6a.option_starts(), m6a.reference_starts(), m6a_qual, diff --git a/src/subcommands/center.rs b/src/subcommands/center.rs index 2f286e55..dd392ce5 100644 --- a/src/subcommands/center.rs +++ b/src/subcommands/center.rs @@ -260,21 +260,37 @@ impl CenteredFiberData { Vec>, Vec>, Vec>, + Vec>, + Vec>, Vec, ) { let (m6a, _, m6a_qual) = self.centered_for_type("m6a"); let (cpg, _, cpg_qual) = self.centered_for_type("cpg"); let (nuc_st, nuc_en, _) = self.centered_for_type("nuc"); - let (msp_st, msp_en, fire) = self.centered_for_type("msp"); + let (msp_st, msp_en, _) = self.centered_for_type("msp"); + let (fire_st, fire_en, fire_qual) = self.centered_for_type("fire"); ( - m6a, m6a_qual, cpg, cpg_qual, nuc_st, nuc_en, msp_st, msp_en, fire, + m6a, m6a_qual, cpg, cpg_qual, nuc_st, nuc_en, msp_st, msp_en, fire_st, fire_en, + fire_qual, ) } pub fn write(&self) -> String { - let (m6a, m6a_qual, cpg, cpg_qual, nuc_st, nuc_en, msp_st, msp_en, fire) = self.grab_data(); + let ( + m6a, + m6a_qual, + cpg, + cpg_qual, + nuc_st, + nuc_en, + msp_st, + msp_en, + fire_st, + fire_en, + fire_qual, + ) = self.grab_data(); format!( - "{}{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n", + "{}{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n", self.leading_columns(), join_by_str_option(&m6a, ","), join_by_str(&m6a_qual, ","), @@ -284,7 +300,9 @@ impl CenteredFiberData { join_by_str_option(&nuc_en, ","), join_by_str_option(&msp_st, ","), join_by_str_option(&msp_en, ","), - join_by_str(&fire, ","), + join_by_str_option(&fire_st, ","), + join_by_str_option(&fire_en, ","), + join_by_str(&fire_qual, ","), self.get_sequence(), ) } @@ -308,7 +326,7 @@ impl CenteredFiberData { } pub fn header() -> String { format!( - "{}{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n", + "{}{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n", CenteredFiberData::leading_header(), "centered_m6a_positions", "m6a_qual", @@ -318,6 +336,8 @@ impl CenteredFiberData { "centered_nuc_ends", "centered_msp_starts", "centered_msp_ends", + "centered_fire_starts", + "centered_fire_ends", "fire_qual", "query_sequence" ) @@ -336,12 +356,25 @@ impl CenteredFiberData { pub fn write_long(&self) -> String { let mut rtn = String::new(); - let (m6a, m6a_qual, cpg, cpg_qual, nuc_st, nuc_en, msp_st, msp_en, fire) = self.grab_data(); + let ( + m6a, + m6a_qual, + cpg, + cpg_qual, + nuc_st, + nuc_en, + msp_st, + msp_en, + fire_st, + fire_en, + fire_qual, + ) = self.grab_data(); for (t, vals) in [ ("m6a", (m6a, None, Some(m6a_qual))), ("5mC", (cpg, None, Some(cpg_qual))), ("nuc", (nuc_st, Some(nuc_en), None)), - ("msp", (msp_st, Some(msp_en), Some(fire))), + ("msp", (msp_st, Some(msp_en), None)), + ("fire", (fire_st, Some(fire_en), Some(fire_qual))), ] { let starts = vals.0.iter().collect::>(); let ends: Vec> = match vals.1 { diff --git a/src/subcommands/decorator.rs b/src/subcommands/decorator.rs index 9d797c74..f9208b67 100644 --- a/src/subcommands/decorator.rs +++ b/src/subcommands/decorator.rs @@ -166,10 +166,12 @@ pub fn fire_decorators(fiber: &FiberseqData) -> Vec> { map.insert(color, vec![]); } - let msp = fiber.msp(); - let ref_starts = msp.reference_starts(); - let ref_lengths = msp.reference_lengths(); - let quals = fiber.fire_qual(); + // FIRE is its own annotation type — color decorators by FIRE precision + // directly. Non-FIRE MSPs are not decorated here + let fire = fiber.fire(); + let ref_starts = fire.reference_starts(); + let ref_lengths = fire.reference_lengths(); + let quals = fire.qual(); for ((pos, length), qual) in ref_starts.iter().zip(ref_lengths.iter()).zip(quals.iter()) { if let (Some(p), Some(l)) = (pos, length) { diff --git a/src/subcommands/fire.rs b/src/subcommands/fire.rs index 5cbf471e..71be43ad 100644 --- a/src/subcommands/fire.rs +++ b/src/subcommands/fire.rs @@ -24,9 +24,11 @@ pub fn add_fire_to_rec( precisions.reverse(); } - // Use the FiberseqData's already-loaded MA object; no record - // re-read. MSP coords come from rec.annotations directly. - let (starts, lens): (Vec, Vec) = { + // FIRE is the filtered subset of MSPs with non-zero precision — + // the MSPs whose XGB prediction crossed the "this is a regulatory + // element" threshold. Build that subset from the per-MSP coords + // and their paired precisions, keeping only entries with p > 0. + let (fire_starts, fire_lens, fire_quals): (Vec, Vec, Vec) = { let Some(msp) = rec.annotations.get_type(ma_io::MSP_TYPE) else { log::warn!("FIRE: no msp annotations on record; skipping"); return; @@ -39,17 +41,24 @@ pub fn add_fire_to_rec( ); return; } - ( - msp.annotations.iter().map(|a| a.start).collect(), - msp.annotations.iter().map(|a| a.length).collect(), - ) + let mut s = Vec::new(); + let mut l = Vec::new(); + let mut q = Vec::new(); + for (a, &p) in msp.annotations.iter().zip(precisions.iter()) { + if p > 0 { + s.push(a.start); + l.push(a.length); + q.push(p); + } + } + (s, l, q) }; // Drop any pre-existing fire annotations so a re-run replaces, rather // than appends to, the previous call. rec.annotations .annotation_types .retain(|t| t.name != ma_io::FIRE_TYPE); - ma_io::add_fire_annotations(&mut rec.annotations, &starts, &lens, &precisions); + ma_io::add_fire_annotations(&mut rec.annotations, &fire_starts, &fire_lens, &fire_quals); rec.serialize_annotations(); diff --git a/src/subcommands/footprint.rs b/src/subcommands/footprint.rs index 4a2fe414..563f2eac 100644 --- a/src/subcommands/footprint.rs +++ b/src/subcommands/footprint.rs @@ -114,8 +114,9 @@ impl<'a> ReferenceMotif<'a> { pub struct Footprint<'a> { pub n_spanning_fibers: usize, pub n_spanning_msps: usize, + pub n_spanning_fires: usize, pub has_spanning_msp: Vec, - pub msp_fire_scores: Vec, + pub fire_quals: Vec, pub n_overlapping_nucs: usize, pub has_overlapping_nucleosome: Vec, pub footprint_codes: Vec, @@ -136,42 +137,52 @@ impl<'a> Footprint<'a> { let mut footprint = Self { n_spanning_fibers: fibers.len(), n_spanning_msps: 0, + n_spanning_fires: 0, has_spanning_msp: vec![], - msp_fire_scores: vec![], + fire_quals: vec![], n_overlapping_nucs: 0, has_overlapping_nucleosome: vec![], footprint_codes: vec![], motif, fibers, }; - // add the number of msps that span the footprint - footprint.spanning_msps(); + // count spanning MSPs (any methylated region) and spanning FIREs + // (regulatory element calls) — two independent signals. + footprint.spanning_msps_and_fires(); footprint.establish_footprints(); footprint.overlapping_nucleosomes(); footprint } - fn spanning_msps(&mut self) { + fn spanning_msps_and_fires(&mut self) { for fiber in self.fibers.iter() { + // Spanning MSP — "is there any methylated region spanning the motif?" let mut has_spanning_msp = false; - let mut msp_qual = -1; - let fire_quals = fiber.fire_qual(); - for (idx, msp) in (&fiber.msp()).into_iter().enumerate() { - // skip if there is no mapping of the msp - match (msp.ref_start, msp.ref_end) { - (Some(rs), Some(re)) => { - if self.motif.spans(rs as i64, re as i64) { - self.n_spanning_msps += 1; - has_spanning_msp = true; - msp_qual = fire_quals.get(idx).copied().unwrap_or(0) as i16; - break; - } + for msp in &fiber.msp() { + if let (Some(rs), Some(re)) = (msp.ref_start, msp.ref_end) { + if self.motif.spans(rs as i64, re as i64) { + self.n_spanning_msps += 1; + has_spanning_msp = true; + break; } - _ => continue, } } self.has_spanning_msp.push(has_spanning_msp); - self.msp_fire_scores.push(msp_qual); + + // Spanning FIRE — "is there a regulatory element call spanning + // the motif, and if so what's its precision?" Independent of + // whether any MSP spans. + let mut fire_qual: i16 = -1; + for fire in &fiber.fire() { + if let (Some(rs), Some(re)) = (fire.ref_start, fire.ref_end) { + if self.motif.spans(rs as i64, re as i64) { + self.n_spanning_fires += 1; + fire_qual = fire.qualities.first().copied().unwrap_or(0) as i16; + break; + } + } + } + self.fire_quals.push(fire_qual); } } @@ -259,7 +270,7 @@ impl<'a> Footprint<'a> { pub fn out_bed_header(&self) -> String { let mut out = - "#chrom\tstart\tend\tstrand\tn_spanning_fibers\tn_spanning_msps\tn_overlapping_nucs\t" + "#chrom\tstart\tend\tstrand\tn_spanning_fibers\tn_spanning_msps\tn_spanning_fires\tn_overlapping_nucs\t" .to_string(); out += &self .motif @@ -277,13 +288,14 @@ impl<'a> Footprint<'a> { impl std::fmt::Display for Footprint<'_> { fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result { let mut out = format!( - "{}\t{}\t{}\t{}\t{}\t{}\t{}\t", + "{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t", self.motif.chrom, self.motif.start, self.motif.end + 1, self.motif.strand, self.n_spanning_fibers, self.n_spanning_msps, + self.n_spanning_fires, self.n_overlapping_nucs, ); @@ -308,7 +320,7 @@ impl std::fmt::Display for Footprint<'_> { .map(|x| x.to_string()) .collect::>() .join(","), - self.msp_fire_scores + self.fire_quals .iter() .map(|x| x.to_string()) .collect::>() diff --git a/src/subcommands/pileup.rs b/src/subcommands/pileup.rs index d47f3ea2..c929e267 100644 --- a/src/subcommands/pileup.rs +++ b/src/subcommands/pileup.rs @@ -400,14 +400,15 @@ impl<'a> FireTrack<'a> { self.coverage[pos as usize] += 1; } - // calculate the fire coverage and fire score - let fire_quals = fiber.fire_qual(); - for (idx, info) in (&fiber.msp()).into_iter().enumerate() { + // calculate the fire coverage and fire score. FIRE is its own + // annotation type — already filtered to non-zero precision in + // add_fire_to_rec. MIN_FIRE_QUAL is the stricter pileup-level gate. + for info in &fiber.fire() { let (rs, re) = match (info.ref_start, info.ref_end) { (Some(rs), Some(re)) => (rs as i64, re as i64), _ => continue, }; - let qual = fire_quals.get(idx).copied().unwrap_or(0); + let qual = info.qualities.first().copied().unwrap_or(0); if qual < MIN_FIRE_QUAL { continue; } diff --git a/src/subcommands/validate.rs b/src/subcommands/validate.rs index 050e9b01..c908aca6 100644 --- a/src/subcommands/validate.rs +++ b/src/subcommands/validate.rs @@ -35,7 +35,7 @@ pub fn validate_fiberseq_bam(opts: &mut ValidateOptions) -> Result<()> { for fiber in opts.bam.fibers(&mut bam) { let m6a_okay = !fiber.m6a().is_empty(); let nuc_okay = !fiber.nuc().is_empty(); - n_fire_calls += fiber.fire_qual().iter().filter(|q| **q > 0).count(); + n_fire_calls += fiber.fire().len(); n_aligned += !fiber.record.is_unmapped() as usize; n_phased += fiber.record.aux(b"HP").is_ok() as usize; diff --git a/tests/fibertig_test.rs b/tests/fibertig_test.rs index 645128e7..98f7c81b 100644 --- a/tests/fibertig_test.rs +++ b/tests/fibertig_test.rs @@ -544,7 +544,7 @@ fn build_tagged_record( t.add(*s, *l, Strand::Forward, vec![], name); } } - ma_io::write_annotations(&mut record, &annot, false); + ma_io::write_annotations(&mut record, &annot); record } diff --git a/tests/molecular_annotation.rs b/tests/molecular_annotation.rs index 21c6cc0d..1a33173f 100644 --- a/tests/molecular_annotation.rs +++ b/tests/molecular_annotation.rs @@ -4,10 +4,11 @@ //! - Reading legacy `ns/nl/as/al/aq` produces the same MolecularAnnotations //! shape (counts, coords, qualities) as direct raw tag access. //! - Writing MA tags then reading them back yields equal annotations. -//! - `--legacy=true` produces both MA and legacy tags; `--legacy=false` -//! strips legacy tags from the output. //! - Reverse-aligned records keep coordinates in molecular orientation. //! - Records with both MA and legacy tags resolve to the MA version. +//! +//! Legacy-write paths are intentionally not exercised here — fibertools-rs +//! reads legacy tags but never emits them post-MA-migration. use std::path::PathBuf; @@ -87,16 +88,7 @@ fn ma_write_then_read_roundtrips() { for record in read_records(fixture) { let original = read_annotations(&record).unwrap(); let mut converted = record.clone(); - write_annotations(&mut converted, &original, false); - - // Legacy tags must be gone after non-legacy write. - for tag in [b"ns", b"nl", b"as", b"al", b"aq"] { - assert!( - converted.aux(tag).is_err(), - "{fixture}: legacy {} should be stripped", - std::str::from_utf8(tag).unwrap() - ); - } + write_annotations(&mut converted, &original); let round = read_annotations(&converted).unwrap(); assert_eq!( @@ -107,60 +99,6 @@ fn ma_write_then_read_roundtrips() { } } -#[test] -fn legacy_write_emits_both_tag_sets() { - for fixture in FIXTURES { - for record in read_records(fixture) { - let original = read_annotations(&record).unwrap(); - let mut both = record.clone(); - write_annotations(&mut both, &original, true); - - // MA tag present. - assert!(both.aux(b"MA").is_ok(), "{fixture}: MA expected"); - - // Legacy tags also present where applicable. - if original.get_type(NUC_TYPE).is_some() { - assert!(both.aux(b"ns").is_ok(), "{fixture}: ns expected"); - assert!(both.aux(b"nl").is_ok(), "{fixture}: nl expected"); - } - if original.get_type(MSP_TYPE).is_some() { - assert!(both.aux(b"as").is_ok(), "{fixture}: as expected"); - assert!(both.aux(b"al").is_ok(), "{fixture}: al expected"); - } - } - } -} - -#[test] -fn legacy_write_inverse_roundtrip() { - // fixture → legacy write into a fresh record (with MA stripped) → re-read - // via the legacy path → equal annotations. - for fixture in FIXTURES { - for record in read_records(fixture) { - let original = read_annotations(&record).unwrap(); - let mut fresh = record.clone(); - // Wipe everything, then write legacy-only. - for tag in [ - b"MA", b"AL", b"AQ", b"AN", b"ns", b"nl", b"as", b"al", b"aq", - ] { - fresh.remove_aux(tag).ok(); - } - write_annotations(&mut fresh, &original, true); - // Strip MA so the read path falls back to legacy. - fresh.remove_aux(b"MA").ok(); - fresh.remove_aux(b"AL").ok(); - fresh.remove_aux(b"AQ").ok(); - fresh.remove_aux(b"AN").ok(); - - let round = read_annotations(&fresh).unwrap(); - assert_eq!( - round.annotation_types, original.annotation_types, - "{fixture}: legacy inverse roundtrip" - ); - } - } -} - #[test] fn ma_takes_precedence_over_legacy() { // Build a record with both MA and legacy tags, with intentionally @@ -234,99 +172,6 @@ fn missing_annotations_yield_empty_container() { assert_eq!(annot.read_length, blank.seq_len() as u32); } -#[test] -fn fire_qual_matches_legacy_and_ma_paths() { - // Pre-MA fibertools wrote FIRE precisions onto the MSP `aq` tag, so - // `msp.qual()` returned the FIRE precision. Post-MA, those precisions - // live on the separate `fire+P` annotation type and `msp.qual()` is - // empty. `FiberseqData::fire_qual()` must return the same per-MSP - // precision vector regardless of which on-disk format the BAM uses. - use fibertools_rs::fiber::FiberseqData; - use fibertools_rs::utils::input_bam::FiberFilters; - use fibertools_rs::utils::ma_io::{add_fire_annotations, add_msp_annotations, FIRE_TYPE}; - - let filters = FiberFilters::default(); - let mut legacy_count = 0; - for record in read_records("NAPA.bam") { - let legacy_aq = raw_u8(&record, b"aq"); - if legacy_aq.is_none() || legacy_aq.as_ref().unwrap().iter().all(|&q| q == 0) { - continue; - } - legacy_count += 1; - - // Legacy path: msp.qual() holds the precisions; no fire type yet. - let legacy_fsd = FiberseqData::new(record.clone(), None, &filters); - assert!( - legacy_fsd.fire().is_empty(), - "legacy fixture should not have a fire annotation type yet" - ); - let legacy_qual = legacy_fsd.fire_qual(); - assert_eq!( - legacy_qual, - legacy_fsd.msp().qual(), - "legacy fire_qual must equal msp.qual()" - ); - assert!( - legacy_qual.iter().any(|&q| q > 0), - "legacy fixture should expose nonzero FIRE precisions" - ); - - // Reshape to the post-FIRE MA layout (msp+ with no qualities, fire+P - // carrying the same precisions) — this is what `ft fire` produces - // post-migration. fire_qual() must yield the same vector. - let original = read_annotations(&record).unwrap(); - let mut reshaped = original.clone(); - // Drop the legacy msp+Q type and re-add msp+ without qualities. - reshaped.annotation_types.retain(|t| t.name != MSP_TYPE); - let msp_starts: Vec = original - .get_type(MSP_TYPE) - .unwrap() - .annotations - .iter() - .map(|a| a.start) - .collect(); - let msp_lens: Vec = original - .get_type(MSP_TYPE) - .unwrap() - .annotations - .iter() - .map(|a| a.length) - .collect(); - let msp_quals: Vec = original - .get_type(MSP_TYPE) - .unwrap() - .annotations - .iter() - .map(|a| a.qualities[0]) - .collect(); - add_msp_annotations(&mut reshaped, &msp_starts, &msp_lens, None); - add_fire_annotations(&mut reshaped, &msp_starts, &msp_lens, &msp_quals); - - let mut ma_only = record.clone(); - write_annotations(&mut ma_only, &reshaped, false); - let ma_fsd = FiberseqData::new(ma_only, None, &filters); - assert!( - !ma_fsd.fire().is_empty(), - "post-FIRE MA layout must expose a fire annotation type" - ); - assert_eq!( - ma_fsd.msp().qual().iter().filter(|q| **q > 0).count(), - 0, - "post-FIRE MA layout must not carry FIRE precisions on msp" - ); - assert_eq!( - ma_fsd.annotations.get_type(FIRE_TYPE).unwrap().annotations.len(), - ma_fsd.msp().len(), - "fire and msp must be 1:1" - ); - assert_eq!( - ma_fsd.fire_qual(), - legacy_qual, - "fire_qual must match across legacy and MA-only formats" - ); - } - assert!(legacy_count > 0, "expected at least one fixture with aq"); -} #[test] fn add_nucleosomes_is_idempotent_on_rerun() { diff --git a/tests/regression/extract.rs b/tests/regression/extract.rs index c507e444..2fb8ea3d 100644 --- a/tests/regression/extract.rs +++ b/tests/regression/extract.rs @@ -76,7 +76,9 @@ fn extract_all_napa() { "nuc_lengths", "msp_starts", "msp_lengths", - "fire", + "fire_starts", + "fire_lengths", + "fire_qual", "m6a", ] )); diff --git a/tests/regression/snapshots/regression__extract__extract_all_napa.snap b/tests/regression/snapshots/regression__extract__extract_all_napa.snap index bfe1ee8e..b5f129ff 100644 --- a/tests/regression/snapshots/regression__extract__extract_all_napa.snap +++ b/tests/regression/snapshots/regression__extract__extract_all_napa.snap @@ -1,159 +1,160 @@ --- source: tests/regression/extract.rs -expression: "select_tsv_cols(&out,\n&[\"#ct\", \"st\", \"en\", \"fiber\", \"nuc_starts\", \"nuc_lengths\", \"msp_starts\",\n\"msp_lengths\", \"fire\", \"m6a\",])" +assertion_line: 68 +expression: "select_tsv_cols(&out,\n&[\"#ct\", \"st\", \"en\", \"fiber\", \"nuc_starts\", \"nuc_lengths\", \"msp_starts\",\n\"msp_lengths\", \"fire_starts\", \"fire_lengths\", \"fire_qual\", \"m6a\",])" --- -#ct st en fiber nuc_starts nuc_lengths msp_starts msp_lengths fire m6a -chr19 47480179 47512478 m54329U_210814_130637/54723395/ccs 57,268,452,643,818,1024,1305,1522,1660,1847,2039,2276,2398,2583,2764,2919,3076,3270,3418,3558,3860,4238,4590,4761,4937,5123,5326,5510,5670,5861,5992,6129,6806,7087,7256,7498,7703,7921,8095,8277,8465,8634,9043,9384,9560,9750,10049,10189,10330,10571,10777,10957,11115,11300,11525,11697,11880,12091,12246,12435,12628,12859,13236,13583,13783,14139,14300,14503,14672,14859,15048,15175,15376,15630,15984,16087,16268,16464,16623,16784,16955,17141,17514,17762,17886,18057,18227,18437,18651,18904,19033,19231,19409,19620,19784,20036,20185,20363,20541,20758,20910,21132,21316,21497,21645,21870,22205,22399,22589,22775,23124,23291,23507,23719,23900,24068,24232,24465,24681,24878,25075,25264,25448,25651,25881,26228,26394,26641,26801,27025,27223,27457,27598,27723,27964,28168,28415,28623,28759,28938,29127,29697,29968,30121,30322,30515,30714,30889,31087,31311,31683,31894, 210,136,119,100,145,133,128,122,135,118,130,93,151,125,144,129,120,108,101,142,279,197,117,134,162,149,159,125,155,130,91,511,115,131,103,116,138,112,141,138,125,257,111,126,128,259,139,130,125,103,114,110,142,136,122,144,141,106,132,146,148,92,116,150,144,122,145,151,125,116,121,145,169,108,102,127,133,144,154,150,142,136,124,88,138,121,152,161,131,88,151,142,137,163,154,84,116,118,112,99,142,145,148,147,132,292,139,148,141,121,108,136,121,148,155,163,143,141,139,164,106,144,135,125,84,131,146,159,148,127,135,128,106,116,112,106,105,76,109,188,116,195,152,150,153,148,129,158,79,120,145,95, 56,267,404,571,743,963,1157,1433,1644,1795,1965,2169,2369,2549,2708,2908,3048,3196,3378,3519,3700,4139,4435,4707,4895,5099,5272,5485,5635,5825,5991,6083,6640,6921,7218,7359,7614,7841,8033,8236,8415,8590,8891,9154,9510,9688,10009,10188,10319,10455,10674,10891,11067,11257,11436,11647,11841,12021,12197,12378,12581,12776,12951,13352,13733,13927,14261,14445,14654,14797,14975,15169,15320,15545,15738,16086,16214,16401,16608,16777,16934,17097,17277,17638,17850,18024,18178,18379,18598,18782,18992,19184,19373,19546,19783,19938,20120,20301,20481,20653,20857,21052,21277,21464,21644,21777,22162,22344,22547,22730,22896,23232,23427,23628,23867,24055,24231,24375,24606,24820,25042,25181,25408,25583,25776,25965,26359,26540,26800,26949,27152,27358,27585,27704,27839,28076,28274,28520,28699,28868,29126,29243,29892,30120,30271,30475,30663,30843,31047,31166,31431,31828, 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-chr19 47491845 47513484 m84039_230401_034725_s4/80545237/ccs 189,359,450,580,1279,1378,1852,2061,2186,2282,2420,2594,2922,3242,3334,3557,3785,3933,4097,4243,4417,4678,4773,5060,5229,5391,5694,5816,6031,6208,6517,6639,6777,6853,7214,7370,7629,7863,8254,8412,8521,8636,8758,8909,9043,9372,9658,9871,10007,10150,10482,11163,11382,11792,11887,12031,12190,12368,12588,12842,12980,13250,13408,13575,13774,14080,14297,14603,14756,14868,15032,15155,15249,15381,15628,15842,16015,16146,16274,16463,17146,17635,17733,18029,18227,18331,18572,18667,18769,18961,19282,19621,19952,20139,20366,20606,20821,21145,21257, 169,83,129,698,98,392,208,102,75,116,166,190,319,87,128,139,147,133,145,133,241,82,199,168,101,302,121,214,176,188,121,123,75,314,155,258,233,390,143,108,101,119,148,133,311,230,212,135,142,329,675,211,409,94,121,158,140,219,253,137,269,157,157,198,305,216,305,136,111,163,122,93,129,213,206,172,129,127,158,643,488,97,295,179,103,240,91,101,188,318,248,330,184,146,192,214,323,101,103, 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-chr19 47492760 47515497 m54329U_210326_192251/174784613/ccs 77,295,497,666,901,1056,1257,1499,1695,1878,2084,2231,2415,2573,2766,2946,3167,3334,3517,3764,3931,4106,4307,4482,4674,4904,5062,5316,5484,5632,5801,5965,6050,6144,6352,6530,6706,6855,7028,7170,7370,7518,7682,7878,8060,8206,8379,8823,8957,9230,9452,9608,9962,10283,10486,10646,10822,10977,11121,11361,11503,11636,11858,12076,12263,12453,12659,12811,12994,13211,13429,13615,13784,13971,14199,14387,14596,14780,14974,15142,15345,15515,15701,16028,16244,16409,16732,16932,17117,17470,17679,17878,18084,18287,18471,18684,18875,19075,19240,19453,19623,19793,19981,20222,20394,20575,20729,20900,21032,21227,21405,21606,21726, 139,113,107,128,102,92,107,125,139,141,116,145,143,150,130,136,105,100,138,106,139,145,113,116,124,81,147,107,85,141,138,84,76,155,107,125,117,133,116,133,130,154,141,148,135,136,136,100,252,135,127,272,292,125,115,156,139,143,143,129,98,135,115,160,153,128,111,166,157,141,128,136,128,135,115,144,138,103,126,125,117,131,302,146,112,281,138,155,267,145,151,114,143,151,135,118,136,136,132,110,128,156,122,105,129,124,131,129,154,132,127,114,134, 216,408,604,794,1003,1148,1364,1624,1834,2019,2200,2376,2558,2723,2896,3082,3272,3434,3655,3870,4070,4251,4420,4598,4798,4985,5209,5423,5569,5773,5939,6049,6126,6299,6459,6655,6823,6988,7144,7303,7500,7672,7823,8026,8195,8342,8515,8923,9209,9365,9579,9880,10254,10408,10601,10802,10961,11120,11264,11490,11601,11771,11973,12236,12416,12581,12770,12977,13151,13352,13557,13751,13912,14106,14314,14531,14734,14883,15100,15267,15462,15646,16003,16174,16356,16690,16870,17087,17384,17615,17830,17992,18227,18438,18606,18802,19011,19211,19372,19563,19751,19949,20103,20327,20523,20699,20860,21029,21186,21359,21532,21720, 79,89,62,107,53,109,135,71,44,65,31,39,15,43,50,85,62,83,109,61,36,56,62,76,106,77,107,61,63,28,26,1,18,53,71,51,32,40,26,67,18,10,55,34,11,37,308,34,21,87,29,82,29,78,45,20,16,1,97,13,35,87,103,27,37,78,41,17,60,77,58,33,59,93,73,65,46,91,42,78,53,55,25,70,53,42,62,30,86,64,48,92,60,33,78,73,64,29,81,60,42,32,119,67,52,30,40,3,41,46,74,6, 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-chr19 47492987 47512813 m84039_230401_031619_s3/197857390/ccs 175,392,610,777,1103,1263,1684,1863,1983,2193,2368,2812,3060,3274,3438,3535,3708,3848,4215,4421,4689,5037,5174,5283,5375,5592,5806,5971,6230,6433,6670,6795,6940,7044,7259,7775,7903,8036,8214,8439,8675,8854,9063,9235,9340,9431,9596,9685,9977,10134,10414,10558,10710,10912,11128,11330,11569,11710,11997,12137,12636,12913,13280,13524,13673,13894,14202,14308,14489,14669,14788,14907,15002,15087,15320,15499,15642,15865,15982,16069,16456,16748,17017,17132,17259,17471,17650,17748,18032,18425,18555,18847,19246, 146,179,166,140,158,375,178,118,146,147,124,247,213,159,92,109,108,345,145,190,294,136,79,91,121,170,164,128,202,207,110,104,103,136,154,127,110,177,224,162,167,146,169,104,90,164,88,291,155,108,126,151,171,155,195,224,140,286,139,262,276,303,242,148,144,185,105,97,179,111,79,94,84,169,135,121,190,114,86,304,169,256,114,75,103,175,93,278,357,114,237,398,346, 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-chr19 47493395 47519143 m54329U_210813_020940/167053480/ccs 248,445,658,856,1011,1189,1330,1576,1763,2021,2220,2409,2588,2783,2979,3150,3336,3499,3705,3920,4088,4274,4459,4707,4915,5093,5323,5561,5909,6077,6442,6607,6823,7567,7685,7914,8066,8258,8435,8707,8895,9079,9291,9446,9623,9823,10008,10163,10416,10610,10773,10921,11095,11293,11525,11745,11907,12127,12314,12510,12667,12835,13038,13224,13394,13558,13766,14015,14150,14341,14483,14692,14856,15028,15195,15348,15600,15772,15982,16160,16351,16546,16733,16953,17161,17524,17703,17881,18066,18370,18653,18786,19041,19238,19380,19585,20151,20317,20509,20661,20850,21197,21330,21608,22668,22857,23020,23192,23478,23635,23801,23947,24105,24282,24422,24619,25056,25698, 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-chr19 47493741 47516930 m54329U_210813_020940/81528729/ccs 210,405,585,788,990,1178,1348,1596,1731,1922,2132,2320,2523,2679,2913,3100,3240,3403,3613,3800,3947,4200,4411,4507,4735,4930,5059,5140,5333,5521,5693,5852,6015,6199,6315,6546,6737,6906,7099,7253,7411,7614,7813,8026,8250,8363,8900,9115,9301,9504,9689,9892,10073,10305,10465,10632,10811,11088,11350,11469,11665,11832,12020,12321,12517,12678,12883,13092,13317,13459,13641,13849,14038,14210,14398,14603,14791,14957,15150,15335,15517,15670,15859,16061,16407,16629,16846,17083,17246,17399,17579,17772,18251,18416,18574,18743,18937,19104,19336,19526,19695,19852,20156,20321,20463,20721,20912,21038,21927,22323,22680,22846, 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-chr19 47496001 47518986 m84039_230401_031619_s3/137303312/ccs 154,281,496,697,832,972,1089,1326,1494,1674,1887,2062,2180,2532,2659,2795,2913,3022,3224,3484,3635,4020,4105,4181,4325,4489,4611,4814,4902,5042,5312,5470,5624,5769,6004,6143,6400,6483,6615,6839,7230,7420,7774,8014,8339,8626,9112,9261,9423,9637,9903,10023,10139,10292,10532,10740,10892,11314,11450,11571,11784,11926,12319,12532,12682,12851,12962,13119,13393,13590,13886,14491,14893,15030,15112,15432,15580,15749,16544,16850,16965,17222,17496,17729,17952,18094,18250,18384,18526,18736,18845,18983,19369,19569,19733,20079,20272,20354,20453,20779,20943,21130,21246,21625,21711,21833,21957,22085,22248,22423,22515,22680, 126,125,121,117,114,111,96,167,147,205,113,104,309,126,113,117,108,201,211,150,384,84,75,143,89,121,183,76,138,166,157,83,100,171,138,123,79,83,161,177,151,218,146,86,208,483,145,161,206,265,118,115,116,239,204,151,395,131,120,146,141,357,212,88,162,110,156,273,89,295,604,390,136,81,272,147,168,715,305,114,200,273,232,222,141,153,133,107,205,106,137,356,199,163,345,100,79,98,259,163,186,99,355,85,121,99,123,162,174,91,111,148, 129,280,406,617,814,946,1083,1185,1493,1641,1879,2000,2166,2489,2658,2772,2912,3021,3223,3435,3634,4019,4104,4180,4324,4414,4610,4794,4890,5040,5208,5469,5553,5724,5940,6142,6266,6479,6566,6776,7016,7381,7638,7920,8100,8547,9109,9257,9422,9629,9902,10021,10138,10255,10531,10736,10891,11287,11445,11570,11717,11925,12283,12531,12620,12844,12961,13118,13392,13482,13885,14490,14881,15029,15111,15384,15579,15748,16464,16849,16964,17165,17495,17728,17951,18093,18247,18383,18491,18731,18842,18982,19339,19568,19732,20078,20179,20351,20452,20712,20942,21129,21229,21601,21710,21832,21932,22080,22247,22422,22514,22626, 25,1,90,80,18,26,6,141,1,33,8,62,14,43,1,23,1,1,1,49,1,1,1,1,1,75,1,20,12,2,104,1,71,45,64,1,134,4,49,63,214,39,136,94,239,79,3,4,1,8,1,2,1,37,1,4,1,27,5,1,67,1,36,1,62,7,1,1,1,108,1,1,12,1,1,48,1,1,80,1,1,57,1,1,1,1,3,1,35,5,3,1,30,1,1,1,93,3,1,67,1,1,17,24,1,1,25,5,1,1,1,54, 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3,4,49,103,129,135,153,194,280,406,427,450,459,495,534,617,619,635,679,696,814,831,882,946,971,1083,1088,1185,1206,1239,1246,1257,1266,1283,1325,1493,1545,1641,1660,1673,1879,1886,2000,2004,2050,2061,2166,2179,2489,2531,2582,2658,2705,2713,2772,2794,2912,3021,3223,3435,3450,3483,3522,3634,4019,4104,4180,4266,4324,4414,4436,4461,4471,4488,4526,4610,4794,4811,4813,4890,4897,4901,5040,5041,5208,5211,5229,5234,5241,5311,5469,5553,5572,5604,5619,5623,5724,5728,5735,5757,5768,5940,6003,6142,6190,6205,6266,6276,6310,6333,6335,6397,6399,6479,6482,6566,6576,6579,6606,6607,6610,6614,6776,6810,6811,6836,6838,7016,7035,7041,7066,7112,7119,7146,7157,7162,7166,7221,7228,7229,7335,7381,7384,7386,7389,7410,7412,7419,7638,7679,7681,7690,7713,7744,7762,7770,7772,7773,7825,7920,7922,7969,7984,8006,8013,8100,8102,8134,8170,8184,8186,8192,8194,8197,8215,8222,8223,8228,8232,8278,8285,8287,8289,8305,8308,8313,8321,8325,8327,8338,8547,8557,8625,9109,9111,9257,9260,9309,9422,9629,9633,9636,9902,10021,10022,10138,10255,10256,10257,10291,10531,10736,10739,10816,10891,11287,11292,11296,11313,11407,11445,11449,11479,11570,11717,11722,11728,11783,11925,12283,12317,12318,12531,12620,12641,12681,12844,12850,12874,12944,12961,13118,13392,13482,13496,13547,13554,13574,13589,13885,14490,14881,14892,15029,15111,15384,15431,15579,15748,16464,16480,16481,16487,16491,16496,16499,16543,16849,16964,17165,17221,17495,17728,17951,17984,18093,18131,18215,18247,18249,18297,18383,18448,18491,18498,18501,18516,18525,18731,18735,18842,18844,18883,18951,18982,19339,19355,19368,19568,19732,20078,20138,20176,20179,20182,20255,20257,20271,20351,20353,20452,20712,20727,20733,20745,20749,20778,20942,21129,21229,21245,21601,21624,21710,21832,21932,21953,21956,21987,22052,22080,22084,22200,22247,22422,22514,22533,22603,22626,22642,22657,22679,22780,22828,22836,22850,22865,22875,22903,22942,22960,22978,22979,22981, -chr19 47496027 47511981 m84008_230107_003043_s1/182523563/ccs 166,336,571,741,942,1143,1321,1516,1693,1890,2096,2249,2418,2641,2837,3034,3236,3400,3593,3763,3929,4110,4335,4485,4722,4923,5107,5292,5467,5646,5807,6006,6200,6391,6594,6784,7004,7142,7350,7535,7704,7864,8049,8218,8353,8432,8573,9055,9403,9606,9954,10114,10304,10503,10686,10860,11044,11221,11456,11673,11835,12039,12255,12405,12584,12794,12950,13098,13494,13685,13849,14073,14226,14464,14614,14830,15015,15219,15423,15651, 119,153,99,110,108,105,129,109,123,127,130,152,164,160,156,130,136,149,127,101,155,173,132,189,144,94,184,144,141,129,175,149,187,172,156,157,113,140,145,107,127,109,119,108,78,100,481,314,153,297,130,142,133,136,125,142,143,137,115,113,124,137,89,137,146,128,147,334,151,121,150,139,200,119,190,151,176,133,153,120, 83,285,489,670,851,1050,1248,1450,1625,1816,2017,2226,2401,2582,2801,2993,3164,3372,3549,3720,3864,4084,4283,4467,4674,4866,5017,5291,5436,5608,5775,5982,6155,6387,6563,6750,6941,7117,7282,7495,7642,7831,7973,8168,8326,8431,8532,9054,9369,9556,9903,10084,10256,10437,10639,10811,11002,11187,11358,11571,11786,11959,12176,12344,12542,12730,12922,13097,13432,13645,13806,13999,14212,14426,14583,14804,14981,15191,15352,15576,15771, 83,51,82,71,91,93,73,66,68,74,79,23,17,59,36,41,72,28,44,43,65,26,52,18,48,57,90,1,31,38,32,24,45,4,31,34,63,25,68,40,62,33,76,50,27,1,41,1,34,50,51,30,48,66,47,49,42,34,98,102,49,80,79,61,42,64,28,1,62,40,43,74,14,38,31,26,34,28,71,75,86, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 82,91,97,100,112,117,127,131,134,140,149,156,158,160,165,285,286,290,294,301,303,308,309,312,313,316,322,326,328,335,364,489,498,503,521,525,532,536,538,543,545,550,551,556,558,570,670,673,675,684,686,690,695,696,700,707,717,722,726,729,732,734,736,740,851,862,865,875,882,888,901,904,906,908,910,916,919,927,931,935,939,941,1050,1056,1077,1081,1084,1086,1089,1091,1094,1097,1100,1103,1105,1110,1112,1123,1135,1142,1248,1251,1256,1260,1263,1267,1272,1275,1278,1285,1291,1294,1298,1300,1304,1306,1309,1312,1320,1450,1463,1466,1471,1475,1477,1479,1482,1484,1490,1495,1497,1502,1515,1625,1637,1644,1645,1652,1656,1675,1676,1692,1774,1816,1826,1829,1834,1837,1838,1840,1862,1866,1867,1869,1871,1887,1889,1981,2017,2023,2034,2037,2042,2046,2048,2052,2054,2058,2060,2063,2066,2071,2076,2078,2095,2226,2229,2233,2243,2248,2401,2409,2410,2415,2417,2468,2582,2587,2606,2608,2617,2622,2623,2629,2630,2633,2640,2677,2801,2807,2813,2817,2819,2836,2993,2997,2998,3000,3004,3030,3033,3164,3170,3174,3187,3190,3195,3200,3202,3217,3223,3225,3235,3372,3387,3391,3393,3398,3399,3549,3556,3559,3564,3577,3581,3584,3586,3592,3720,3731,3734,3736,3740,3755,3762,3864,3866,3898,3904,3906,3928,4046,4084,4109,4283,4285,4301,4305,4307,4322,4334,4467,4480,4484,4674,4677,4680,4686,4689,4691,4712,4721,4866,4868,4872,4877,4878,4881,4883,4885,4888,4890,4893,4897,4900,4915,4922,5017,5041,5045,5047,5070,5073,5082,5085,5088,5090,5091,5092,5093,5095,5096,5103,5106,5291,5436,5438,5439,5445,5446,5449,5457,5463,5466,5574,5608,5610,5611,5614,5615,5618,5620,5623,5626,5633,5637,5639,5642,5645,5775,5780,5803,5806,5982,5990,5997,6003,6005,6155,6170,6175,6177,6180,6184,6189,6191,6193,6197,6199,6387,6390,6563,6565,6567,6569,6585,6593,6750,6758,6763,6765,6768,6775,6783,6941,6948,6951,6958,6963,6972,6974,6977,6979,6984,6989,7003,7117,7119,7128,7131,7135,7138,7141,7282,7309,7320,7325,7327,7329,7331,7337,7340,7349,7495,7497,7531,7534,7642,7646,7650,7675,7678,7688,7690,7692,7703,7802,7831,7833,7844,7847,7853,7856,7861,7863,7973,7989,7991,7993,8012,8013,8016,8040,8048,8168,8184,8190,8194,8204,8217,8326,8344,8348,8352,8431,8532,8537,8554,8556,8572,9054,9369,9387,9389,9394,9402,9556,9567,9569,9571,9578,9589,9591,9595,9601,9605,9903,9907,9915,9917,9921,9926,9927,9929,9953,10084,10089,10104,10108,10113,10256,10263,10296,10298,10303,10390,10437,10447,10463,10476,10482,10488,10493,10496,10502,10639,10665,10685,10811,10814,10817,10819,10830,10854,10856,10859,11002,11008,11014,11017,11019,11022,11030,11038,11043,11187,11189,11197,11199,11201,11207,11210,11217,11220,11358,11368,11385,11393,11395,11397,11401,11404,11412,11414,11418,11421,11424,11430,11439,11455,11571,11575,11578,11582,11585,11589,11591,11593,11602,11604,11607,11608,11618,11621,11625,11627,11629,11631,11636,11645,11651,11666,11672,11786,11790,11796,11798,11800,11802,11817,11821,11830,11834,11870,11959,11962,11965,11988,11991,11993,12004,12008,12012,12016,12019,12038,12176,12180,12182,12185,12192,12195,12199,12228,12231,12234,12237,12239,12241,12243,12254,12344,12363,12370,12376,12380,12383,12394,12396,12401,12404,12542,12544,12545,12548,12552,12557,12562,12564,12567,12572,12574,12575,12581,12583,12730,12734,12740,12741,12747,12763,12764,12766,12768,12773,12775,12793,12840,12922,12933,12934,12939,12944,12946,12949,13097,13432,13440,13442,13443,13446,13449,13453,13454,13456,13464,13467,13472,13493,13645,13647,13661,13668,13675,13677,13680,13684,13806,13815,13820,13833,13835,13837,13841,13848,13999,14001,14011,14015,14017,14020,14026,14028,14030,14036,14038,14040,14072,14212,14215,14217,14222,14225,14426,14431,14441,14463,14583,14605,14606,14608,14613,14804,14807,14819,14829,14981,14988,14990,15011,15014,15191,15195,15209,15211,15212,15216,15218,15257,15352,15356,15362,15371,15374,15377,15379,15382,15385,15387,15391,15397,15409,15416,15419,15422,15576,15582,15586,15588,15590,15591,15595,15597,15601,15606,15627,15644,15650,15771,15773,15777,15780,15791,15794,15815,15828,15833,15845,15853,15856, -chr19 47496290 47515520 m84008_230107_003043_s1/206769025/ccs 167,370,561,792,965,1372,1562,1752,1953,2160,2416,2606,2780,2984,3185,3375,3527,3726,3956,4119,4332,4507,4707,4911,5070,5290,5456,5636,5848,6034,6212,6409,6595,6766,6939,7092,7339,7518,7701,7868,8054,8238,8439,8609,8781,8983,9161,9350,9572,9755,9996,10143,10310,10535,10727,10907,11110,11310,11461,11661,11857,12064,12225,12523,12720,12889,13066,13258,13461,13628,13820,14016,14206,14382,14541,14769,14986,15158,15400,15605,15792,15979,16079,16344,16559,16730,16932,17117,17336,17489,17680,17828,18027,18324,18540, 161,141,152,131,123,122,111,140,107,118,118,119,147,120,122,104,166,150,98,125,152,179,151,139,142,112,143,186,172,177,190,138,134,158,152,168,165,137,130,127,136,138,150,136,166,142,183,144,124,155,146,141,189,170,156,141,151,150,133,135,155,114,276,136,127,169,147,124,107,165,136,146,175,158,148,167,100,122,108,101,110,82,175,149,138,108,146,131,98,119,139,138,208,118,97, 129,328,511,713,923,1088,1494,1673,1892,2060,2278,2534,2725,2927,3104,3307,3479,3693,3876,4054,4244,4484,4686,4858,5050,5212,5402,5599,5822,6020,6211,6402,6547,6729,6924,7091,7260,7504,7655,7831,7995,8190,8376,8589,8745,8947,9125,9344,9494,9696,9910,10142,10284,10499,10705,10883,11048,11261,11460,11594,11796,12012,12178,12501,12659,12847,13058,13213,13382,13568,13793,13956,14162,14381,14540,14689,14936,15086,15280,15508,15706,15902,16061,16254,16493,16697,16838,17078,17248,17434,17608,17819,17966,18235,18442, 38,42,50,79,42,284,68,79,61,100,138,72,55,57,81,68,48,33,80,65,88,23,21,53,20,78,54,37,26,14,1,7,48,37,15,1,79,14,46,37,59,48,63,20,36,36,36,6,78,59,86,1,26,36,22,24,62,49,1,67,61,52,47,22,61,42,8,45,79,60,27,60,44,1,1,80,50,72,120,97,86,77,18,90,66,33,94,39,88,55,72,9,61,89,98, 0,0,0,0,0,0,0,0,0,0,245,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 129,134,166,328,334,340,342,346,349,355,360,361,363,364,369,446,511,517,522,535,537,539,544,547,560,713,716,719,722,723,728,730,733,738,744,751,757,758,760,762,764,765,766,769,772,777,784,788,791,923,930,931,933,937,940,942,945,946,953,957,959,964,1088,1092,1120,1128,1133,1146,1149,1165,1168,1170,1175,1184,1246,1249,1283,1309,1318,1321,1331,1333,1358,1360,1366,1371,1494,1496,1500,1517,1518,1523,1526,1527,1529,1532,1537,1539,1561,1673,1675,1677,1682,1684,1687,1690,1694,1695,1698,1705,1707,1712,1717,1720,1722,1724,1726,1727,1729,1732,1733,1735,1739,1740,1749,1751,1847,1892,1896,1897,1899,1901,1908,1909,1911,1916,1919,1924,1931,1933,1934,1947,1952,2028,2060,2072,2076,2090,2092,2105,2111,2113,2129,2134,2135,2137,2139,2142,2143,2146,2148,2155,2157,2159,2244,2278,2281,2283,2284,2287,2310,2312,2315,2323,2326,2329,2332,2339,2341,2347,2350,2355,2358,2362,2379,2390,2403,2404,2410,2415,2534,2536,2540,2546,2561,2564,2567,2572,2575,2585,2587,2600,2603,2605,2725,2730,2732,2735,2736,2750,2751,2756,2760,2767,2771,2779,2834,2927,2932,2941,2943,2949,2962,2971,2977,2981,2983,3052,3104,3114,3119,3123,3125,3138,3139,3163,3165,3178,3183,3184,3307,3311,3314,3316,3322,3325,3328,3330,3333,3336,3337,3339,3346,3348,3359,3360,3362,3366,3374,3417,3451,3479,3493,3495,3498,3506,3510,3511,3521,3524,3526,3569,3693,3694,3701,3703,3708,3715,3717,3725,3876,3879,3892,3932,3955,4054,4072,4078,4079,4086,4087,4089,4092,4095,4099,4104,4108,4110,4114,4118,4244,4249,4261,4274,4275,4282,4286,4289,4290,4296,4301,4303,4313,4331,4484,4492,4506,4686,4688,4690,4702,4706,4858,4859,4863,4870,4881,4889,4892,4903,4910,5050,5061,5063,5069,5096,5212,5238,5258,5260,5262,5266,5271,5273,5277,5289,5402,5425,5429,5432,5435,5436,5438,5440,5446,5455,5599,5635,5822,5829,5832,5843,5847,6020,6031,6033,6211,6402,6408,6547,6549,6553,6571,6575,6576,6594,6729,6730,6732,6765,6924,6931,6934,6938,7091,7141,7260,7278,7301,7307,7311,7316,7331,7338,7504,7508,7517,7655,7661,7665,7668,7673,7680,7682,7685,7690,7693,7700,7831,7836,7838,7862,7867,7995,7998,8001,8010,8029,8038,8039,8047,8053,8190,8192,8195,8202,8212,8237,8376,8378,8384,8388,8390,8392,8394,8400,8421,8423,8438,8589,8608,8745,8757,8773,8776,8780,8947,8967,8970,8973,8982,9125,9149,9154,9160,9344,9349,9494,9497,9500,9505,9524,9529,9535,9549,9552,9558,9565,9571,9696,9698,9702,9704,9721,9743,9745,9754,9910,9915,9928,9974,9995,10142,10284,10309,10499,10501,10513,10519,10524,10529,10532,10534,10599,10705,10720,10726,10883,10906,11048,11074,11077,11078,11088,11095,11099,11105,11109,11261,11267,11271,11284,11291,11300,11309,11460,11594,11595,11598,11615,11623,11626,11628,11631,11632,11636,11637,11640,11641,11646,11647,11652,11653,11660,11796,11803,11812,11822,11830,11838,11856,12012,12015,12018,12024,12034,12039,12056,12058,12060,12063,12178,12182,12188,12195,12210,12212,12215,12221,12224,12501,12522,12659,12662,12664,12666,12669,12677,12682,12707,12710,12719,12847,12852,12854,12856,12874,12877,12884,12888,13058,13065,13213,13241,13243,13247,13252,13254,13257,13382,13389,13435,13441,13446,13454,13457,13460,13536,13568,13573,13590,13593,13595,13627,13793,13802,13819,13956,13976,13982,13985,13995,13998,14005,14010,14011,14015,14162,14174,14192,14200,14205,14381,14540,14689,14717,14718,14723,14728,14732,14735,14742,14744,14750,14756,14762,14768,14936,14938,14977,14980,14985,15032,15086,15088,15097,15102,15105,15107,15111,15114,15117,15118,15121,15124,15126,15128,15131,15134,15138,15141,15143,15153,15157,15280,15283,15292,15294,15300,15313,15315,15320,15326,15328,15331,15335,15344,15346,15347,15349,15355,15359,15361,15367,15379,15399,15508,15511,15512,15514,15520,15556,15567,15574,15579,15584,15604,15706,15717,15720,15730,15731,15737,15741,15745,15758,15765,15772,15775,15791,15902,15917,15921,15925,15927,15931,15934,15974,15978,16061,16070,16075,16078,16254,16256,16258,16265,16268,16271,16288,16290,16292,16295,16314,16329,16331,16333,16335,16337,16343,16493,16494,16496,16501,16503,16504,16507,16509,16514,16517,16524,16530,16536,16539,16540,16543,16545,16552,16556,16558,16697,16700,16705,16707,16713,16715,16722,16724,16727,16729,16838,16840,16844,16846,16847,16850,16853,16855,16858,16863,16865,16869,16871,16872,16875,16879,16890,16895,16899,16919,16921,16922,16923,16925,16929,16931,17078,17082,17091,17094,17101,17108,17109,17112,17116,17248,17253,17258,17265,17279,17288,17290,17292,17318,17320,17323,17324,17326,17328,17335,17434,17438,17444,17448,17467,17470,17488,17608,17612,17616,17620,17624,17633,17642,17645,17648,17652,17655,17677,17679,17819,17822,17827,17966,17972,17986,17992,17993,17996,17998,18001,18004,18009,18018,18026,18235,18238,18246,18248,18254,18267,18269,18271,18274,18287,18288,18294,18295,18297,18299,18305,18312,18316,18320,18322,18323,18442,18449,18453,18455,18457,18460,18461,18469,18471,18475,18479,18488,18495,18505,18507,18511,18512,18513,18533,18539,18637,18643,18645,18649,18653,18654,18656,18660,18679,18682,18684,18686,18695,18706,18710,18713,18720,18731,18735,18736,18747,18763,18769,18782,18784,18818,18837,18839,18841,18846,18853,18854,18861,18866,18868,18878,18884,18886,18887,18895,18896,18903,18917,18922,18924,18927,18930,18935,18942,18948,18950,18953,18958,18959,18967,18978,18990,18994,18996,19000,19003,19006,19013,19016,19020,19021,19023,19026,19029,19034,19039,19045,19057,19082,19084,19093,19098,19109,19113,19120,19123,19141,19145,19147,19149,19150,19152,19162, -chr19 47496312 47517829 m64076_221119_202646/144639565/ccs 222,428,646,777,1050,1231,1418,1601,1794,1974,2182,2373,2568,2734,2918,3095,3275,3417,3622,3818,3997,4197,4328,5245,5468,5586,5758,5923,6130,6283,6478,6802,7190,7331,7540,7746,7906,8077,8262,8444,8638,8836,9019,9219,9350,9532,9715,9907,10060,10284,10457,10669,10863,11062,11232,11413,11589,11783,11977,12123,12302,12483,12661,12845,13137,13318,13492,13672,13888,14061,14255,14460,14766,14974,15198,15389,15603,15771,15935,16108,16350,16522,16644,16863,17014,17166,17357,17579,17871,18043,18354,18500,19382,19559,19719,19910,20085,20266,20448,20651,20852,20999,21169, 157,99,130,127,93,116,113,127,147,121,132,127,103,126,79,121,137,177,166,133,118,130,912,141,117,110,114,158,111,142,285,330,140,166,145,129,138,161,155,139,132,132,113,91,143,163,144,138,159,149,146,131,138,122,147,165,167,140,135,137,163,129,145,284,144,134,141,125,151,134,149,295,166,148,131,148,140,140,159,124,161,111,140,129,151,146,185,291,135,285,145,112,132,140,127,127,128,136,156,144,146,105,138, 165,379,527,776,904,1143,1347,1531,1728,1941,2095,2314,2500,2671,2860,2997,3216,3412,3594,3788,3951,4115,4327,5240,5386,5585,5696,5872,6081,6241,6425,6763,7132,7330,7497,7685,7875,8044,8238,8417,8583,8770,8968,9132,9310,9493,9695,9859,10045,10219,10433,10603,10800,11001,11184,11379,11578,11756,11923,12112,12260,12465,12612,12806,13129,13281,13452,13633,13797,14039,14195,14404,14755,14932,15122,15329,15537,15743,15911,16094,16232,16511,16633,16784,16992,17165,17312,17542,17870,18006,18328,18499,18612,19514,19699,19846,20037,20213,20402,20604,20795,20998,21104,21307, 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16,23,24,34,165,175,185,188,191,193,198,200,203,208,217,221,379,384,387,389,398,404,409,410,414,416,423,427,527,530,535,540,554,560,565,568,582,584,589,590,595,596,600,602,604,606,609,612,613,615,618,620,622,641,643,645,776,812,838,904,918,921,923,927,930,934,938,940,945,955,960,963,966,990,997,1000,1006,1009,1013,1015,1019,1021,1024,1027,1035,1040,1049,1143,1146,1149,1151,1156,1160,1162,1165,1169,1172,1175,1178,1186,1190,1194,1195,1197,1199,1205,1210,1212,1217,1219,1222,1230,1347,1352,1359,1367,1369,1371,1373,1376,1380,1384,1390,1396,1398,1399,1417,1531,1535,1536,1541,1544,1549,1552,1555,1561,1567,1574,1577,1581,1584,1586,1600,1728,1732,1734,1738,1745,1749,1752,1761,1763,1767,1769,1773,1793,1941,1944,1947,1958,1966,1973,2095,2097,2103,2116,2124,2125,2128,2132,2137,2141,2143,2146,2147,2154,2164,2172,2177,2181,2314,2316,2329,2332,2337,2340,2344,2345,2348,2351,2355,2357,2361,2372,2500,2516,2522,2525,2528,2538,2539,2543,2546,2548,2549,2551,2567,2642,2671,2677,2688,2690,2700,2708,2715,2716,2719,2721,2725,2733,2787,2860,2864,2869,2872,2879,2881,2885,2889,2895,2897,2902,2908,2915,2917,2997,3004,3007,3030,3032,3047,3050,3054,3058,3062,3065,3067,3068,3071,3072,3073,3077,3094,3216,3217,3223,3229,3238,3241,3244,3250,3252,3264,3274,3412,3416,3594,3597,3601,3613,3619,3621,3788,3791,3795,3797,3800,3817,3951,3953,3962,3968,3969,3975,3980,3985,3996,4115,4132,4133,4137,4138,4140,4147,4150,4152,4156,4158,4169,4173,4175,4177,4179,4183,4189,4196,4327,5240,5244,5327,5386,5388,5398,5405,5415,5418,5422,5449,5452,5467,5540,5585,5696,5706,5715,5720,5722,5723,5726,5728,5732,5735,5738,5744,5755,5757,5872,5876,5877,5879,5880,5887,5889,5892,5894,5901,5906,5908,5910,5914,5916,5918,5920,5922,6081,6084,6086,6106,6127,6129,6241,6245,6249,6253,6256,6260,6263,6266,6269,6274,6276,6279,6282,6397,6425,6429,6432,6436,6437,6439,6441,6442,6444,6447,6451,6457,6462,6463,6469,6472,6477,6763,6777,6779,6783,6801,7132,7142,7147,7162,7163,7167,7170,7180,7181,7187,7189,7330,7452,7497,7501,7510,7512,7516,7520,7539,7631,7685,7687,7690,7692,7706,7725,7745,7875,7884,7892,7897,7898,7899,7900,7905,8044,8051,8076,8238,8240,8256,8261,8417,8421,8423,8425,8427,8429,8443,8583,8587,8589,8600,8602,8606,8612,8632,8637,8679,8770,8795,8797,8799,8816,8829,8835,8968,8977,8981,8982,8986,8988,8992,8994,8996,9001,9018,9132,9139,9145,9147,9148,9153,9156,9159,9164,9173,9175,9179,9185,9187,9193,9205,9218,9310,9316,9318,9322,9330,9334,9337,9341,9342,9344,9346,9347,9349,9493,9504,9508,9510,9515,9517,9523,9525,9528,9530,9531,9599,9695,9697,9701,9709,9714,9859,9862,9872,9886,9890,9893,9895,9901,9906,10045,10049,10052,10054,10055,10059,10099,10219,10225,10227,10238,10242,10246,10250,10266,10283,10433,10438,10453,10456,10603,10610,10612,10618,10619,10625,10632,10633,10638,10642,10655,10668,10800,10824,10829,10834,10838,10844,10862,11001,11007,11010,11019,11020,11024,11026,11027,11031,11034,11040,11046,11061,11184,11192,11206,11208,11214,11215,11218,11220,11222,11227,11231,11379,11382,11384,11387,11390,11405,11412,11578,11580,11588,11756,11760,11763,11775,11777,11782,11923,11938,11941,11946,11955,11959,11961,11964,11972,11976,12112,12114,12122,12260,12266,12280,12282,12285,12292,12295,12299,12301,12465,12482,12612,12616,12624,12626,12631,12632,12634,12636,12640,12646,12652,12655,12660,12806,12808,12814,12816,12819,12826,12827,12833,12834,12835,12837,12841,12844,13129,13136,13281,13285,13291,13294,13300,13304,13308,13317,13452,13464,13466,13471,13473,13475,13491,13633,13635,13648,13650,13666,13671,13797,13799,13801,13803,13807,13810,13814,13819,13821,13826,13827,13842,13845,13849,13851,13854,13856,13859,13860,13866,13868,13880,13887,14039,14045,14047,14060,14195,14198,14200,14204,14205,14207,14211,14214,14217,14238,14240,14242,14246,14248,14249,14254,14404,14405,14411,14414,14416,14418,14422,14425,14429,14432,14435,14441,14443,14447,14452,14459,14755,14763,14765,14932,14943,14947,14973,15122,15124,15125,15130,15132,15135,15138,15148,15169,15170,15174,15197,15329,15338,15343,15345,15346,15348,15352,15358,15360,15366,15376,15378,15383,15384,15386,15388,15419,15537,15544,15549,15551,15553,15555,15561,15563,15566,15569,15572,15575,15577,15602,15743,15752,15757,15760,15770,15911,15913,15918,15920,15921,15923,15934,16094,16100,16107,16232,16238,16244,16248,16254,16258,16260,16267,16271,16274,16277,16290,16291,16292,16294,16296,16299,16301,16307,16308,16310,16315,16318,16335,16337,16341,16345,16347,16349,16511,16513,16521,16633,16635,16643,16685,16784,16799,16804,16813,16819,16821,16825,16826,16828,16831,16832,16835,16842,16844,16848,16850,16851,16854,16857,16859,16862,16937,16992,16993,16998,17000,17013,17139,17165,17312,17324,17327,17332,17334,17336,17338,17339,17346,17349,17356,17542,17544,17546,17548,17550,17554,17556,17558,17564,17573,17578,17870,18006,18009,18023,18037,18042,18328,18340,18353,18499,18612,18620,18623,18624,18628,18630,18643,18645,18649,18655,18659,18660,18662,18664,18666,18685,18686,18688,18690,18692,18693,18697,18701,18712,18716,18717,18722,18726,18737,18741,18742,18803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-chr19 47496383 47518082 m54329U_210813_020940/178063722/ccs 78,257,495,630,817,1001,1194,1372,1613,1835,2062,2206,2407,2540,2761,2969,3175,3359,3529,3731,3883,4127,4321,4501,4692,4900,5117,5278,5493,5659,5847,6066,6272,6420,6646,6847,7016,7210,7370,7547,7770,7935,8134,8319,8531,8717,8918,9101,9291,9483,9651,9836,10022,10106,10214,10443,10645,10879,11067,11230,11427,11628,11755,12009,12400,12697,12874,13073,13278,13439,13619,13804,13991,14183,14410,14626,14809,15015,15213,15442,15609,15786,15971,16155,16358,16545,16687,16889,17049,17220,17403,17572,17762,17938,18096,18247,18489,19216,19414,19586,19788,19963,20134,20303,20487,20680,20848,21032, 145,166,126,159,152,145,146,168,131,111,82,155,113,153,144,138,124,150,154,137,199,160,153,178,139,135,120,156,145,135,184,141,147,158,173,155,174,157,145,170,139,169,121,144,177,172,135,150,139,135,132,171,83,83,156,116,136,96,118,99,121,126,126,277,251,148,171,133,151,122,143,156,191,179,153,123,113,134,137,104,131,169,160,175,132,109,138,117,148,125,141,161,153,150,111,136,102,119,120,135,142,151,147,137,157,145,169,168, 223,423,621,789,969,1146,1340,1540,1744,1946,2144,2361,2520,2693,2905,3107,3299,3509,3683,3868,4082,4287,4474,4679,4831,5035,5237,5434,5638,5794,6031,6207,6419,6578,6819,7002,7190,7367,7515,7717,7909,8104,8255,8463,8708,8889,9053,9251,9430,9618,9783,10007,10105,10189,10370,10559,10781,10975,11185,11329,11548,11754,11881,12286,12651,12845,13045,13206,13429,13561,13762,13960,14182,14362,14563,14749,14922,15149,15350,15546,15740,15955,16131,16330,16490,16654,16825,17006,17197,17345,17544,17733,17915,18088,18207,18383,18591,19335,19534,19721,19930,20114,20281,20440,20644,20825,21017,21200, 34,72,9,28,32,48,32,73,91,116,62,46,20,68,64,68,60,20,48,15,45,34,27,13,69,82,41,59,21,53,35,65,1,68,28,14,20,3,32,53,26,30,64,68,9,29,48,40,53,33,53,15,1,25,73,86,98,92,45,98,80,1,128,114,46,29,28,72,10,58,42,31,1,48,63,60,93,64,92,63,46,16,24,28,55,33,64,43,23,58,28,29,23,8,40,106,625,79,52,67,33,20,22,47,36,23,15,36, 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-chr19 47498629 47511783 m54329U_210326_192251/74844661/ccs 206,364,553,721,900,1060,1271,1436,1622,1766,1952,2120,2292,2484,2689,2876,3050,3233,3417,3604,3792,3976,4185,4303,4516,4866,5046,5224,5550,5715,5868,6071,6221,6396,6564,6743,6906,7077,7305,7434,7655,7831,7999,8199,8385,8604,8803,8960,9141,9340,9525,9703,10080,10250,10433,10591,10777,10966,11141,11293,11508,11707,11897,12163,12320,12496,12707,12873, 128,136,124,142,148,177,120,158,143,156,144,161,151,164,137,115,154,138,143,162,142,150,117,142,291,151,148,298,132,150,156,145,139,138,127,122,123,133,80,153,139,127,179,170,133,134,115,149,145,134,130,321,137,170,157,143,102,143,147,138,156,105,148,75,133,135,141,134, 136,334,500,677,863,1048,1237,1391,1594,1765,1922,2096,2281,2443,2648,2826,2991,3204,3371,3560,3766,3934,4126,4302,4445,4807,5017,5194,5522,5682,5865,6024,6216,6360,6534,6691,6865,7029,7210,7385,7587,7794,7958,8178,8369,8518,8738,8918,9109,9286,9474,9655,10024,10217,10420,10590,10734,10879,11109,11288,11431,11664,11812,12045,12238,12453,12631,12848,13007, 70,30,53,44,37,12,34,45,28,1,30,24,11,41,41,50,59,29,46,44,26,42,59,1,71,59,29,30,28,33,3,47,5,36,30,52,41,48,95,49,68,37,41,21,16,86,65,42,32,54,51,48,56,33,13,1,43,87,32,5,77,43,85,118,82,43,76,25,24, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,243,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,243,0,0,0,0,0, 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-chr19 47498655 47517467 m64076_210328_012155/132450463/ccs 112,270,455,648,877,1036,1214,1417,1628,1792,1975,2187,2368,2557,2768,2969,3168,3391,3581,3798,3981,4221,4422,4646,4848,5029,5238,5420,5603,5795,5967,6150,6356,6543,6708,6913,7080,7273,7474,7676,7973,8214,8360,8588,8783,8971,9121,9304,9586,9736,9934,10115,10289,10492,10619,10830,11101,11264,11487,11706,11907,12102,12323,12515,12717,12886,13104,13320,13501,13737,13937,14111,14330,14539,14723,14960,15155,15383,16002,16207,16580,17010,17190,17334,17560,17747,17897,18084,18245,18422,18559, 151,128,110,113,99,177,136,163,144,140,150,117,151,142,134,130,141,96,123,116,139,142,131,146,129,139,136,145,111,171,160,147,132,142,131,139,137,144,143,115,101,87,137,128,121,75,117,117,88,116,127,162,148,126,169,136,107,117,94,139,123,131,117,143,135,132,129,120,113,90,122,122,121,112,138,102,159,579,114,97,110,131,136,174,110,121,138,111,130,114,122, 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-chr19 47498684 47513031 m84039_230401_031619_s3/78972603/ccs 108,310,494,656,1093,1274,1460,1691,1849,2056,2682,2937,3076,3263,3454,3797,4023,4170,4343,4521,4723,4887,5082,5283,5445,5629,5787,5972,6162,6373,6539,6732,6911,7137,7299,7561,7731,7855,8061,8250,8616,8776,8971,9148,9354,9551,9913,10063,10256,10424,10593,11450,11639,11848,12063,12254,12387,12809,12996,13536,13760,13982, 94,109,108,132,101,104,137,92,135,125,93,77,126,120,136,140,110,125,139,123,116,86,115,129,101,125,137,120,116,118,113,86,130,82,141,79,95,113,105,108,101,118,78,93,82,131,110,136,121,116,115,75,113,81,102,81,135,140,112,112,108,98, 202,419,602,788,1194,1378,1597,1783,1984,2181,2775,3014,3202,3383,3590,3937,4133,4295,4482,4644,4839,4973,5197,5412,5546,5754,5924,6092,6278,6491,6652,6818,7041,7219,7440,7640,7826,7968,8166,8358,8717,8894,9049,9241,9436,9682,10023,10199,10377,10540,10708,11525,11752,11929,12165,12335,12522,12949,13108,13648,13868,14080, 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-chr19 47499085 47514363 m54329U_210326_192251/105579375/ccs 206,421,608,823,1061,1168,1329,1489,1653,1855,2065,2210,2427,2633,2830,3031,3170,3392,3601,3770,3924,4113,4365,4479,4758,4898,5086,5433,5650,5813,6027,6235,6409,6563,6768,6940,7133,7351,7555,7760,7966,8159,8351,8548,8693,8918,9074,9270,9446,9699,9887,10066,10201,10414,10574,10785,10963,11180,11354,11550,11741,11937,12129,12316,12481,12713,12860,13232,13468,13651,13856,14078,14228,14351,14528,14700,14857,15050,15184, 129,127,132,127,76,160,93,141,123,138,106,103,121,128,131,92,150,153,106,135,162,166,108,107,80,119,122,137,125,135,92,121,148,164,124,143,157,140,167,137,132,152,89,136,156,112,139,158,101,125,127,126,170,126,180,144,159,148,175,102,145,154,156,142,149,140,152,128,131,142,138,101,122,141,127,90,111,107,147, 134,335,548,740,950,1137,1328,1422,1630,1776,1993,2171,2313,2548,2761,2961,3123,3320,3545,3707,3905,4086,4279,4473,4586,4838,5017,5208,5570,5775,5948,6119,6356,6557,6727,6892,7083,7290,7491,7722,7897,8098,8311,8440,8684,8849,9030,9213,9428,9547,9824,10014,10192,10371,10540,10754,10929,11122,11328,11529,11652,11886,12091,12285,12458,12630,12853,13012,13360,13599,13793,13994,14179,14350,14492,14655,14790,14968,15157,15331, 72,86,60,83,111,31,1,67,23,79,72,39,114,85,69,70,47,72,56,63,19,27,86,6,172,60,69,225,80,38,79,116,53,6,41,48,50,61,64,38,69,61,40,108,9,69,44,57,18,152,63,52,9,43,34,31,34,58,26,21,89,51,38,31,23,83,7,220,108,52,63,84,49,1,36,45,67,82,27,25, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,242,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 134,135,139,145,147,150,156,160,161,167,171,175,176,181,185,191,193,205,335,336,343,347,349,352,354,355,359,375,379,381,385,389,394,396,397,400,401,404,407,415,420,548,551,554,555,557,564,578,580,583,586,589,600,601,604,607,714,740,743,759,761,765,767,771,801,802,805,806,813,815,817,820,822,863,950,955,965,969,975,994,997,1000,1024,1055,1056,1060,1137,1150,1156,1163,1167,1232,1328,1422,1434,1445,1485,1488,1542,1630,1632,1635,1652,1776,1796,1797,1799,1801,1804,1807,1811,1813,1816,1818,1822,1827,1829,1844,1846,1849,1851,1854,1993,1999,2005,2006,2008,2019,2028,2061,2064,2171,2174,2177,2180,2185,2186,2201,2203,2209,2313,2315,2344,2350,2352,2372,2376,2377,2381,2387,2392,2393,2396,2398,2399,2403,2409,2410,2412,2423,2425,2426,2548,2551,2562,2569,2571,2572,2576,2579,2581,2584,2587,2589,2594,2598,2600,2603,2604,2606,2608,2612,2616,2617,2621,2622,2625,2630,2632,2761,2768,2770,2773,2776,2784,2793,2796,2814,2816,2817,2818,2829,2861,2961,2966,2968,2972,2974,2977,2984,2987,2999,3001,3003,3005,3007,3030,3123,3126,3127,3134,3136,3139,3141,3153,3155,3157,3160,3161,3163,3165,3167,3169,3215,3218,3283,3320,3381,3388,3391,3545,3549,3552,3556,3558,3560,3563,3567,3569,3571,3572,3596,3597,3600,3707,3713,3719,3737,3740,3744,3747,3759,3761,3763,3769,3832,3905,3909,3920,3923,4086,4089,4091,4094,4097,4100,4103,4107,4110,4112,4279,4280,4285,4286,4289,4291,4302,4304,4306,4310,4329,4334,4341,4364,4473,4475,4477,4478,4509,4512,4586,4588,4640,4642,4645,4648,4675,4679,4682,4686,4706,4707,4753,4757,4838,4843,4849,4851,4860,4865,4866,4870,4872,4876,4887,4897,5017,5027,5032,5033,5039,5057,5062,5066,5068,5071,5074,5075,5078,5082,5085,5208,5210,5212,5213,5216,5219,5230,5233,5237,5240,5243,5245,5249,5251,5316,5346,5350,5378,5382,5402,5404,5407,5422,5425,5432,5570,5571,5576,5581,5582,5585,5595,5597,5610,5612,5614,5617,5633,5635,5639,5645,5647,5649,5775,5778,5788,5791,5793,5795,5796,5798,5800,5808,5811,5812,5948,5954,5968,5972,5995,5998,6002,6026,6119,6136,6143,6149,6152,6154,6163,6169,6171,6174,6178,6183,6187,6190,6192,6194,6210,6213,6227,6234,6356,6363,6364,6368,6371,6372,6373,6376,6377,6382,6384,6387,6394,6398,6404,6408,6557,6562,6727,6729,6732,6736,6744,6750,6751,6754,6755,6756,6759,6761,6767,6892,6898,6901,6907,6911,6919,6925,6930,6931,6938,6939,7033,7083,7102,7105,7109,7110,7112,7114,7119,7128,7132,7206,7290,7294,7304,7311,7328,7330,7334,7340,7345,7346,7350,7406,7491,7508,7512,7517,7519,7521,7532,7534,7538,7541,7542,7551,7554,7722,7726,7727,7732,7738,7747,7759,7793,7897,7927,7932,7933,7934,7936,7939,7943,7944,7949,7961,7965,8098,8102,8107,8108,8119,8133,8158,8311,8314,8318,8320,8321,8325,8327,8328,8332,8335,8341,8347,8348,8350,8440,8446,8504,8509,8519,8523,8528,8530,8547,8684,8686,8689,8690,8692,8849,8854,8857,8858,8864,8869,8870,8877,8880,8890,8897,8917,9030,9034,9054,9058,9061,9068,9073,9213,9220,9228,9245,9248,9258,9265,9269,9428,9438,9445,9547,9567,9568,9571,9573,9591,9593,9596,9630,9632,9633,9646,9648,9651,9655,9657,9680,9682,9683,9688,9690,9694,9696,9698,9824,9840,9846,9847,9850,9853,9886,10014,10029,10031,10036,10039,10059,10063,10065,10192,10200,10371,10373,10375,10377,10380,10404,10407,10410,10413,10451,10540,10558,10560,10563,10564,10568,10570,10573,10754,10757,10759,10762,10765,10776,10779,10784,10892,10929,10935,10937,10939,10942,10948,10954,10955,10960,10962,11122,11127,11140,11144,11149,11179,11328,11353,11529,11538,11540,11546,11549,11582,11652,11654,11703,11706,11709,11722,11727,11731,11733,11735,11739,11740,11886,11891,11894,11895,11897,11901,11913,11916,11923,11927,11930,11936,12091,12093,12095,12097,12103,12105,12118,12123,12128,12241,12285,12289,12312,12315,12458,12475,12477,12480,12630,12643,12647,12649,12652,12656,12658,12661,12662,12663,12667,12669,12671,12672,12674,12683,12688,12691,12704,12706,12712,12853,12856,12857,12859,12934,13012,13018,13021,13023,13030,13033,13035,13040,13046,13056,13059,13061,13063,13066,13131,13134,13137,13190,13192,13199,13214,13215,13219,13221,13224,13225,13227,13231,13360,13391,13405,13409,13411,13413,13415,13422,13425,13431,13437,13440,13441,13444,13446,13450,13462,13467,13599,13607,13609,13622,13625,13628,13635,13642,13645,13650,13699,13793,13802,13805,13806,13810,13814,13817,13826,13839,13840,13847,13853,13855,13994,14001,14005,14008,14013,14025,14028,14033,14051,14054,14077,14179,14183,14184,14186,14189,14190,14193,14195,14200,14202,14206,14209,14212,14217,14224,14227,14278,14350,14492,14498,14502,14504,14506,14507,14524,14527,14655,14659,14672,14677,14679,14680,14682,14684,14687,14688,14690,14692,14696,14699,14790,14793,14794,14831,14833,14852,14853,14856,14968,14974,14977,14983,14986,14990,14994,14997,15003,15013,15016,15019,15023,15028,15032,15040,15043,15049,15157,15159,15165,15167,15174,15180,15183,15331,15338,15339,15341,15345,15347,15356, -chr19 47499130 47525626 m84008_230107_003043_s1/89002147/ccs 87,243,435,645,828,1021,1206,1409,1578,1802,1952,2119,2295,2479,2654,2734,2854,3015,3177,3329,3508,3696,3911,4081,4268,4438,4637,4813,5005,5197,5368,5542,5712,5927,6169,6342,6543,6773,6965,7157,7354,7586,7775,7931,8130,8386,8573,8785,8927,9124,9305,9476,9683,9852,10027,10376,10579,10724,10984,11129,11396,11531,11688,11853,12094,12290,12431,12653,12808,12958,13130,13282,13746,13929,14104,14290,14474,14644,14838,15000,15080,15203,15385,15511,15713,16634,17018,17164,17295,17494,17687,17832,18088,18257,18412,18604,18736,18896,19205,19358,19613,19809,20020,20244,20468,20634,20838,21000,21181,21351,21533,21741,21952,22155,22340,22563,22688,22892,23105,23310,23494,23711,23884,24088,24416,24637,24851,25003,25212,25429,25613,25854,26016,26172,26276, 127,142,131,119,115,147,122,128,113,117,131,138,151,153,79,104,116,161,148,97,118,141,107,105,151,122,118,136,138,135,125,169,161,119,123,117,119,119,145,113,126,103,127,130,171,118,136,98,165,93,136,153,118,138,289,92,111,127,127,136,98,92,143,144,116,137,144,118,124,108,110,250,125,88,128,147,123,132,119,79,122,128,113,135,106,383,145,130,151,179,144,160,103,130,134,131,145,211,108,125,76,133,123,111,101,143,102,131,98,157,177,95,121,147,135,96,173,146,150,106,134,75,123,205,152,89,89,153,144,122,137,126,152,103,93, 214,385,566,764,943,1168,1328,1537,1691,1919,2083,2257,2446,2632,2733,2838,2970,3176,3325,3426,3626,3837,4018,4186,4419,4560,4755,4949,5143,5332,5493,5711,5873,6046,6292,6459,6662,6892,7110,7270,7480,7689,7902,8061,8301,8504,8709,8883,9092,9217,9441,9629,9801,9990,10316,10468,10690,10851,11111,11265,11494,11623,11831,11997,12210,12427,12575,12771,12932,13066,13240,13532,13871,14017,14232,14437,14597,14776,14957,15079,15202,15331,15498,15646,15819,17017,17163,17294,17446,17673,17831,17992,18191,18387,18546,18735,18881,19107,19313,19483,19689,19942,20143,20355,20569,20777,20940,21131,21279,21508,21710,21836,22073,22302,22475,22659,22861,23038,23255,23416,23628,23786,24007,24293,24568,24726,24940,25156,25356,25551,25750,25980,26168,26275,26369, 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-chr19 47499206 47516044 m54329U_210813_020940/137365885/ccs 223,589,747,947,1154,1329,1529,1732,1928,2108,2283,2491,2661,2869,3032,3250,3411,3650,3832,4013,4196,4345,4550,4756,4942,5135,5310,5516,5726,5858,6096,6301,6564,6740,6876,7039,7245,7453,7643,7806,8028,8195,8700,8870,9069,9234,9413,9795,9975,10507,10682,10868,11044,11199,11388,11602,11795,11975,12212,12395,12589,12774,12945,13134,13294,13453,13870,14050,14222,14391,14550,14754,14939,15093,15262,15410,15617,16464, 100,96,150,142,111,142,138,137,151,136,147,144,176,132,183,100,139,121,110,115,148,140,131,145,147,160,136,180,116,200,135,106,112,85,121,159,132,111,128,164,117,475,141,147,99,157,148,96,291,136,129,111,123,154,157,157,137,127,87,157,93,136,149,113,158,155,125,164,147,151,128,124,138,137,127,130,106,138, 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9,13,15,17,22,24,27,30,31,33,39,43,164,168,171,173,174,184,193,195,200,203,208,209,212,214,220,222,323,329,347,363,368,370,380,382,387,389,401,402,404,406,407,412,415,429,475,478,481,483,494,497,502,511,516,517,518,522,525,527,534,536,541,542,544,547,552,555,576,580,585,588,685,687,690,692,696,704,707,719,721,725,727,739,743,746,897,905,913,925,938,946,1089,1091,1094,1096,1105,1110,1118,1124,1128,1130,1139,1153,1265,1276,1282,1284,1286,1292,1296,1307,1312,1313,1318,1320,1328,1471,1474,1478,1482,1485,1488,1492,1494,1497,1500,1503,1506,1509,1512,1514,1517,1521,1525,1528,1641,1667,1674,1676,1679,1681,1685,1690,1692,1705,1707,1709,1712,1714,1717,1721,1724,1731,1869,1871,1882,1886,1887,1891,1894,1895,1900,1906,1909,1920,1924,1927,2079,2083,2084,2088,2107,2244,2249,2251,2252,2257,2258,2261,2263,2264,2268,2274,2275,2282,2430,2436,2441,2444,2446,2449,2452,2454,2457,2459,2465,2482,2490,2635,2638,2641,2644,2649,2656,2657,2660,2837,2841,2844,2847,2860,2866,2868,3001,3006,3010,3019,3029,3031,3215,3218,3236,3238,3249,3350,3361,3362,3383,3385,3388,3391,3395,3402,3406,3410,3550,3556,3564,3566,3571,3572,3578,3581,3586,3593,3596,3598,3600,3603,3608,3611,3615,3619,3632,3634,3638,3642,3644,3649,3771,3776,3779,3781,3799,3802,3805,3814,3831,3942,3945,3953,3959,3966,3968,3977,3983,3999,4000,4005,4008,4010,4012,4128,4131,4148,4157,4159,4164,4165,4170,4174,4177,4180,4182,4185,4188,4192,4195,4344,4485,4487,4490,4493,4503,4506,4508,4513,4516,4524,4527,4531,4539,4549,4681,4700,4703,4705,4709,4715,4717,4721,4729,4732,4734,4738,4739,4742,4744,4746,4748,4751,4755,4901,4906,4910,4912,4915,4921,4922,4926,4929,4934,4939,4941,5089,5091,5098,5101,5109,5113,5117,5121,5123,5130,5134,5295,5297,5299,5309,5446,5448,5483,5485,5487,5495,5497,5499,5509,5515,5696,5700,5705,5710,5715,5725,5842,5857,6058,6065,6072,6078,6081,6084,6090,6095,6231,6245,6254,6258,6260,6261,6264,6266,6269,6272,6277,6281,6284,6286,6288,6292,6298,6300,6407,6418,6422,6424,6430,6434,6439,6442,6446,6449,6453,6454,6456,6458,6459,6461,6468,6473,6477,6478,6479,6481,6483,6497,6504,6517,6520,6521,6527,6531,6532,6535,6540,6543,6545,6546,6547,6550,6552,6553,6555,6557,6563,6676,6682,6691,6694,6696,6697,6703,6711,6714,6717,6719,6721,6723,6725,6726,6736,6739,6825,6838,6843,6845,6849,6852,6857,6864,6868,6875,6997,7001,7010,7015,7017,7020,7023,7025,7028,7031,7033,7038,7144,7198,7200,7202,7203,7206,7209,7212,7214,7217,7218,7219,7221,7224,7234,7244,7377,7394,7405,7411,7412,7417,7428,7446,7452,7564,7567,7569,7576,7580,7585,7589,7600,7609,7611,7623,7624,7629,7642,7771,7772,7783,7786,7800,7805,7970,7971,7973,7989,7993,8000,8015,8020,8025,8027,8084,8145,8168,8170,8186,8191,8194,8670,8699,8841,8845,8847,8860,8864,8867,8869,9017,9024,9028,9032,9034,9038,9057,9063,9068,9168,9175,9197,9203,9212,9223,9225,9233,9391,9393,9396,9412,9561,9563,9568,9589,9592,9593,9595,9597,9602,9604,9606,9614,9654,9703,9704,9723,9727,9743,9745,9751,9755,9757,9771,9775,9778,9791,9794,9891,9904,9906,9911,9915,9918,9931,9938,9949,9956,9957,9961,9963,9965,9970,9974,10266,10283,10285,10289,10293,10312,10315,10317,10322,10327,10332,10404,10417,10420,10421,10429,10435,10440,10442,10450,10455,10458,10461,10464,10474,10478,10481,10486,10490,10491,10506,10643,10644,10649,10662,10681,10811,10818,10820,10821,10822,10828,10830,10835,10837,10840,10841,10842,10844,10846,10849,10851,10853,10855,10857,10867,10979,10981,10984,10986,10996,11002,11003,11008,11010,11019,11030,11035,11043,11167,11168,11173,11176,11198,11273,11353,11371,11373,11387,11545,11548,11560,11565,11571,11572,11577,11578,11580,11583,11586,11592,11594,11601,11759,11764,11785,11790,11792,11794,11932,11936,11943,11946,11949,11951,11962,11967,11969,11972,11974,12102,12108,12110,12120,12130,12133,12136,12141,12143,12148,12156,12157,12160,12171,12185,12191,12206,12211,12299,12307,12316,12318,12323,12326,12332,12335,12336,12339,12340,12343,12347,12349,12352,12367,12370,12371,12377,12382,12386,12391,12394,12511,12552,12557,12561,12562,12564,12567,12570,12577,12583,12588,12682,12685,12690,12712,12724,12740,12747,12749,12757,12761,12764,12767,12773,12910,12917,12934,12937,12944,13066,13094,13097,13102,13115,13131,13133,13247,13258,13275,13290,13293,13414,13452,13608,13614,13629,13633,13634,13637,13639,13641,13649,13672,13676,13678,13751,13759,13765,13768,13793,13798,13801,13803,13805,13809,13812,13814,13820,13825,13827,13830,13833,13834,13835,13842,13844,13847,13858,13869,13929,13995,14015,14019,14022,14025,14027,14032,14034,14049,14175,14214,14221,14369,14379,14390,14542,14548,14549,14678,14693,14700,14710,14716,14722,14725,14728,14738,14742,14744,14747,14753,14878,14883,14896,14905,14907,14910,14913,14917,14938,15077,15090,15092,15230,15233,15236,15241,15243,15261,15389,15391,15409,15540,15563,15566,15570,15574,15576,15578,15581,15582,15585,15588,15590,15592,15597,15600,15616,15723,15727,15735,15737,15738,15739,15743,15747,15752,15766,15774,15775,15777,15781,15787,15800,15801,15803,15805,15807,15808,15812,15816,15831,15837,15841,15856,15918,15926,15928,15936,15939,15948,15958,15960,15962,15965,15967,16016,16017,16024,16027,16029,16031,16033,16038,16043,16045,16047,16048,16051,16053,16056,16060,16063,16065,16069,16071,16074,16075,16079,16080,16081,16085,16087,16088,16112,16116,16118,16122,16125,16128,16129,16142,16143,16145,16148,16151,16161,16167,16179,16185,16204,16206,16208,16212,16214,16216,16218,16221,16223,16228,16230,16232,16236,16239,16241,16255,16268,16270,16272,16275,16280,16283,16285,16289,16304,16307,16309,16316,16318,16320,16321,16324,16326,16328,16332,16333,16334,16341,16343,16347,16353,16354,16355,16359,16360,16362,16365,16405,16410,16412,16417,16420,16424,16426,16428,16433,16439,16449,16450,16452,16456,16458,16460,16463,16602,16610,16620,16626,16628,16635,16637,16639,16647,16651,16654,16657, -chr19 47499682 47516253 m54329U_210323_190418/100861377/ccs 142,269,474,678,852,1217,1364,1521,1687,1852,1998,2185,2369,2556,2761,2987,3142,3353,3443,3632,3821,3985,4174,4359,4543,4713,4946,5110,5340,5528,5699,5915,6080,6293,6506,6681,6869,7100,7281,7466,7610,7840,8030,8199,8381,8614,8728,8927,9213,9364,9528,9697,9852,10011,10194,10341,10533,10757,10910,11091,11261,11422,11591,11761,11942,12129,12337,12494,12648,12788,12955,13250,13399,13581,13774,14028,14160,14334,14544,14709,14883,15061,15231,15391,15753,15889,16293, 126,153,145,84,133,146,127,121,86,124,118,123,97,156,130,113,127,84,147,113,134,124,119,128,135,130,116,127,120,117,124,132,151,125,92,107,139,134,115,118,132,95,105,99,97,89,122,198,136,122,168,110,106,91,123,98,127,102,137,127,109,120,122,146,137,108,115,116,119,130,122,98,148,110,123,86,143,101,126,91,105,108,110,159,82,364,102, 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-chr19 47499852 47513988 m54329U_210323_190418/40634447/ccs 119,294,489,658,869,1050,1265,1420,1571,1724,1929,2098,2454,2606,2833,3031,3242,3389,3574,3813,3983,4193,4380,4548,4777,4962,5169,5335,5519,5690,5788,5900,6125,6300,6488,6655,6831,7026,7222,7391,7604,7802,8032,8185,8386,8578,8767,8970,9142,9273,9407,9625,9789,9974,10156,10330,10528,10713,10892,11077,11265,11422,11620,11811,11971,12200,12348,12501,12665,12841,13064,13250,13403,13588,13779,13973, 133,118,112,153,88,122,115,142,149,130,168,333,151,207,146,135,138,134,166,120,137,137,143,156,158,141,149,117,166,93,75,143,143,134,140,168,141,167,111,109,110,117,120,127,145,143,159,119,97,129,124,163,162,136,131,135,131,155,148,147,150,189,115,159,112,85,134,149,152,164,141,135,152,146,128,104, 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31,32,38,40,42,43,45,47,51,58,59,62,65,74,76,80,82,85,94,97,98,101,104,107,115,118,252,278,280,291,293,412,414,419,423,424,429,430,435,436,437,441,443,444,446,448,449,451,453,454,457,460,462,464,478,482,484,488,601,608,609,611,613,617,619,623,625,638,640,644,646,650,657,811,815,818,828,832,836,839,842,843,846,848,851,854,857,860,863,866,868,957,959,1007,1013,1015,1020,1023,1027,1029,1032,1034,1038,1045,1049,1172,1178,1190,1192,1194,1198,1204,1209,1213,1214,1215,1216,1218,1221,1222,1224,1228,1230,1231,1235,1238,1239,1240,1244,1248,1250,1253,1259,1264,1380,1382,1392,1395,1398,1401,1403,1404,1410,1412,1419,1562,1565,1568,1570,1720,1723,1854,1857,1861,1866,1867,1868,1872,1876,1879,1882,1883,1885,1887,1890,1893,1896,1899,1902,1905,1907,1910,1913,1916,1919,1924,1928,2097,2431,2432,2453,2605,2813,2815,2817,2818,2821,2822,2825,2827,2828,2829,2832,2979,2988,2992,2996,2998,3001,3003,3005,3007,3029,3030,3166,3169,3172,3176,3178,3181,3185,3186,3188,3189,3192,3195,3196,3201,3207,3209,3212,3214,3215,3217,3218,3221,3241,3380,3387,3388,3523,3532,3535,3537,3540,3543,3547,3550,3553,3555,3556,3561,3563,3566,3568,3570,3573,3740,3746,3752,3754,3758,3759,3761,3764,3766,3768,3769,3773,3776,3777,3783,3788,3790,3791,3793,3795,3797,3799,3812,3933,3937,3945,3946,3955,3959,3963,3967,3978,3982,4120,4135,4152,4154,4157,4159,4175,4182,4192,4330,4333,4336,4344,4346,4353,4377,4379,4474,4523,4526,4529,4531,4533,4537,4539,4542,4543,4545,4547,4704,4708,4710,4715,4718,4720,4723,4725,4726,4732,4737,4738,4740,4742,4771,4773,4775,4776,4935,4937,4940,4943,4957,4959,4961,5103,5108,5112,5114,5115,5121,5129,5131,5135,5136,5138,5139,5144,5147,5150,5161,5165,5168,5318,5321,5323,5325,5327,5329,5334,5452,5453,5457,5459,5463,5465,5467,5472,5478,5485,5496,5499,5502,5504,5507,5508,5513,5518,5685,5688,5689,5783,5787,5863,5867,5876,5879,5886,5890,5891,5894,5899,6043,6047,6052,6062,6064,6070,6073,6076,6078,6080,6082,6084,6085,6090,6092,6096,6101,6104,6123,6124,6268,6275,6277,6283,6287,6288,6295,6297,6299,6434,6438,6447,6455,6458,6469,6474,6475,6478,6483,6484,6487,6628,6633,6635,6644,6647,6649,6654,6823,6830,6972,6974,6975,6980,6986,6992,6997,7000,7002,7005,7007,7008,7010,7013,7017,7021,7022,7025,7193,7199,7205,7208,7210,7221,7333,7352,7356,7363,7378,7380,7383,7385,7388,7390,7500,7514,7523,7526,7531,7533,7535,7550,7554,7557,7560,7561,7564,7567,7571,7573,7574,7577,7581,7585,7591,7593,7597,7598,7603,7714,7716,7720,7722,7728,7732,7733,7734,7737,7740,7742,7744,7746,7748,7749,7755,7763,7764,7766,7768,7771,7775,7778,7782,7784,7786,7791,7792,7795,7797,7800,7801,7919,7920,7923,7928,7930,7933,7936,7938,7941,7943,7948,7949,7954,7957,7962,7963,7966,7969,7971,7976,7979,7980,7983,7989,7993,8007,8010,8014,8017,8019,8023,8027,8030,8031,8077,8152,8155,8157,8158,8161,8165,8169,8176,8181,8184,8312,8316,8320,8331,8335,8336,8338,8342,8344,8345,8348,8352,8354,8369,8373,8375,8378,8385,8531,8538,8540,8546,8553,8557,8560,8562,8564,8568,8570,8571,8574,8577,8721,8732,8736,8738,8739,8742,8744,8745,8746,8751,8756,8758,8761,8766,8926,8928,8933,8954,8957,8958,8960,8962,8969,9089,9093,9094,9097,9113,9117,9120,9121,9123,9128,9129,9132,9141,9239,9262,9265,9270,9272,9402,9406,9531,9533,9535,9537,9538,9540,9542,9544,9546,9551,9556,9558,9565,9568,9570,9571,9574,9576,9580,9584,9588,9590,9593,9596,9598,9604,9610,9614,9616,9619,9624,9788,9951,9953,9955,9959,9971,9973,10110,10113,10115,10128,10130,10135,10139,10144,10146,10149,10151,10155,10287,10290,10299,10304,10307,10318,10320,10322,10329,10465,10477,10478,10480,10483,10485,10491,10498,10499,10500,10503,10505,10507,10511,10513,10525,10527,10659,10669,10672,10675,10678,10680,10683,10685,10689,10690,10691,10694,10695,10697,10701,10712,10868,10870,10873,10877,10879,10881,10884,10885,10891,11040,11041,11043,11047,11056,11062,11067,11069,11073,11076,11224,11233,11244,11246,11256,11259,11263,11264,11415,11418,11421,11611,11613,11616,11619,11735,11754,11755,11759,11762,11766,11768,11772,11773,11779,11780,11781,11783,11785,11787,11788,11792,11794,11797,11798,11801,11803,11805,11807,11808,11810,11970,12083,12088,12091,12098,12102,12108,12111,12115,12117,12118,12120,12121,12123,12125,12129,12132,12135,12141,12146,12147,12150,12152,12155,12157,12160,12161,12164,12165,12167,12169,12174,12176,12179,12185,12199,12285,12290,12292,12293,12297,12298,12300,12301,12304,12311,12323,12325,12331,12334,12335,12339,12344,12347,12482,12485,12489,12497,12498,12500,12650,12652,12653,12657,12660,12664,12817,12819,12821,12823,12827,12829,12831,12833,12836,12840,13005,13007,13016,13020,13022,13025,13026,13029,13031,13038,13042,13044,13048,13052,13063,13205,13210,13213,13219,13227,13249,13277,13385,13388,13391,13402,13555,13560,13587,13734,13739,13749,13751,13755,13758,13760,13763,13776,13778,13907,13924,13927,13930,13935,13936,13946,13949,13951,13953,13956,13972,14077,14082,14103,14107,14111,14114,14120,14129,14132,14135, -chr19 47500098 47516399 m84008_230107_003043_s1/220005464/ccs 96,310,474,626,809,1003,1164,1330,1574,1724,1896,2124,2317,2504,2679,2872,3078,3256,3442,3775,3925,4092,4282,4501,4703,4917,5119,5367,5522,5693,5933,6114,6284,6482,6651,6831,7042,7247,7405,7602,7764,7923,8110,8253,8407,8595,8778,8967,9175,9360,9539,9699,9896,10106,10301,10490,10695,10914,11127,11352,11548,12004,12167,12534,13000,13210,13453,13647,13917,14087,14251,14399,14597,14800,15523,15715,15851,16102, 151,101,131,148,139,114,130,141,95,140,187,130,126,134,131,143,105,108,265,103,144,166,168,136,137,148,139,98,151,140,100,129,138,123,164,158,149,110,109,117,153,137,142,134,139,109,132,124,101,118,119,151,116,81,114,129,137,113,103,100,114,110,110,132,93,108,99,106,86,97,122,95,109,101,118,95,111,129, 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248,433,634,843,1040,1248,1418,1624,1786,2019,2224,2389,2640,2810,3037,3226,3409,3588,3774,4153,4343,4532,4767,5175,5340,5519,5694,5873,6138,6338,6532,6713,6896,7092,7282,7478,7668,7859,8081,8379,8581,8799,8960,9129,9324,9490,9679,9857,10040,10203,10402,10607,10812,11023,11328,11619,11814,11993,12241,12407,12729,12860,13078,13213,13375,13533,13669,13973,14527, 75,85,87,88,77,13,60,7,94,41,26,108,13,87,40,23,42,36,71,20,48,80,70,37,1,33,57,115,40,61,32,26,39,32,31,25,35,65,29,76,76,27,58,60,34,35,38,1,38,59,45,50,71,49,151,76,40,105,20,1,1,63,1,28,1,11,176,18,99, 0,0,0,0,0,0,0,0,0,0,0,243,0,243,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,245,0,0,244,0,0,0,0,0,0,0,0,250,0,0, 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-chr19 47501338 47519083 m84039_230404_003541_s3/198186026/ccs 141,356,526,698,896,1083,1294,1465,1665,1889,2073,2283,2454,2641,2861,3055,3248,3619,3801,4002,4202,4405,4629,4803,4887,4982,5228,5436,5616,5803,6012,6205,6400,6596,6792,7042,7167,7368,7542,7733,7916,8071,8222,8421,8651,8807,8991,9195,9391,9580,9780,9980,10346,10557,10740,10963,11086,11472,11561,11755,11917,12297,12373,12593,12743,12942,13118,13308,13465,14316,14459,14624,14796,15012,15206,15377,15542,15728,15937,16108,16238,16316,16562,17105,17258,17450, 158,125,155,164,124,146,103,164,141,115,200,162,131,124,124,135,309,155,157,119,143,141,149,83,90,142,131,159,161,175,149,154,95,134,126,97,113,87,115,116,135,127,130,146,113,144,141,136,133,150,166,319,137,106,170,122,240,88,185,130,275,75,146,116,99,139,118,99,125,142,126,121,148,174,153,138,145,147,125,105,77,215,273,152,142,140, 94,299,481,681,862,1020,1229,1397,1629,1806,2004,2273,2445,2585,2765,2985,3190,3557,3774,3958,4121,4345,4546,4778,4886,4977,5124,5359,5595,5777,5978,6161,6359,6495,6730,6918,7139,7280,7455,7657,7849,8051,8198,8352,8567,8764,8951,9132,9331,9524,9730,9946,10299,10483,10663,10910,11085,11326,11560,11746,11885,12192,12372,12519,12709,12842,13081,13236,13407,13590,14458,14585,14745,14944,15186,15359,15515,15687,15875,16062,16213,16315,16531,16835,17257,17400,17590, 47,57,45,17,34,63,65,68,36,83,69,10,9,56,96,70,58,62,27,44,81,60,83,25,1,5,104,77,21,26,34,44,41,101,62,124,28,88,87,76,67,20,24,69,84,43,40,63,60,56,50,34,47,74,77,53,1,146,1,9,32,105,1,74,34,100,37,72,58,726,1,39,51,68,20,18,27,41,62,46,25,1,31,270,1,50,34, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,248,0,0,0,0,0,0,0,0,0,0,0,0,0,250,0,0,0, 0,2,3,5,6,94,107,110,112,117,118,123,127,134,137,140,299,302,306,309,311,314,317,322,324,328,330,333,334,336,338,355,481,497,498,500,503,506,514,525,681,690,695,697,862,867,869,872,876,895,1020,1021,1023,1057,1059,1082,1229,1233,1247,1249,1252,1255,1270,1283,1285,1293,1397,1420,1430,1435,1460,1464,1629,1640,1643,1645,1664,1806,1809,1811,1830,1832,1833,1844,1872,1874,1888,2004,2006,2012,2021,2029,2034,2038,2041,2044,2046,2049,2052,2056,2059,2065,2070,2072,2273,2275,2278,2282,2445,2451,2453,2585,2606,2615,2628,2631,2632,2640,2765,2774,2776,2779,2790,2840,2860,2985,2990,3006,3008,3018,3020,3030,3033,3036,3044,3052,3054,3190,3202,3207,3215,3217,3225,3227,3230,3232,3247,3557,3566,3569,3577,3579,3589,3591,3614,3618,3702,3774,3776,3792,3798,3800,3958,3972,3977,4001,4121,4129,4147,4149,4155,4157,4161,4163,4165,4173,4184,4190,4194,4201,4345,4350,4381,4385,4391,4395,4396,4399,4404,4546,4548,4553,4560,4567,4569,4603,4608,4614,4620,4622,4627,4628,4750,4778,4780,4786,4790,4797,4800,4802,4886,4977,4981,5080,5124,5126,5131,5136,5138,5147,5150,5152,5157,5170,5176,5182,5190,5196,5200,5202,5204,5206,5223,5227,5359,5379,5391,5398,5400,5405,5408,5409,5410,5415,5417,5430,5433,5435,5475,5595,5596,5601,5609,5615,5777,5802,5978,5980,6003,6011,6119,6161,6195,6199,6200,6204,6359,6361,6382,6394,6395,6399,6495,6497,6536,6544,6552,6557,6565,6571,6576,6589,6591,6595,6730,6733,6740,6743,6745,6749,6752,6762,6776,6779,6781,6791,6918,6923,6932,6936,6938,6941,6943,6946,6953,6960,6962,6968,6972,6975,6982,6988,6991,7000,7021,7041,7139,7158,7166,7280,7295,7322,7344,7346,7347,7352,7354,7367,7455,7463,7480,7509,7510,7513,7516,7528,7530,7539,7541,7657,7660,7685,7702,7712,7717,7726,7728,7730,7732,7849,7852,7876,7893,7902,7915,8051,8064,8067,8070,8198,8218,8221,8352,8395,8401,8409,8412,8414,8420,8567,8569,8578,8582,8589,8591,8600,8601,8612,8614,8618,8634,8638,8645,8648,8650,8735,8764,8767,8771,8776,8778,8780,8786,8789,8793,8798,8806,8920,8951,8966,8969,8970,8979,8984,8990,9103,9132,9151,9154,9156,9166,9174,9177,9182,9194,9331,9351,9354,9355,9362,9367,9369,9378,9380,9384,9390,9524,9535,9567,9571,9574,9579,9730,9736,9742,9744,9751,9754,9755,9757,9761,9762,9765,9767,9770,9774,9779,9946,9949,9952,9960,9963,9968,9970,9974,9976,9979,10299,10301,10303,10305,10306,10322,10327,10345,10483,10486,10489,10490,10492,10508,10514,10520,10523,10526,10528,10540,10545,10548,10551,10556,10623,10663,10677,10687,10694,10710,10714,10716,10718,10735,10736,10739,10910,10946,10953,10956,10957,10962,11085,11326,11328,11352,11371,11376,11379,11380,11397,11400,11402,11405,11410,11417,11418,11420,11421,11423,11424,11430,11441,11457,11471,11560,11746,11749,11754,11838,11885,11888,11890,11892,11895,11897,11904,11908,11910,11912,11914,11916,12192,12207,12210,12211,12214,12217,12219,12221,12231,12236,12239,12241,12243,12252,12255,12257,12258,12260,12271,12273,12275,12279,12291,12296,12372,12404,12519,12521,12529,12533,12535,12543,12547,12550,12552,12557,12561,12564,12565,12567,12572,12574,12576,12583,12585,12589,12592,12709,12718,12742,12842,12854,12859,12870,12872,12874,12877,12879,12886,12888,12893,12896,12897,12900,12901,12903,12904,12906,12912,12914,12920,12922,12926,12929,12931,12941,13081,13085,13097,13100,13104,13105,13107,13109,13117,13236,13238,13243,13247,13251,13253,13255,13258,13260,13268,13272,13273,13292,13294,13297,13305,13307,13407,13409,13430,13440,13456,13464,13590,13607,13609,13616,13624,13628,13630,13634,13638,13639,13641,13645,13651,13664,13665,13667,13669,13671,13672,13682,13691,13698,13705,13716,13720,13721,13728,13782,13790,13800,13803,13812,13822,13824,13829,13831,13838,13839,13840,13846,13856,13859,13863,13864,13869,13871,13880,13881,13888,13891,13893,13895,13897,13902,13907,13909,13911,13912,13915,13920,13927,13933,13935,13938,13939,13943,13944,13945,13985,13988,13991,13992,13995,14005,14006,14011,14014,14024,14050,14066,14068,14070,14078,14080,14083,14108,14117,14126,14130,14132,14134,14137,14142,14145,14166,14169,14178,14182,14187,14191,14193,14198,14200,14206,14207,14208,14209,14212,14213,14218,14219,14221,14269,14271,14276,14279,14281,14283,14285,14287,14292,14308,14315,14458,14585,14595,14599,14605,14609,14621,14623,14702,14745,14754,14765,14774,14775,14784,14795,14944,14947,14952,14955,14957,14960,14962,14965,14988,14989,14998,15001,15003,15011,15186,15193,15201,15203,15205,15359,15360,15365,15374,15376,15515,15518,15521,15524,15526,15530,15531,15534,15538,15541,15687,15698,15711,15721,15727,15875,15878,15883,15899,15901,15909,15913,15917,15918,15921,15927,15929,15936,16062,16068,16070,16072,16074,16076,16085,16107,16213,16227,16229,16235,16237,16315,16531,16532,16549,16552,16561,16835,16841,16845,16852,16855,16867,16874,16877,16879,16880,16886,16891,16893,16898,16901,16902,16906,16909,16911,16912,16916,16917,16923,16924,16926,16928,16934,16935,16937,16940,16941,16945,16947,16948,16952,16955,16958,16961,16962,16964,16967,16970,16975,16977,16986,16989,16991,16993,16996,16999,17005,17007,17011,17015,17020,17038,17039,17041,17043,17045,17049,17052,17053,17055,17057,17065,17069,17071,17073,17077,17080,17082,17104,17216,17257,17364,17400,17410,17415,17418,17421,17425,17435,17441,17444,17446,17449,17590,17604,17616,17623,17728,17732, -chr19 47501400 47513749 m54329U_210323_190418/100534861/ccs 205,406,596,784,942,1127,1347,1508,1699,1861,2061,2233,2431,2638,2824,2993,3178,3345,3520,3710,3936,4097,4327,4517,4671,4877,5038,5264,5612,5825,6005,6204,6391,6583,6752,6937,7150,7331,7505,7677,7886,8043,8264,8399,8595,8743,9000,9174,9414,9780,9974,10182,10346,10578,10771,10910,11105,11367,11551,11753,11920, 132,166,150,100,159,139,149,169,137,183,142,178,166,149,137,135,152,152,184,152,152,150,126,120,174,132,163,315,167,136,147,154,149,150,159,166,141,140,159,173,153,162,111,159,135,186,138,162,328,113,146,150,179,122,122,139,121,137,143,117,136, 187,337,572,746,884,1101,1266,1496,1677,1836,2044,2203,2411,2597,2787,2961,3128,3330,3497,3704,3862,4088,4247,4453,4637,4845,5009,5201,5579,5779,5961,6152,6358,6540,6733,6911,7103,7291,7471,7664,7850,8039,8205,8375,8558,8730,8929,9138,9336,9742,9893,10120,10332,10525,10700,10893,11049,11226,11504,11694,11870,12056, 18,69,24,38,58,26,81,12,22,25,17,30,20,41,37,32,50,15,23,6,74,9,80,64,34,32,29,63,33,46,44,52,33,43,19,26,47,40,34,13,36,4,59,24,37,13,71,36,78,38,81,62,14,53,71,17,56,141,47,59,50,38, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,243,0,0,0,0, 7,10,15,17,20,22,187,188,191,193,196,198,203,204,231,337,339,342,345,348,354,359,362,368,371,376,378,384,385,387,392,393,396,397,399,402,405,572,576,578,579,592,595,746,749,752,755,761,768,774,777,783,884,900,905,906,921,923,934,936,941,1101,1107,1113,1114,1116,1126,1266,1268,1272,1273,1275,1297,1304,1306,1307,1309,1311,1313,1317,1318,1320,1324,1326,1329,1330,1336,1346,1496,1497,1499,1504,1507,1677,1691,1698,1836,1839,1843,1860,2044,2045,2047,2058,2060,2203,2210,2222,2225,2232,2411,2424,2426,2430,2597,2600,2602,2605,2613,2619,2630,2631,2637,2787,2790,2792,2799,2823,2961,2968,2982,2990,2992,3128,3131,3134,3140,3143,3145,3149,3153,3155,3163,3168,3170,3171,3177,3330,3332,3344,3497,3500,3506,3513,3519,3704,3707,3709,3862,3875,3884,3885,3888,3893,3894,3898,3903,3905,3911,3913,3935,4088,4090,4092,4096,4247,4251,4254,4258,4263,4264,4273,4309,4322,4325,4326,4453,4463,4465,4468,4470,4474,4481,4487,4489,4492,4493,4501,4508,4516,4637,4644,4646,4651,4663,4670,4845,4851,4859,4862,4876,5009,5010,5013,5016,5019,5021,5026,5028,5031,5033,5037,5201,5203,5218,5219,5221,5224,5226,5235,5263,5579,5580,5582,5587,5591,5594,5608,5611,5779,5796,5798,5824,5961,5967,5973,5978,5980,5982,5986,6001,6004,6152,6155,6156,6160,6162,6166,6168,6179,6180,6183,6186,6188,6190,6192,6195,6203,6309,6358,6363,6366,6367,6370,6375,6380,6383,6390,6470,6540,6544,6547,6549,6552,6553,6567,6578,6581,6582,6677,6733,6736,6739,6751,6911,6913,6916,6917,6922,6923,6927,6933,6936,7103,7109,7116,7119,7123,7131,7133,7136,7147,7149,7291,7298,7312,7316,7319,7321,7330,7471,7477,7483,7485,7492,7504,7664,7666,7670,7672,7674,7676,7850,7854,7859,7865,7871,7873,7882,7885,8009,8039,8042,8072,8151,8205,8215,8217,8228,8231,8232,8237,8241,8259,8263,8375,8380,8396,8398,8558,8571,8573,8578,8582,8585,8594,8730,8733,8737,8742,8929,8943,8947,8965,8969,8971,8984,8992,8999,9138,9141,9167,9171,9173,9336,9339,9341,9350,9354,9357,9360,9361,9364,9366,9368,9372,9377,9379,9383,9384,9390,9392,9413,9742,9744,9752,9761,9779,9893,9899,9921,9923,9926,9933,9937,9941,9943,9945,9946,9949,9954,9970,9973,10120,10123,10125,10129,10131,10133,10136,10139,10146,10148,10149,10152,10153,10160,10165,10178,10181,10306,10332,10339,10345,10525,10528,10533,10536,10537,10543,10547,10553,10556,10577,10700,10712,10715,10719,10723,10725,10727,10730,10735,10737,10738,10740,10742,10743,10745,10746,10749,10756,10760,10768,10770,10893,10895,10900,10906,10909,11049,11054,11055,11069,11080,11085,11086,11092,11101,11104,11226,11242,11258,11260,11262,11264,11266,11268,11272,11274,11276,11278,11281,11285,11289,11309,11314,11319,11322,11324,11327,11328,11330,11338,11350,11353,11359,11360,11366,11504,11506,11508,11510,11512,11513,11517,11523,11529,11532,11544,11545,11547,11550,11694,11697,11701,11704,11707,11709,11711,11712,11716,11719,11726,11728,11731,11752,11870,11884,11889,11891,11896,11919,12056,12071,12091,12094, -chr19 47501413 47515667 m54329U_210810_004956/24643281/ccs 191,388,582,790,947,1175,1351,1550,1754,1906,2083,2282,2477,2691,2872,3167,3366,3580,3795,3980,4159,4344,4550,4793,4979,5169,5357,5560,5770,5932,6156,6378,6551,6768,6979,7156,7356,7558,7766,8111,8333,8496,8691,8874,9090,9291,9494,9679,9916,10063,10259,10467,10654,10846,10980,11146,11423,11642,11758,11966,12161,12357,12607,12777,13273,13431,14203,14349,14622,14769,14973,15146,15360,15571,15827,16123,16323,16503,16700,16908,17229,17379,17552,17695,17873,18234,18472,18859,19020,19233,19336,19557,19717,19920,20069,20308,20456,20679,21086,21488,21608,21783,22081,22318,22483,22643,22824,22986,23377,23498,23680, 119,145,111,115,140,119,136,149,132,167,161,151,143,136,278,190,163,143,141,159,142,162,150,137,150,166,137,155,145,173,146,139,153,155,121,134,119,125,281,145,162,141,108,154,148,136,125,147,146,153,115,118,139,133,149,164,140,88,142,136,155,104,140,463,113,111,102,173,76,129,144,121,101,147,262,161,150,147,117,130,128,172,87,119,132,137,125,75,93,76,138,101,135,148,162,139,172,192,285,113,143,148,210,125,138,127,155,88,75,181,318, 131,310,533,693,905,1087,1294,1487,1699,1886,2073,2244,2433,2620,2827,3150,3357,3529,3723,3936,4139,4301,4506,4700,4930,5129,5335,5494,5715,5915,6105,6302,6517,6704,6923,7100,7290,7475,7683,8047,8256,8495,8637,8799,9028,9238,9427,9619,9826,10062,10216,10374,10585,10793,10979,11129,11310,11563,11730,11900,12102,12316,12461,12747,13240,13386,13542,14305,14522,14698,14898,15117,15267,15461,15718,16089,16284,16473,16650,16817,17038,17357,17551,17639,17814,18005,18371,18597,18934,19113,19309,19474,19658,19852,20068,20231,20447,20628,20871,21371,21601,21751,21931,22291,22443,22621,22770,22979,23074,23452,23679,23998, 60,78,49,97,42,88,57,63,55,20,10,38,44,71,45,17,9,51,72,44,20,43,44,93,49,40,22,66,55,17,51,76,34,64,56,56,66,83,83,64,77,1,54,75,62,53,67,60,90,1,43,93,69,53,1,17,113,79,28,66,59,41,146,30,33,45,661,44,100,71,75,29,93,110,109,34,39,30,50,91,191,22,1,56,59,229,101,262,86,120,27,83,59,68,1,77,9,51,215,117,7,32,150,27,40,22,54,7,303,46,1,54, 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-chr19 47501574 47511800 m84039_230404_003541_s3/123732821/ccs 172,356,573,747,1084,1254,1434,1662,1849,2011,2195,2417,2818,3015,3233,3422,3632,4024,4194,4375,4536,4688,4847,5047,5209,5412,5747,5886,6037,6262,6438,6980,7169,7327,7459,7643,7890,8139,8334,8490,8635,8838,9055,9234,9430,9774,9916, 143,173,150,287,116,153,136,119,144,175,131,400,158,170,159,149,128,133,180,88,108,142,162,149,153,245,138,145,128,120,446,132,136,131,162,246,171,131,97,138,155,121,140,162,291,91,140, 135,315,529,723,1034,1200,1407,1570,1781,1993,2186,2326,2817,2976,3185,3392,3571,3760,4157,4374,4463,4644,4830,5009,5196,5362,5657,5885,6031,6165,6382,6884,7112,7305,7458,7621,7889,8061,8270,8431,8628,8790,8959,9195,9396,9721,9865,10056, 37,41,44,24,50,54,27,92,68,18,9,91,1,39,48,30,61,264,37,1,73,44,17,38,13,50,90,1,6,97,56,96,57,22,1,22,1,78,64,59,7,48,96,39,34,53,51,3, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,245,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 1,2,4,5,6,135,139,141,144,154,161,163,165,168,171,315,323,344,355,462,529,538,547,551,554,557,566,572,723,728,734,743,746,1034,1049,1051,1055,1057,1081,1083,1200,1214,1219,1221,1224,1228,1231,1235,1236,1239,1247,1253,1407,1409,1433,1570,1573,1581,1584,1587,1594,1596,1608,1636,1638,1653,1661,1781,1802,1805,1808,1810,1813,1820,1823,1829,1834,1836,1842,1848,1993,2006,2008,2010,2135,2186,2194,2326,2329,2332,2334,2344,2346,2350,2358,2361,2363,2367,2416,2817,2976,2980,2982,2990,2992,2995,2997,3009,3012,3014,3082,3185,3206,3208,3211,3214,3228,3232,3317,3392,3406,3412,3421,3571,3592,3594,3596,3600,3603,3629,3631,3760,3773,3775,3784,3787,3789,3792,3800,3801,3815,3818,3827,3845,3875,3895,3898,3910,3913,3915,3917,3921,3927,3929,3931,3939,3945,3947,3949,3950,3954,3956,3959,3960,3967,3994,4023,4157,4161,4162,4165,4170,4193,4374,4463,4470,4475,4481,4484,4487,4489,4496,4503,4516,4535,4644,4649,4652,4657,4660,4665,4670,4676,4684,4687,4830,4834,4835,4838,4844,4846,5009,5020,5026,5028,5035,5036,5046,5196,5208,5241,5362,5365,5375,5376,5377,5382,5385,5398,5404,5409,5411,5657,5684,5690,5695,5705,5713,5718,5722,5746,5777,5885,6031,6032,6036,6165,6169,6173,6177,6179,6184,6196,6201,6204,6206,6209,6211,6216,6222,6225,6239,6244,6251,6257,6261,6382,6383,6388,6394,6395,6399,6402,6433,6437,6884,6893,6924,6932,6937,6940,6942,6947,6952,6954,6957,6961,6963,6971,6975,6977,6979,7028,7112,7134,7136,7143,7152,7165,7168,7305,7314,7326,7416,7458,7621,7642,7889,8061,8075,8106,8108,8110,8113,8118,8123,8129,8138,8270,8276,8281,8309,8333,8431,8454,8462,8481,8489,8628,8634,8790,8792,8803,8805,8808,8811,8817,8823,8825,8830,8833,8837,8959,8977,8987,8991,8996,9011,9014,9015,9054,9114,9195,9199,9203,9204,9209,9210,9212,9215,9218,9222,9224,9226,9228,9231,9233,9396,9407,9409,9421,9422,9426,9429,9721,9726,9729,9734,9736,9745,9749,9773,9865,9880,9883,9915,10056,10058,10205,10215, -chr19 47501949 47517076 m64076_210328_012155/98043755/ccs 127,287,456,879,1175,1343,1558,1733,1883,2190,2451,2644,2817,2988,3271,3478,3659,3862,4047,4273,4442,4605,4807,5001,5159,5375,5553,5770,5932,6130,6292,6501,6683,6873,7068,7234,7543,7749,7935,8101,8307,8465,8645,8814,8995,9173,9374,9562,9733,9914,10115,10469,10637,10932,11120,11292,11494,11695,11884,12191,12347,12499,12674,12905,13706,13881,14033,14222,14436,14578,14802,14978, 143,162,123,252,167,150,130,147,287,115,104,103,127,110,121,81,130,119,133,104,128,148,118,124,123,116,108,113,124,141,144,116,148,148,120,278,147,100,119,141,124,147,114,115,102,131,120,100,134,119,112,117,268,117,116,126,107,132,306,136,151,123,97,108,116,123,148,136,113,174,110,118, 86,270,449,579,1131,1342,1493,1688,1880,2170,2305,2555,2747,2944,3098,3392,3559,3789,3981,4180,4377,4570,4753,4925,5125,5282,5491,5661,5883,6056,6271,6436,6617,6831,7021,7188,7512,7690,7849,8054,8242,8431,8612,8759,8929,9097,9304,9494,9662,9867,10033,10227,10586,10905,11049,11236,11418,11601,11827,12190,12327,12498,12622,12771,13013,13822,14004,14181,14358,14549,14752,14912, 41,17,7,300,44,1,65,45,3,20,146,89,70,44,173,86,100,73,66,93,65,35,54,76,34,93,62,109,49,74,21,65,66,42,47,46,31,59,86,47,65,34,33,55,66,76,70,68,71,47,82,242,51,27,71,56,76,94,57,1,20,1,52,134,693,59,29,41,78,29,50,66, 0,0,0,0,0,0,0,0,0,0,243,0,0,0,246,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,248,0,0,0,0,0,0,0, 86,87,90,92,95,96,99,102,104,105,107,108,115,117,119,121,123,125,126,270,272,274,277,278,280,284,286,449,451,455,579,582,592,595,598,601,603,606,610,614,617,618,621,625,628,631,634,635,639,641,644,647,649,651,656,658,677,683,687,755,757,758,760,764,771,772,774,775,780,781,825,830,831,837,840,845,855,857,859,861,862,865,866,867,870,874,876,878,1131,1145,1151,1152,1156,1159,1161,1162,1163,1166,1169,1174,1342,1493,1499,1500,1502,1505,1506,1507,1510,1513,1523,1526,1530,1531,1534,1535,1538,1549,1557,1688,1698,1704,1720,1724,1725,1730,1732,1880,1882,2170,2172,2175,2178,2179,2182,2186,2189,2305,2313,2314,2317,2320,2325,2327,2328,2330,2333,2334,2337,2338,2340,2341,2343,2345,2349,2351,2352,2354,2358,2361,2362,2364,2366,2369,2377,2381,2383,2386,2390,2392,2393,2394,2398,2399,2401,2404,2406,2409,2410,2414,2416,2419,2423,2426,2432,2434,2436,2440,2442,2445,2446,2448,2450,2555,2556,2558,2561,2562,2568,2573,2576,2579,2583,2586,2588,2589,2592,2598,2601,2603,2607,2611,2613,2619,2623,2626,2629,2636,2643,2747,2753,2755,2757,2759,2761,2763,2765,2769,2770,2771,2772,2774,2775,2778,2780,2782,2784,2786,2788,2790,2792,2794,2796,2798,2800,2802,2804,2806,2813,2816,2944,2948,2953,2959,2960,2962,2965,2969,2970,2975,2979,2981,2983,2985,2987,3098,3115,3117,3121,3122,3124,3127,3140,3142,3143,3146,3152,3163,3165,3167,3168,3170,3172,3174,3176,3180,3183,3187,3189,3193,3194,3195,3197,3200,3202,3203,3205,3206,3208,3210,3211,3213,3214,3220,3223,3225,3227,3229,3231,3234,3236,3240,3243,3245,3246,3249,3254,3261,3263,3270,3392,3396,3397,3399,3402,3405,3411,3416,3419,3421,3424,3430,3447,3454,3474,3477,3559,3561,3563,3571,3572,3573,3579,3582,3586,3588,3591,3592,3599,3603,3604,3605,3607,3610,3626,3628,3638,3650,3653,3658,3789,3793,3794,3797,3803,3806,3810,3813,3815,3818,3820,3826,3835,3837,3842,3847,3850,3852,3854,3856,3859,3861,3948,3981,3996,4000,4005,4010,4014,4019,4020,4022,4024,4027,4028,4034,4046,4180,4183,4190,4197,4198,4200,4202,4206,4209,4211,4216,4228,4236,4239,4241,4263,4272,4377,4381,4390,4392,4396,4397,4410,4414,4416,4420,4431,4432,4436,4439,4440,4441,4472,4570,4576,4582,4587,4590,4593,4596,4597,4602,4604,4753,4755,4756,4760,4765,4766,4769,4771,4775,4776,4780,4783,4789,4793,4796,4799,4801,4806,4876,4925,4949,4954,4969,4971,4973,4976,4981,4984,4988,4990,4997,5000,5125,5129,5133,5138,5139,5143,5145,5150,5152,5154,5158,5214,5282,5284,5292,5294,5296,5302,5305,5306,5312,5315,5316,5319,5321,5323,5325,5328,5330,5334,5335,5336,5338,5340,5344,5348,5351,5353,5357,5359,5363,5364,5366,5374,5491,5495,5497,5500,5501,5506,5508,5510,5514,5517,5520,5523,5526,5531,5532,5535,5539,5552,5661,5668,5670,5672,5675,5677,5679,5682,5686,5688,5690,5695,5696,5699,5701,5704,5705,5713,5718,5722,5724,5726,5728,5729,5733,5761,5767,5769,5883,5887,5895,5897,5899,5911,5912,5914,5918,5927,5931,6056,6059,6061,6062,6065,6069,6086,6089,6101,6102,6106,6110,6114,6116,6117,6119,6124,6129,6271,6291,6436,6443,6445,6458,6461,6462,6465,6467,6470,6473,6479,6482,6493,6495,6500,6617,6626,6641,6643,6644,6645,6647,6651,6656,6661,6663,6666,6676,6681,6682,6831,6833,6839,6846,6859,6863,6865,6867,6872,7021,7024,7025,7027,7032,7033,7038,7043,7045,7048,7049,7051,7053,7056,7061,7067,7188,7196,7208,7216,7219,7226,7231,7233,7512,7522,7539,7542,7690,7699,7700,7705,7706,7710,7712,7715,7720,7725,7728,7731,7734,7735,7740,7741,7748,7849,7866,7890,7896,7902,7905,7908,7913,7914,7919,7932,7934,8054,8058,8069,8072,8073,8075,8077,8081,8082,8088,8090,8091,8092,8095,8096,8098,8100,8242,8243,8249,8254,8256,8258,8261,8266,8270,8273,8278,8284,8288,8290,8295,8301,8306,8431,8444,8455,8459,8464,8612,8614,8616,8619,8626,8630,8632,8638,8644,8759,8772,8777,8781,8783,8789,8795,8800,8806,8813,8885,8929,8943,8944,8946,8950,8959,8962,8965,8970,8972,8976,8979,8989,8990,8994,9097,9111,9114,9121,9123,9125,9127,9129,9130,9135,9139,9141,9147,9149,9156,9159,9160,9162,9166,9167,9170,9172,9304,9309,9312,9314,9316,9318,9321,9324,9335,9354,9357,9373,9494,9506,9508,9514,9516,9519,9522,9554,9561,9662,9669,9674,9676,9684,9688,9695,9697,9710,9711,9713,9717,9729,9730,9732,9867,9871,9873,9891,9894,9895,9897,9913,10033,10039,10045,10050,10051,10054,10056,10059,10061,10064,10065,10068,10069,10071,10073,10078,10080,10083,10089,10093,10100,10103,10113,10114,10227,10229,10235,10250,10251,10257,10263,10265,10267,10274,10281,10285,10296,10306,10316,10388,10391,10395,10398,10406,10410,10416,10422,10426,10433,10435,10437,10440,10442,10444,10446,10448,10452,10457,10459,10461,10462,10464,10465,10468,10586,10587,10589,10594,10596,10599,10603,10609,10615,10618,10620,10622,10626,10628,10636,10905,10906,10911,10913,10921,10931,11049,11065,11070,11073,11077,11079,11081,11082,11084,11086,11092,11097,11099,11102,11105,11106,11107,11114,11116,11119,11236,11238,11239,11242,11245,11247,11254,11257,11261,11263,11264,11267,11270,11271,11275,11276,11280,11282,11291,11418,11419,11423,11443,11445,11447,11449,11451,11455,11456,11458,11461,11466,11470,11474,11493,11601,11604,11616,11619,11628,11640,11644,11645,11648,11650,11652,11653,11657,11661,11664,11666,11669,116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-chr19 47501977 47526503 m54329U_210814_130637/126552497/ccs 180,473,653,836,946,1308,1514,1664,1861,2052,2222,2368,2564,2757,2935,3116,3320,3467,3655,3869,4054,4230,4403,4623,4817,5007,5252,5421,5637,5813,6000,6185,6353,6536,6731,6954,7133,7299,7493,7625,7870,8078,8244,8428,8592,8820,8982,9141,9282,9477,9705,10445,10800,11007,11163,11336,11483,11670,11827,11994,12176,12342,12842,13665,13867,14144,14332,14488,14689,14881,15211,15392,15584,15752,15971,16210,16400,16571,16759,17076,17234,17417,17561,17704,17922,18124,18330,18535,18711,18848,19068,19271,19459,19638,19818,20023,20170,20365,20580,20748,20936,21069,21402,21621,21805,21994,22197,22399,22594,22779,22971,23122,23277,23479,23636,23877,24026,24297, 292,133,126,109,361,134,118,120,131,131,145,151,126,177,114,150,121,150,186,139,144,148,159,114,133,146,87,96,112,106,114,112,147,145,142,98,125,94,119,143,134,115,146,125,159,127,114,140,180,183,726,289,154,155,122,144,143,126,140,158,130,443,99,92,235,112,153,128,133,277,142,161,167,187,165,133,141,137,316,141,140,114,129,166,146,152,136,148,136,170,136,136,138,122,158,143,162,150,127,153,123,297,153,120,110,127,146,140,137,115,126,147,158,151,143,144,198,97, 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-chr19 47502029 47515967 m54329U_210326_192251/65864044/ccs 207,395,587,758,906,1092,1305,1475,1688,1880,2022,2261,2453,2637,2831,3011,3184,3375,3546,3742,3965,4156,4385,4581,4754,4936,5107,5295,5472,5633,5825,5993,6380,6590,6710,6894,7096,7262,7472,7671,7844,8025,8208,8414,8618,8810,9018,9212,9415,9629,9836,10009,10195,10393,10565,10755,10999,11123,11303,11437,11646,11805,11969,12146,12338,12555,12701,13651, 162,131,142,112,156,159,114,160,141,141,147,137,129,145,133,146,140,115,162,143,113,140,125,107,114,108,132,126,117,112,125,288,100,77,152,151,133,140,134,145,144,126,140,138,136,155,131,135,125,145,98,146,152,143,136,131,84,179,133,166,123,137,140,149,127,115,244,98, 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7,10,12,15,16,19,22,28,176,178,189,190,192,194,197,200,204,206,316,369,371,375,391,394,526,534,537,538,541,545,548,551,554,559,561,564,567,569,571,573,578,579,582,586,729,732,740,742,747,748,754,757,870,875,878,883,884,886,888,891,892,896,897,901,905,1016,1062,1064,1069,1073,1076,1080,1083,1086,1091,1251,1254,1259,1261,1271,1272,1278,1285,1304,1419,1423,1447,1460,1461,1465,1466,1468,1472,1474,1635,1638,1643,1644,1649,1651,1653,1655,1657,1658,1664,1666,1669,1672,1676,1682,1687,1829,1838,1840,1842,1845,1846,1847,1850,1854,1860,1868,1879,2021,2169,2176,2222,2231,2233,2234,2237,2250,2257,2260,2398,2404,2412,2415,2420,2422,2423,2424,2426,2452,2582,2584,2594,2598,2599,2602,2636,2782,2784,2785,2797,2809,2811,2827,2829,2830,2964,2970,2972,2984,2988,2991,2996,3010,3157,3175,3183,3324,3335,3338,3340,3343,3349,3353,3357,3358,3366,3374,3490,3498,3501,3505,3507,3510,3511,3518,3523,3526,3529,3538,3545,3708,3712,3713,3716,3721,3731,3733,3736,3741,3885,3893,3896,3899,3901,3903,3905,3907,3908,3912,3914,3918,3928,3932,3940,3945,3946,3952,3953,3960,3964,4078,4081,4084,4088,4090,4094,4097,4099,4102,4105,4109,4110,4111,4117,4119,4121,4125,4126,4128,4130,4135,4155,4296,4300,4309,4311,4315,4316,4318,4333,4335,4339,4341,4343,4344,4345,4348,4350,4351,4355,4359,4360,4367,4384,4510,4513,4516,4517,4522,4524,4532,4535,4537,4539,4543,4547,4566,4570,4574,4580,4688,4690,4695,4711,4712,4715,4718,4720,4725,4735,4745,4750,4753,4868,4873,4890,4895,4907,4909,4916,4919,4929,4935,5044,5057,5069,5073,5077,5083,5087,5096,5104,5106,5239,5243,5245,5248,5250,5258,5264,5268,5271,5277,5279,5294,5421,5428,5430,5434,5437,5440,5443,5446,5451,5455,5460,5471,5589,5591,5594,5596,5598,5601,5605,5609,5615,5618,5620,5623,5624,5632,5745,5750,5752,5763,5765,5776,5779,5798,5801,5802,5805,5811,5824,5950,5954,5957,5975,5978,5980,5981,5984,5988,5992,6281,6283,6289,6292,6309,6312,6316,6318,6321,6324,6325,6331,6332,6336,6339,6342,6347,6354,6363,6376,6379,6480,6488,6493,6508,6510,6513,6522,6527,6533,6584,6589,6667,6669,6670,6675,6677,6681,6683,6685,6686,6690,6691,6693,6695,6698,6700,6703,6704,6706,6709,6862,6864,6871,6883,6885,6893,7045,7051,7053,7095,7229,7233,7236,7237,7248,7250,7252,7258,7261,7402,7417,7424,7431,7433,7436,7438,7441,7443,7446,7450,7455,7467,7471,7606,7609,7610,7615,7616,7619,7621,7624,7625,7629,7631,7632,7647,7663,7667,7670,7816,7821,7824,7827,7843,7988,7992,7994,7996,8001,8007,8009,8010,8014,8017,8019,8024,8151,8168,8170,8189,8192,8198,8200,8205,8207,8348,8350,8354,8358,8363,8366,8369,8375,8381,8388,8391,8395,8413,8552,8555,8558,8567,8568,8570,8573,8574,8578,8593,8603,8610,8613,8617,8754,8758,8762,8763,8768,8769,8771,8774,8777,8781,8783,8785,8787,8803,8805,8809,8965,8966,8968,8971,8972,8976,8980,8981,8985,8988,8996,9001,9003,9006,9010,9016,9017,9149,9153,9172,9179,9180,9183,9197,9201,9204,9211,9347,9351,9355,9360,9362,9369,9372,9374,9376,9380,9382,9386,9388,9391,9394,9397,9399,9402,9405,9407,9411,9414,9540,9543,9568,9571,9573,9574,9577,9582,9585,9589,9596,9602,9606,9608,9615,9617,9628,9774,9779,9783,9785,9787,9791,9793,9797,9800,9811,9814,9815,9817,9820,9823,9835,9934,9941,9943,9944,9948,9952,9955,9958,9964,9969,9975,9978,9980,10008,10155,10168,10171,10177,10180,10183,10185,10187,10192,10194,10347,10348,10351,10355,10358,10362,10366,10368,10374,10383,10386,10392,10536,10538,10546,10550,10554,10557,10558,10560,10564,10592,10701,10704,10706,10710,10720,10727,10730,10732,10735,10747,10748,10750,10751,10753,10754,10886,10892,10899,10905,10911,10914,10926,10927,10929,10939,10994,10996,10998,11083,11086,11089,11098,11101,11108,11110,11113,11122,11302,11436,11603,11605,11609,11616,11617,11621,11622,11626,11628,11629,11631,11636,11637,11639,11641,11643,11645,11769,11773,11778,11780,11783,11794,11799,11802,11804,11942,11948,11957,11963,11967,11968,12109,12118,12123,12126,12127,12145,12295,12302,12306,12307,12309,12314,12317,12320,12335,12337,12465,12477,12488,12491,12494,12495,12498,12502,12506,12510,12513,12516,12535,12537,12538,12544,12548,12554,12670,12674,12678,12683,12685,12694,12700,12945,12958,12960,12964,12966,12970,12974,12975,12977,12979,12981,13000,13001,13003,13005,13007,13008,13012,13027,13031,13041,13052,13056,13057,13064,13067,13071,13074,13076,13078,13084,13090,13091,13101,13104,13105,13106,13119,13127,13129,13137,13140,13149,13159,13161,13163,13166,13168,13175,13176,13177,13183,13185,13186,13188,13190,13195,13196,13200,13201,13206,13217,13218,13225,13228,13230,13232,13240,13245,13247,13249,13250,13254,13256,13259,13263,13266,13268,13272,13274,13277,13278,13282,13283,13284,13288,13290,13291,13315,13319,13321,13322,13325,13328,13331,13332,13335,13338,13341,13344,13345,13346,13348,13351,13354,13359,13364,13370,13382,13388,13390,13397,13406,13407,13409,13411,13415,13417,13419,13421,13424,13426,13431,13433,13435,13437,13439,13442,13444,13446,13449,13458,13471,13473,13475,13476,13478,13483,13485,13486,13490,13507,13510,13512,13519,13520,13521,13523,13524,13526,13528,13532,13533,13534,13539,13540,13541,13543,13548,13550,13553,13554,13555,13559,13560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-chr19 47502070 47519370 m84039_230404_003541_s3/182191703/ccs 166,351,528,744,880,1061,1243,1431,1612,1759,1968,2152,2322,2516,2732,2958,3140,3333,3525,3704,3896,4074,4248,4414,4611,4792,4948,5133,5324,5513,5764,5934,6111,6308,6526,6672,6839,6999,7171,7374,7567,7758,7930,8112,8267,8468,8655,8819,9009,9220,9413,9610,9813,9962,10165,10325,10779,10968,11182,11413,11565,11740,11910,12162,12282,12466,12585,12827,13571,13692,13983,14133,14231,14371,14567,14869,15066,15158,15455,15642,15857,15983,16241,16443,16631,16816,17003, 95,123,142,87,138,134,107,115,123,165,136,121,151,137,148,135,148,127,126,132,139,133,128,137,130,140,150,136,160,135,93,127,137,129,92,133,126,167,126,108,121,133,153,142,163,104,132,108,127,133,141,108,106,123,113,301,108,104,140,109,124,161,132,105,138,118,153,102,120,104,108,87,139,148,114,148,91,169,106,114,109,117,110,134,130,138,114, 261,474,670,831,1018,1195,1350,1546,1735,1924,2104,2273,2473,2653,2880,3093,3288,3460,3651,3836,4035,4207,4376,4551,4741,4932,5098,5269,5484,5648,5857,6061,6248,6437,6618,6805,6965,7166,7297,7482,7688,7891,8083,8254,8430,8572,8787,8927,9136,9353,9554,9718,9919,10085,10278,10626,10887,11072,11322,11522,11689,11901,12042,12267,12420,12584,12738,12929,13691,13796,14091,14220,14370,14519,14681,15017,15157,15327,15561,15756,15966,16100,16351,16577,16761,16954,17117, 90,54,74,49,43,48,81,66,24,44,48,49,43,79,78,47,45,65,53,60,39,41,38,60,51,16,35,55,29,116,77,50,60,89,54,34,34,5,77,85,70,39,29,13,38,83,32,82,84,60,56,95,43,80,47,153,81,110,91,43,51,9,120,15,46,1,89,642,1,187,42,11,1,48,188,49,1,128,81,101,17,141,92,54,55,49,49, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,245,0,0,0,0,0,0,0,0,0,0,0,246,0,248,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,2,4,5,61,66,70,76,79,94,98,107,113,115,120,122,123,137,140,144,153,156,157,159,161,163,165,261,263,289,291,295,311,322,325,327,347,350,474,482,486,490,493,494,497,501,504,507,510,515,517,520,523,525,527,670,685,696,710,713,718,723,725,728,743,831,842,844,853,857,861,879,1018,1025,1032,1035,1047,1052,1060,1195,1205,1207,1210,1217,1221,1227,1236,1242,1350,1372,1373,1375,1376,1383,1386,1388,1404,1421,1430,1546,1550,1560,1565,1570,1610,1611,1735,1739,1758,1924,1927,1929,1932,1946,1957,1967,2104,2115,2123,2127,2135,2151,2273,2285,2290,2294,2297,2300,2303,2305,2307,2311,2316,2319,2321,2473,2481,2483,2491,2493,2496,2515,2653,2670,2686,2707,2709,2712,2715,2731,2880,2884,2893,2896,2899,2901,2903,2907,2908,2910,2911,2913,2916,2919,2921,2928,2931,2937,2940,2945,2957,3030,3093,3095,3097,3104,3106,3110,3124,3130,3132,3139,3288,3290,3293,3302,3303,3309,3319,3323,3332,3432,3460,3495,3519,3524,3651,3658,3662,3663,3666,3671,3678,3683,3684,3694,3703,3836,3848,3854,3856,3861,3867,3870,3875,3894,3895,4035,4037,4041,4044,4046,4049,4052,4056,4063,4064,4066,4068,4073,4207,4216,4227,4232,4244,4247,4376,4382,4383,4385,4387,4390,4392,4402,4404,4407,4413,4551,4560,4578,4582,4584,4592,4596,4599,4610,4741,4744,4749,4755,4756,4766,4769,4774,4777,4779,4791,4875,4932,4947,5098,5102,5103,5121,5122,5125,5130,5132,5269,5277,5295,5300,5302,5304,5315,5323,5484,5488,5490,5495,5496,5508,5510,5512,5648,5654,5660,5665,5669,5673,5677,5679,5684,5687,5691,5696,5698,5701,5709,5711,5761,5763,5857,5868,5870,5873,5874,5878,5879,5882,5888,5894,5895,5899,5902,5916,5920,5923,5926,5929,5933,6061,6065,6072,6088,6092,6104,6106,6110,6248,6254,6257,6276,6278,6281,6284,6287,6291,6305,6307,6437,6440,6447,6452,6454,6457,6461,6463,6466,6468,6470,6471,6475,6477,6479,6486,6488,6491,6499,6503,6505,6506,6513,6525,6618,6620,6624,6634,6636,6641,6643,6649,6665,6668,6671,6805,6807,6810,6814,6826,6838,6965,6978,6986,6988,6992,6994,6996,6998,7166,7170,7297,7308,7331,7334,7343,7347,7351,7353,7365,7373,7482,7485,7490,7506,7508,7511,7515,7528,7534,7536,7550,7551,7566,7688,7692,7696,7698,7703,7707,7709,7714,7716,7722,7726,7757,7814,7891,7902,7907,7912,7914,7929,8083,8085,8092,8097,8099,8111,8254,8261,8262,8266,8374,8430,8438,8441,8443,8446,8448,8452,8454,8457,8467,8572,8574,8609,8615,8618,8619,8631,8633,8654,8787,8790,8799,8802,8803,8805,8809,8818,8927,8945,8947,8949,8955,8956,8961,8966,8970,8973,8982,8984,8986,8988,8994,8998,9000,9006,9008,9136,9156,9171,9175,9177,9180,9186,9196,9213,9216,9219,9353,9367,9373,9375,9378,9381,9412,9528,9554,9556,9560,9567,9569,9572,9581,9588,9589,9591,9603,9609,9653,9718,9722,9724,9736,9750,9753,9754,9756,9774,9784,9787,9790,9792,9796,9798,9804,9812,9919,9938,9948,9951,9958,9961,10085,10087,10093,10096,10097,10101,10108,10109,10113,10115,10118,10123,10146,10149,10154,10164,10278,10285,10286,10289,10291,10293,10300,10304,10315,10318,10324,10626,10631,10635,10636,10639,10641,10645,10647,10655,10656,10658,10659,10660,10662,10665,10677,10682,10683,10685,10686,10688,10691,10692,10694,10697,10706,10709,10712,10715,10722,10726,10728,10729,10736,10741,10765,10767,10778,10887,10889,10896,10909,10911,10914,10917,10921,10926,10929,10931,10933,10935,10937,10948,10953,10958,10961,10962,10963,10967,11072,11086,11088,11092,11095,11111,11117,11119,11120,11136,11139,11143,11144,11145,11147,11150,11153,11179,11181,11322,11335,11337,11339,11341,11342,11343,11348,11356,11360,11364,11369,11371,11372,11374,11377,11383,11387,11389,11409,11412,11522,11538,11540,11544,11552,11556,11557,11561,11563,11564,11689,11692,11696,11697,11708,11711,11713,11715,11718,11722,11725,11729,11734,11739,11901,11909,11997,12042,12046,12049,12053,12057,12060,12067,12071,12076,12078,12081,12083,12086,12093,12097,12104,12114,12115,12117,12119,12125,12144,12161,12267,12271,12275,12281,12420,12423,12426,12427,12429,12433,12437,12440,12443,12458,12463,12465,12584,12695,12738,12752,12755,12770,12772,12783,12787,12789,12804,12826,12929,12937,12941,12947,12956,12960,12966,12981,12985,12986,13019,13022,13029,13032,13055,13068,13087,13089,13091,13094,13096,13103,13105,13111,13114,13116,13118,13124,13128,13129,13145,13146,13153,13158,13160,13162,13167,13172,13174,13176,13177,13180,13185,13189,13194,13198,13203,13204,13208,13209,13210,13214,13217,13240,13244,13246,13250,13253,13256,13257,13260,13263,13289,13295,13313,13315,13330,13331,13333,13335,13339,13341,13343,13345,13348,13350,13355,13357,13359,13361,13363,13366,13368,13370,13373,13395,13399,13400,13402,13407,13431,13434,13436,13450,13452,13456,13458,13463,13467,13474,13477,13483,13486,13489,13521,13534,13541,13543,13544,13546,13548,13550,13552,13557,13570,13691,13763,13796,13799,13807,13811,13821,13832,13842,13843,13846,13852,13855,13857,13860,13864,13870,13872,13876,13878,13880,13882,13886,13888,13906,13910,13915,13917,13921,13923,13938,13939,13940,13943,13944,13946,13947,13956,13958,13960,13963,13976,13979,13982,14091,14093,14096,14099,14102,14104,14108,14119,14132,14220,14222,14225,14230,14370,14519,14522,14525,14539,14543,14546,14547,14552,14554,14561,14563,14565,14566,14681,14702,14706,14707,14714,14720,14723,14733,14735,14744,14749,14780,14791,14799,14803,14824,14868,15017,15023,15025,15030,15040,15042,15045,15047,15050,15060,15062,15063,15065,15157,15201,15327,15337,15339,15341,15342,15357,15358,15363,15375,15383,15385,15388,15392,15395,15396,15398,15400,15403,15404,15409,15410,15413,15415,15421,15425,15432,15435,15438,15454,15496,15561,15564,15568,15569,15572,15575,15576,15578,15579,15580,15583,15592,15593,15595,15599,15607,15612,15613,15615,15619,15622,15630,15632,15637,15639,15641,15756,15760,15763,15767,15771,15774,15775,15776,15778,15782,15794,15801,15803,15813,15814,15817,15823,15826,15829,15850,15854,15856,15966,15979,15982,16100,16104,16106,16122,16124,16128,16130,16132,16137,16139,16145,16151,16152,16156,16158,16163,16166,16167,16171,16174,16177,16188,16189,16191,16193,16195,16196,16199,16202,16203,16210,16213,16223,16240,16351,16354,16356,16364,16365,16367,16370,16373,16379,16381,16389,16394,16396,16424,16430,16432,16442,16577,16581,16583,16585,16589,16591,16593,16599,16603,16606,16608,16611,16613,16617,16620,16625,16628,16630,16761,16770,16774,16777,16779,16782,16785,16788,16790,16793,16798,16801,16811,16815,16954,16962,16966,16973,16978,16998,17001,17002,17117,17122,17129,17131,17135,17137,17143,17149,17154,17165,17279,17281,17282,17283, -chr19 47502157 47518509 m84039_230404_003541_s3/211359295/ccs 58,311,429,770,965,1140,1343,1530,1729,1889,2098,2292,2463,2645,2893,3063,3269,3380,3522,3665,3806,3984,4112,4194,4405,4508,4612,4753,4935,5107,5300,5500,5690,5951,6102,6314,6457,6662,6822,7030,7217,7395,7586,7778,7948,8147,8333,8552,8722,8938,9144,9349,9539,9700,9804,9913,10125,10247,10455,10673,10854,11015,11187,11382,11560,11767,11922,12101,12319,12523,12654,13495,13645,14053,14265,14440,14598,14734,14862,15041,15251,15654,15786, 195,92,327,164,162,193,145,144,141,208,190,170,181,159,169,172,110,141,140,115,169,127,78,153,102,100,140,156,147,169,81,150,145,98,167,123,163,156,204,186,165,153,133,155,154,161,197,158,138,141,148,132,147,103,80,117,116,192,192,131,138,131,145,161,133,120,148,154,106,123,143,149,314,153,149,157,135,127,178,207,383,131,224, 253,403,756,934,1127,1333,1488,1674,1870,2097,2288,2462,2644,2804,3062,3235,3379,3521,3662,3780,3975,4111,4190,4347,4507,4608,4752,4909,5082,5276,5381,5650,5835,6049,6269,6437,6620,6818,7026,7216,7382,7548,7719,7933,8102,8308,8530,8710,8860,9079,9292,9481,9686,9803,9884,10030,10241,10439,10647,10804,10992,11146,11332,11543,11693,11887,12070,12255,12425,12646,12797,13644,13959,14206,14414,14597,14733,14861,15040,15248,15634,15785, 58,26,14,31,13,10,42,55,19,1,4,1,1,89,1,34,1,1,3,26,9,1,4,58,1,4,1,26,25,24,119,40,116,53,45,20,42,4,4,1,13,38,59,15,45,25,22,12,78,65,57,58,14,1,29,95,6,16,26,50,23,41,50,17,74,35,31,64,98,8,698,1,94,59,26,1,1,1,1,3,20,1, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,251,0,0,0,0,0,0,0,0,0,0,0, 0,1,3,4,33,43,57,253,301,310,403,406,414,423,428,756,769,934,937,944,954,964,1127,1129,1139,1333,1342,1488,1501,1522,1523,1529,1674,1678,1682,1693,1703,1705,1719,1725,1728,1870,1884,1885,1888,2097,2288,2290,2291,2462,2644,2804,2812,2814,2818,2824,2827,2832,2844,2848,2851,2853,2856,2858,2875,2879,2883,2888,2892,3015,3062,3235,3239,3244,3268,3379,3466,3521,3662,3664,3780,3785,3804,3805,3863,3975,3979,3983,4071,4111,4190,4191,4193,4241,4347,4374,4379,4381,4394,4400,4404,4431,4507,4608,4611,4752,4909,4914,4915,4919,4921,4930,4934,5082,5088,5091,5099,5101,5104,5106,5206,5276,5277,5284,5286,5290,5293,5296,5299,5381,5383,5434,5445,5447,5480,5488,5499,5617,5650,5662,5668,5670,5672,5674,5686,5687,5689,5835,5837,5838,5841,5845,5849,5856,5861,5864,5881,5894,5898,5899,5908,5910,5911,5913,5918,5921,5923,5927,5930,5932,5950,6049,6072,6076,6078,6096,6101,6269,6274,6310,6313,6437,6440,6445,6456,6620,6637,6639,6641,6646,6654,6658,6661,6818,6821,7026,7029,7216,7382,7394,7548,7568,7584,7585,7719,7723,7745,7758,7776,7777,7901,7933,7947,8102,8132,8135,8145,8146,8194,8247,8308,8322,8327,8330,8332,8530,8551,8710,8713,8716,8721,8764,8822,8860,8862,8866,8867,8872,8873,8877,8884,8891,8893,8895,8899,8917,8937,9079,9086,9088,9091,9124,9127,9130,9143,9255,9292,9323,9324,9348,9481,9491,9502,9512,9514,9520,9538,9686,9696,9699,9710,9772,9803,9884,9886,9890,9892,9912,9997,10030,10035,10055,10057,10058,10061,10073,10075,10078,10080,10082,10086,10089,10097,10102,10104,10107,10122,10124,10241,10246,10439,10454,10647,10652,10660,10672,10804,10807,10816,10820,10822,10825,10828,10830,10832,10837,10840,10846,10848,10851,10853,10992,11003,11005,11006,11009,11012,11014,11119,11146,11147,11160,11164,11174,11186,11332,11336,11338,11341,11344,11345,11350,11352,11357,11381,11468,11543,11544,11546,11548,11550,11552,11557,11559,11693,11695,11697,11699,11701,11703,11717,11721,11723,11724,11726,11729,11731,11735,11748,11757,11759,11763,11766,11887,11892,11906,11908,11910,11921,12070,12074,12078,12080,12088,12094,12096,12100,12255,12266,12268,12274,12278,12279,12281,12283,12289,12291,12299,12318,12425,12427,12429,12432,12434,12445,12446,12463,12465,12467,12470,12478,12480,12492,12496,12507,12511,12515,12520,12522,12603,12646,12653,12763,12797,12803,12807,12812,12814,12816,12837,12838,12840,12842,12844,12845,12849,12853,12855,12864,12871,12874,12878,12893,12927,12930,12937,12940,12955,12963,12965,12973,12976,12995,12997,13002,13004,13013,13019,13021,13022,13024,13026,13029,13032,13036,13037,13042,13044,13053,13054,13061,13064,13066,13068,13070,13075,13080,13082,13084,13085,13088,13093,13097,13100,13102,13106,13108,13111,13118,13122,13125,13148,13152,13154,13158,13161,13164,13165,13168,13171,13174,13177,13184,13187,13197,13203,13223,13240,13241,13249,13251,13253,13258,13260,13265,13267,13269,13273,13278,13280,13292,13305,13307,13309,13310,13312,13317,13320,13326,13341,13344,13346,13355,13357,13360,13362,13366,13367,13368,13373,13374,13375,13377,13381,13383,13384,13387,13389,13396,13399,13431,13444,13446,13451,13453,13454,13456,13458,13460,13462,13475,13478,13480,13483,13484,13486,13492,13494,13552,13582,13644,13959,13963,13964,13966,14001,14003,14006,14009,14012,14014,14033,14042,14044,14052,14206,14208,14214,14217,14221,14222,14239,14264,14382,14414,14417,14419,14430,14439,14597,14629,14689,14698,14733,14861,15040,15248,15250,15634,15645,15649,15653,15785,16010,16026,16029,16031,16048,16051,16053,16054,16060,16061,16065,16067,16072,16075,16076,16080,16083,16085,16086,16090,16091,16096,16097,16099,16101,16103,16106,16108,16110,16113,16114,16115,16120,16121,16125,16128,16131,16134,16135,16137,16140,16143,16148,16150,16152,16154,16157,16162,16164,16166,16169,16178,16180,16184,16187,16188,16193,16195,16196,16204,16207,16211,16212,16214,16216,16218,16222,16225,16226,16228,16230,16231,16238,16241,16242,16244,16246,16250,16260,16261,16262,16264,16278,16326,16327,16328,16329,16332, -chr19 47502336 47514147 m54329U_210323_190418/43647472/ccs 122,341,523,948,1689,2239,2378,2596,2783,2966,3159,3303,3492,3654,3826,4178,4302,4498,4657,4827,5019,5185,5397,5587,5743,5895,6075,6267,6443,6604,6739,7077,7235,7364,7551,7701,7903,8093,8287,8465,8663,8842,9044,9234,9390,10169,10549,10680,10844,11000,11185,11343, 142,114,93,85,86,100,133,123,136,102,100,120,96,115,115,123,140,119,113,123,84,102,95,87,108,130,118,122,133,128,181,127,123,135,120,138,142,141,148,162,129,109,103,96,88,255,80,131,106,149,121,316, 84,264,455,616,1033,1775,2339,2511,2719,2919,3068,3259,3423,3588,3769,3941,4301,4442,4617,4770,4950,5103,5287,5492,5674,5851,6025,6193,6389,6576,6732,6920,7204,7358,7499,7671,7839,8045,8234,8435,8627,8792,8951,9147,9330,9478,10424,10629,10811,10950,11149,11306,11659, 38,77,68,332,656,464,39,85,64,47,91,44,69,66,57,237,1,56,40,57,69,82,110,95,69,44,50,74,54,28,7,157,31,6,52,30,64,48,53,30,36,50,93,87,60,691,125,51,33,50,36,37,90, 0,0,0,246,0,0,0,0,0,0,0,0,0,0,0,248,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,245,0,0,0,0,0,0,0, 84,104,118,120,121,264,271,275,279,282,283,284,286,287,288,290,292,296,298,300,301,307,321,322,324,330,332,340,455,460,462,471,472,475,476,477,480,484,488,494,497,499,500,501,503,505,507,511,513,516,518,520,522,616,620,627,632,634,638,640,645,648,650,654,655,659,660,663,665,666,668,669,671,674,676,677,681,683,685,686,688,689,690,692,695,699,700,702,703,704,706,709,714,719,720,723,726,728,729,731,732,735,741,745,746,748,749,750,753,755,757,759,761,762,766,769,771,772,773,776,777,779,781,784,787,788,789,792,794,795,797,798,800,802,804,807,808,811,814,816,818,819,820,822,825,827,828,830,831,832,835,837,838,842,843,844,845,846,848,849,852,856,859,860,862,864,865,868,869,873,874,877,879,881,883,886,887,888,890,893,894,901,902,904,908,910,912,913,915,916,917,920,921,925,928,932,942,944,947,1033,1039,1043,1046,1049,1051,1054,1057,1058,1061,1064,1067,1069,1070,1075,1077,1078,1080,1082,1083,1084,1087,1092,1103,1104,1106,1107,1109,1110,1112,1113,1115,1116,1117,1120,1123,1125,1133,1136,1140,1141,1144,1145,1148,1151,1158,1161,1165,1167,1224,1228,1229,1231,1234,1237,1239,1247,1249,1251,1254,1261,1268,1272,1273,1275,1278,1280,1282,1283,1287,1290,1291,1297,1302,1304,1305,1307,1309,1311,1313,1326,1329,1330,1331,1333,1334,1335,1339,1341,1343,1345,1347,1348,1354,1356,1359,1362,1366,1372,1374,1375,1377,1382,1383,1385,1386,1387,1389,1393,1396,1397,1400,1405,1408,1415,1416,1418,1420,1421,1424,1426,1431,1434,1436,1437,1442,1446,1448,1450,1452,1456,1458,1459,1461,1464,1465,1468,1472,1476,1477,1480,1481,1491,1495,1499,1508,1510,1512,1513,1518,1528,1530,1584,1586,1590,1598,1601,1603,1607,1608,1611,1613,1615,1617,1620,1621,1624,1633,1636,1637,1645,1648,1650,1652,1654,1657,1662,1665,1678,1684,1688,1775,1781,1784,1787,1790,1791,1795,1798,1800,1803,1807,1808,1810,1812,1814,1823,1824,1827,1828,1834,1835,1836,1839,1840,1842,1845,1847,1848,1850,1853,1856,1858,1861,1865,1911,1914,1922,1923,1926,1929,1934,1936,1937,1939,1942,1943,1946,1947,1949,1950,1952,1954,1958,1960,1961,1963,1967,1970,1971,1973,1975,1978,1982,1986,1990,1992,1995,1999,2002,2003,2007,2008,2010,2011,2013,2015,2018,2019,2023,2025,2028,2032,2035,2038,2057,2059,2111,2118,2127,2129,2134,2152,2162,2165,2166,2168,2171,2172,2176,2178,2183,2186,2189,2193,2196,2199,2202,2208,2211,2213,2217,2221,2223,2236,2238,2339,2344,2348,2351,2354,2355,2357,2361,2365,2367,2369,2371,2373,2375,2377,2511,2512,2515,2521,2524,2526,2529,2539,2541,2544,2545,2546,2547,2554,2563,2566,2569,2570,2572,2575,2579,2580,2581,2583,2585,2595,2619,2659,2719,2721,2725,2731,2734,2737,2773,2780,2782,2919,2923,2926,2928,2933,2941,2942,2954,2960,2964,2965,3068,3071,3086,3088,3093,3094,3095,3099,3101,3103,3107,3110,3115,3116,3124,3128,3130,3131,3133,3134,3136,3139,3158,3259,3261,3264,3267,3269,3272,3278,3291,3295,3299,3302,3423,3424,3426,3443,3453,3454,3455,3458,3460,3462,3464,3467,3469,3470,3491,3588,3603,3607,3610,3612,3615,3617,3621,3626,3627,3629,3631,3634,3635,3641,3642,3644,3646,3649,3651,3653,3769,3772,3776,3778,3782,3785,3787,3789,3790,3793,3797,3800,3802,3804,3805,3807,3809,3813,3814,3816,3818,3822,3823,3825,3941,3942,3944,3948,3952,3957,3961,3964,3965,3966,3968,3970,3971,3973,3978,3979,3983,3984,3985,3988,3993,3994,3997,3999,4003,4004,4006,4008,4017,4020,4021,4023,4027,4029,4031,4032,4033,4036,4038,4039,4043,4046,4047,4048,4055,4059,4062,4067,4071,4073,4075,4076,4079,4082,4083,4085,4087,4091,4092,4094,4095,4097,4099,4100,4103,4107,4109,4110,4113,4117,4123,4128,4131,4133,4138,4143,4145,4148,4154,4157,4163,4164,4168,4177,4301,4442,4449,4453,4454,4458,4461,4462,4464,4466,4473,4482,4484,4485,4490,4491,4492,4496,4497,4617,4620,4622,4624,4626,4629,4633,4639,4645,4647,4652,4656,4770,4774,4784,4787,4791,4793,4796,4799,4801,4804,4808,4809,4813,4818,4820,4822,4826,4950,4954,4965,4969,4972,4976,4980,4985,4987,4999,5001,5004,5008,5011,5018,5103,5106,5107,5112,5114,5116,5120,5123,5126,5129,5132,5137,5138,5141,5146,5149,5153,5157,5160,5168,5176,5179,5184,5287,5293,5295,5301,5306,5309,5310,5318,5320,5322,5323,5327,5329,5331,5333,5334,5338,5340,5341,5342,5347,5353,5356,5361,5363,5366,5368,5371,5372,5374,5378,5381,5382,5389,5395,5396,5492,5502,5504,5511,5516,5517,5519,5523,5528,5532,5536,5539,5540,5543,5546,5551,5564,5586,5674,5685,5690,5693,5703,5705,5706,5710,5714,5718,5720,5723,5742,5851,5853,5878,5882,5884,5887,5894,6025,6039,6041,6043,6046,6048,6054,6061,6065,6072,6074,6193,6195,6202,6204,6205,6209,6211,6212,6218,6220,6226,6227,6229,6231,6232,6238,6240,6241,6242,6244,6246,6247,6248,6250,6252,6253,6254,6259,6264,6266,6389,6392,6397,6399,6400,6403,6404,6405,6408,6411,6415,6417,6420,6424,6428,6431,6436,6442,6576,6578,6580,6581,6583,6595,6599,6600,6603,6732,6734,6736,6738,6920,6938,6939,6941,6942,6944,6947,6996,7037,7039,7041,7043,7044,7046,7050,7062,7064,7070,7073,7076,7204,7224,7227,7228,7232,7234,7358,7363,7499,7504,7510,7515,7516,7521,7522,7523,7527,7528,7529,7534,7536,7538,7541,7542,7548,7550,7671,7690,7700,7839,7841,7844,7845,7851,7853,7856,7858,7862,7863,7865,7868,7869,7872,7874,7875,7880,7885,7887,7889,7902,8045,8048,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-chr19 47502433 47514189 m64076_221119_202646/39062020/ccs 158,472,639,829,996,1194,1354,1494,1702,1864,1998,2183,2374,2556,2749,2933,3139,3309,3510,3685,3864,4190,4399,4555,4837,5010,5167,5348,5532,5701,5892,6049,6262,6398,7059,7237,7402,7564,7757,7936,8076,8218,8412,8607,8786,8947,9143,9338,9491,9649,9778,9992,10148,10341,10486,10665,10796,11067,11210,11383, 313,163,145,135,135,125,139,175,115,129,100,145,147,124,154,157,138,140,118,121,288,124,85,235,106,121,130,162,117,126,113,130,135,614,136,134,127,116,124,139,141,149,140,130,137,131,143,152,126,128,111,108,136,108,120,130,139,95,104,91, 141,471,635,784,964,1131,1319,1493,1669,1817,1993,2098,2328,2521,2680,2903,3090,3277,3449,3628,3806,4152,4314,4484,4790,4943,5131,5297,5510,5649,5827,6005,6179,6397,7012,7195,7371,7529,7680,7881,8075,8217,8367,8552,8737,8923,9078,9286,9490,9617,9777,9889,10100,10284,10449,10606,10795,10935,11162,11314,11474, 17,1,4,45,32,63,35,1,33,47,5,85,46,35,69,30,49,32,61,57,58,38,85,71,47,67,36,51,22,52,65,44,83,1,47,42,31,35,77,55,1,1,45,55,49,24,65,52,1,32,1,103,48,57,37,59,1,132,48,69,186, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,246, 141,147,150,151,155,157,471,635,638,784,786,804,805,807,811,813,815,828,964,967,970,972,973,978,980,983,985,990,995,1131,1140,1150,1152,1154,1157,1163,1164,1169,1171,1175,1181,1186,1193,1319,1334,1337,1345,1349,1351,1353,1493,1669,1673,1682,1684,1693,1698,1701,1817,1825,1826,1829,1832,1837,1840,1842,1849,1855,1857,1861,1863,1993,1995,1997,2098,2104,2110,2115,2119,2123,2125,2127,2135,2138,2140,2141,2152,2155,2157,2181,2182,2328,2334,2349,2351,2354,2357,2373,2521,2526,2535,2541,2543,2545,2549,2555,2680,2699,2701,2714,2715,2718,2722,2725,2735,2737,2741,2743,2748,2873,2903,2910,2913,2916,2918,2922,2927,2930,2932,3090,3092,3093,3097,3099,3102,3103,3110,3113,3115,3118,3130,3137,3138,3277,3281,3290,3293,3305,3308,3449,3455,3457,3461,3476,3484,3487,3490,3492,3496,3498,3505,3509,3628,3632,3639,3643,3646,3650,3652,3659,3671,3674,3678,3684,3806,3808,3813,3819,3827,3830,3834,3839,3843,3844,3846,3850,3859,3863,4152,4157,4161,4163,4169,4179,4189,4314,4324,4326,4330,4339,4342,4344,4351,4355,4360,4363,4375,4384,4386,4387,4398,4484,4496,4498,4501,4502,4504,4505,4508,4510,4518,4519,4520,4524,4525,4531,4535,4536,4541,4547,4554,4790,4800,4802,4804,4810,4814,4820,4827,4829,4831,4836,4943,4945,4947,4958,4965,4966,4969,4973,4976,4979,4983,4985,4989,4993,5009,5131,5148,5151,5155,5160,5166,5297,5316,5320,5322,5327,5330,5339,5344,5347,5510,5511,5516,5521,5531,5649,5658,5661,5663,5668,5671,5674,5678,5681,5684,5685,5688,5700,5827,5850,5856,5858,5862,5865,5869,5871,5875,5881,5884,5891,6005,6013,6019,6027,6030,6036,6038,6041,6048,6179,6204,6206,6220,6222,6225,6229,6231,6256,6261,6364,6397,7012,7018,7024,7027,7029,7036,7050,7053,7058,7195,7196,7205,7207,7210,7211,7217,7225,7233,7236,7371,7401,7529,7536,7543,7547,7550,7554,7559,7563,7680,7685,7698,7702,7707,7709,7714,7715,7728,7730,7733,7737,7739,7742,7744,7747,7754,7756,7881,7891,7893,7898,7907,7908,7911,7913,7915,7924,7933,7935,8075,8146,8217,8367,8374,8384,8389,8393,8411,8552,8569,8572,8580,8585,8590,8594,8600,8601,8606,8737,8741,8742,8747,8749,8756,8760,8763,8767,8781,8785,8923,8931,8932,8935,8939,8944,8946,9078,9091,9093,9095,9101,9108,9111,9114,9115,9118,9127,9132,9134,9142,9286,9292,9294,9295,9298,9301,9307,9318,9323,9333,9337,9490,9617,9619,9625,9627,9631,9635,9645,9648,9777,9889,9901,9904,9905,9907,9911,9917,9920,9923,9927,9930,9931,9934,9936,9938,9941,9945,9949,9951,9958,9963,9966,9969,9975,9991,10100,10110,10111,10116,10119,10121,10123,10127,10129,10133,10137,10147,10284,10286,10289,10290,10292,10300,10310,10312,10315,10319,10320,10321,10327,10328,10340,10449,10451,10459,10463,10466,10470,10472,10485,10606,10612,10617,10620,10622,10631,10634,10637,10642,10656,10659,10664,10795,10935,10940,10944,10946,10948,10950,10952,10956,10957,10962,10967,10971,10975,10980,10982,10984,10986,10987,10993,10994,10998,11001,11002,11005,11009,11014,11016,11017,11019,11022,11023,11028,11032,11034,11036,11054,11057,11066,11162,11183,11185,11189,11201,11206,11209,11314,11327,11331,11334,11337,11349,11353,11356,11358,11360,11382,11474,11477,11482,11484,11489,11490,11496,11499,11502,11506,11507,11512,11516,11518,11521,11527,11531,11536,11546,11562,11571,11642,11644,11652,11660, -chr19 47502578 47527331 m84008_230107_003043_s1/93585759/ccs 207,355,578,779,1020,1185,1381,1557,1750,1895,2091,2281,2715,2860,3036,3241,3384,3590,3754,3985,4196,4396,4583,4762,4952,5146,5351,5520,5702,5889,6111,6316,6479,6606,6938,7099,7258,7475,7688,7869,8061,8231,8470,8629,8849,9072,9243,9456,9705,9896,10065,10377,10630,10831,10994,11172,11324,11470,11661,11824,11967,12114,12255,12469,13025,13258,13401,13601,13760,13906,14115,14296,14454,14629,14777,14988,15307,15557,15707,16160,16299,16489,16687,16942,17100,17248,17418,17736,17963,18110,18288,18463,18645,18835,19098,19261,19433,19619,19841,20029,20216,20358,20526,20871,21079,21278,21439,21627,21944,22111,22521,22694,22877,23071,23262,23492,23805,23906,24089,24338, 115,147,127,121,98,157,110,166,142,195,187,355,127,153,178,139,158,163,178,175,166,164,148,137,126,153,152,131,186,207,160,111,126,273,150,155,172,148,110,127,124,122,136,157,181,135,158,248,128,99,158,190,140,106,155,135,126,130,125,131,114,133,131,116,232,131,199,81,124,155,128,157,141,139,116,318,107,146,335,124,145,135,154,122,118,169,315,165,146,155,106,143,123,126,81,135,154,161,187,147,141,140,284,167,198,127,162,304,144,329,156,165,173,137,131,312,100,119,111,124, 179,322,502,705,900,1118,1342,1491,1723,1892,2090,2278,2636,2842,3013,3214,3380,3542,3753,3932,4160,4362,4560,4731,4899,5078,5299,5503,5651,5888,6096,6271,6427,6605,6879,7088,7254,7430,7623,7798,7996,8185,8353,8606,8786,9030,9207,9401,9704,9833,9995,10223,10567,10770,10937,11149,11307,11450,11600,11786,11955,12081,12247,12386,12585,13257,13389,13600,13682,13884,14061,14243,14453,14595,14768,14893,15306,15414,15703,16042,16284,16444,16624,16841,17064,17218,17417,17733,17901,18109,18265,18394,18606,18768,18961,19179,19396,19587,19780,20028,20176,20357,20498,20810,21038,21277,21405,21601,21931,22088,22440,22677,22859,23050,23208,23393,23804,23905,24025,24200,24462, 28,33,76,74,120,67,39,66,27,3,1,3,79,18,23,27,4,48,1,53,36,34,23,31,53,68,52,17,51,1,15,45,52,1,59,11,4,45,65,71,65,46,117,23,63,42,36,55,1,63,70,154,63,61,57,23,17,20,61,38,12,33,8,83,440,1,12,1,78,22,54,53,1,34,9,95,1,143,4,118,15,45,63,101,36,30,1,3,62,1,23,69,39,67,137,82,37,32,61,1,40,1,28,61,41,1,34,26,13,23,81,17,18,21,54,99,1,1,64,138,73, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,244,0,0,0,0,0,0,0,0,0,0,0,0,249,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,243,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 22,27,29,33,179,192,194,200,206,322,328,331,339,350,354,502,527,530,534,537,540,545,548,577,705,715,721,761,767,778,900,917,918,920,924,926,962,967,969,987,990,998,1019,1118,1121,1144,1146,1148,1153,1160,1165,1180,1181,1184,1342,1346,1350,1354,1369,1371,1373,1376,1377,1380,1491,1498,1534,1543,1551,1556,1723,1749,1892,1894,2090,2278,2280,2636,2639,2642,2682,2695,2705,2714,2842,2849,2859,3013,3023,3029,3032,3035,3214,3216,3221,3240,3380,3383,3542,3545,3560,3562,3564,3568,3573,3578,3589,3753,3932,3938,3940,3944,3948,3951,3954,3957,3958,3961,3963,3984,4160,4167,4183,4189,4195,4362,4368,4372,4379,4395,4560,4572,4574,4576,4582,4731,4758,4761,4899,4903,4907,4916,4927,4936,4945,4951,5078,5102,5115,5117,5120,5121,5123,5127,5144,5145,5299,5307,5312,5325,5326,5350,5503,5506,5508,5510,5513,5516,5519,5651,5669,5688,5693,5701,5888,6096,6098,6104,6110,6172,6271,6281,6299,6315,6394,6427,6435,6449,6456,6478,6605,6879,6919,6924,6930,6937,7088,7095,7098,7254,7257,7430,7437,7441,7447,7456,7459,7461,7474,7623,7628,7630,7633,7639,7644,7655,7661,7663,7668,7680,7687,7798,7810,7816,7817,7820,7823,7828,7840,7868,7960,7996,7998,8001,8002,8031,8033,8052,8055,8060,8185,8189,8190,8195,8196,8198,8201,8208,8212,8214,8217,8219,8222,8230,8266,8353,8358,8402,8407,8409,8418,8448,8453,8460,8467,8469,8606,8609,8624,8628,8786,8828,8831,8833,8837,8840,8843,8844,8847,8848,9030,9032,9034,9039,9041,9052,9057,9061,9062,9066,9071,9207,9212,9214,9216,9236,9239,9240,9242,9368,9401,9403,9413,9415,9444,9447,9448,9455,9704,9807,9833,9845,9850,9856,9859,9887,9895,9995,9998,10001,10030,10045,10062,10064,10223,10225,10230,10232,10236,10254,10269,10274,10276,10281,10287,10291,10298,10299,10302,10310,10330,10376,10567,10569,10573,10575,10576,10579,10584,10595,10599,10605,10609,10629,10770,10772,10775,10777,10779,10780,10782,10784,10786,10788,10793,10795,10798,10803,10822,10823,10830,10937,10948,10955,10959,10964,10976,10981,10986,10988,10993,11149,11151,11165,11168,11171,11307,11323,11450,11457,11469,11571,11600,11605,11619,11631,11642,11643,11647,11649,11650,11658,11660,11786,11787,11801,11803,11818,11823,11922,11955,11960,11966,12081,12089,12094,12098,12113,12247,12254,12386,12411,12414,12416,12418,12419,12423,12427,12429,12438,12442,12443,12445,12463,12467,12468,12559,12585,12586,12618,12627,12637,12639,12641,12648,12658,12663,12666,12670,12675,12689,12690,12695,12698,12720,12724,12736,12737,12740,12743,12746,12750,12751,12753,12756,12775,12810,12818,12820,12822,12824,12829,12834,12836,12838,12842,12847,12849,12861,12876,12878,12879,12881,12886,12910,12913,12915,12922,12923,12924,12926,12931,12936,12945,12957,12962,12964,12967,13021,13022,13024,13257,13389,13400,13600,13682,13687,13690,13693,13696,13704,13709,13713,13714,13716,13722,13723,13729,13736,13737,13751,13759,13884,13885,13887,13899,13905,14061,14100,14102,14109,14114,14243,14247,14255,14263,14265,14266,14268,14273,14288,14293,14295,14453,14595,14598,14606,14609,14610,14616,14628,14768,14769,14771,14776,14893,14909,14913,14916,14933,14941,14949,14953,14956,14957,14959,14967,14969,14985,14987,15306,15414,15417,15436,15444,15449,15455,15458,15465,15481,15484,15487,15491,15494,15496,15501,15503,15507,15509,15515,15556,15703,15706,16042,16058,16060,16104,16106,16108,16111,16119,16138,16159,16231,16253,16284,16298,16444,16448,16455,16473,16488,16624,16644,16655,16670,16678,16681,16684,16686,16841,16853,16874,16881,16891,16902,16904,16909,16913,16923,16927,16933,16935,16941,17064,17071,17081,17083,17087,17094,17099,17218,17226,17247,17417,17733,17735,17901,17924,17939,17953,17962,18109,18265,18267,18282,18287,18394,18397,18405,18411,18416,18418,18427,18441,18462,18495,18606,18611,18637,18640,18644,18768,18777,18780,18782,18785,18788,18793,18797,18808,18809,18813,18824,18830,18834,18866,18961,18964,18986,19004,19008,19009,19012,19016,19020,19022,19034,19037,19054,19067,19081,19083,19095,19097,19179,19190,19216,19221,19223,19225,19252,19260,19396,19416,19430,19432,19587,19606,19613,19618,19780,19788,19790,19791,19810,19817,19840,20028,20139,20176,20215,20357,20498,20525,20810,20814,20815,20824,20831,20844,20846,20851,20868,20870,21038,21040,21044,21047,21048,21073,21078,21277,21405,21409,21423,21428,21438,21601,21626,21931,21943,22088,22090,22094,22101,22106,22108,22110,22440,22452,22453,22455,22456,22499,22501,22504,22520,22677,22678,22688,22691,22693,22859,22876,23050,23067,23070,23208,23210,23215,23217,23220,23227,23261,23393,23398,23407,23437,23449,23478,23484,23491,23804,23905,24025,24031,24036,24041,24071,24077,24084,24088,24200,24204,24206,24228,24252,24256,24265,24269,24272,24288,24290,24294,24298,24299,24301,24326,24337,24462,24468,24470,24473,24476,24495,24497,24500,24522,24526,24527,24534,24650, -chr19 47502663 47516933 m84039_230404_003541_s3/96539427/ccs 158,289,486,669,838,1045,1218,1413,1619,1828,1985,2122,2331,2555,2707,2958,3128,3320,3472,3663,3874,4083,4256,4434,4625,4787,4993,5176,5352,5524,5722,5893,6042,6231,6405,6576,6749,6963,7137,7343,7543,7738,7886,8053,8218,8422,8595,8761,8949,9114,9279,9437,9649,9948,10148,10328,10574,10709,10921,11117,11305,11532,11706,11846,12036,12171,12950,13154,13275,13448,13627,13801,14012, 130,136,117,122,128,98,119,140,138,126,136,178,155,114,147,95,110,103,83,136,127,139,142,190,137,139,151,144,128,132,134,129,139,117,117,128,145,106,126,128,155,110,140,143,161,153,112,150,149,101,121,128,199,139,137,135,128,168,143,123,149,140,139,152,134,126,148,110,126,138,136,169,130, 98,288,425,603,791,966,1143,1337,1553,1757,1954,2121,2300,2486,2669,2854,3053,3238,3423,3555,3799,4001,4222,4398,4624,4762,4926,5144,5320,5480,5656,5856,6022,6181,6348,6522,6704,6894,7069,7263,7471,7698,7848,8026,8196,8379,8575,8707,8911,9098,9215,9400,9565,9848,10087,10285,10463,10702,10877,11064,11240,11454,11672,11845,11998,12170,12297,13098,13264,13401,13586,13763,13970, 60,1,61,66,47,79,75,76,66,71,31,1,31,69,38,104,75,82,49,108,75,82,34,36,1,25,67,32,32,44,66,37,20,50,57,54,45,69,68,80,72,40,38,27,22,43,20,54,38,16,64,37,84,100,61,43,111,7,44,53,65,78,34,1,38,1,653,56,11,47,41,38,42, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,251,0,0,0,0,0,0, 1,3,5,6,98,106,120,123,129,133,135,138,140,153,157,288,425,427,431,439,442,443,454,458,459,465,485,603,613,615,618,625,635,642,644,649,651,668,791,794,816,818,829,835,837,966,976,982,1003,1004,1008,1010,1025,1028,1041,1044,1143,1155,1157,1174,1185,1186,1187,1197,1204,1207,1217,1275,1337,1363,1371,1372,1380,1383,1399,1412,1553,1558,1567,1577,1580,1588,1595,1603,1616,1618,1757,1759,1781,1782,1784,1827,1954,1957,1984,2095,2121,2300,2304,2313,2316,2328,2330,2374,2440,2486,2514,2540,2554,2669,2676,2677,2679,2695,2700,2706,2766,2854,2858,2869,2870,2880,2883,2904,2934,2957,3053,3056,3123,3125,3127,3238,3240,3251,3255,3266,3275,3278,3284,3290,3292,3294,3319,3423,3431,3440,3449,3451,3452,3455,3459,3469,3471,3555,3560,3619,3627,3642,3651,3662,3799,3804,3806,3835,3837,3839,3869,3871,3873,4001,4024,4066,4068,4072,4082,4192,4222,4234,4238,4243,4247,4255,4328,4398,4403,4408,4410,4433,4624,4664,4762,4765,4774,4776,4780,4783,4786,4899,4926,4948,4956,4960,4964,4966,4969,4978,4980,4983,4984,4990,4992,5064,5144,5147,5151,5157,5161,5175,5294,5320,5343,5351,5453,5480,5505,5523,5656,5659,5683,5689,5693,5701,5716,5721,5788,5856,5858,5881,5883,5892,6022,6024,6041,6181,6182,6185,6205,6211,6213,6216,6220,6226,6230,6311,6348,6351,6359,6368,6376,6386,6394,6396,6400,6402,6404,6496,6522,6529,6532,6536,6549,6550,6552,6562,6575,6704,6710,6717,6740,6743,6748,6894,6897,6909,6918,6920,6927,6936,6961,6962,7069,7082,7083,7086,7088,7091,7101,7104,7105,7107,7112,7117,7124,7126,7132,7136,7263,7265,7267,7268,7274,7286,7288,7294,7303,7312,7333,7339,7342,7471,7492,7494,7508,7511,7512,7518,7520,7536,7542,7663,7698,7700,7718,7737,7848,7867,7870,7885,8026,8027,8039,8041,8044,8048,8050,8052,8196,8210,8213,8217,8260,8379,8390,8404,8406,8421,8575,8577,8578,8594,8707,8719,8744,8747,8752,8760,8911,8921,8928,8935,8942,8948,9098,9113,9215,9221,9226,9234,9237,9259,9260,9275,9278,9400,9405,9408,9421,9433,9436,9565,9578,9582,9583,9587,9590,9595,9597,9600,9614,9621,9627,9630,9648,9848,9857,9878,9880,9882,9896,9899,9902,9915,9919,9922,9925,9938,9947,10087,10090,10099,10100,10114,10127,10141,10147,10285,10327,10361,10463,10475,10492,10494,10498,10500,10501,10504,10507,10509,10517,10532,10533,10553,10556,10559,10573,10702,10704,10706,10708,10877,10886,10907,10920,11064,11068,11095,11099,11116,11240,11260,11268,11272,11276,11279,11285,11289,11294,11297,11304,11454,11471,11479,11484,11486,11495,11498,11500,11507,11510,11517,11518,11522,11527,11531,11590,11672,11675,11681,11686,11704,11705,11845,11998,12013,12022,12028,12035,12094,12128,12170,12297,12306,12327,12328,12330,12332,12334,12335,12339,12345,12354,12364,12380,12384,12385,12392,12395,12399,12404,12412,12418,12428,12431,12456,12464,12467,12476,12486,12490,12493,12495,12519,12527,12534,12543,12544,12556,12558,12560,12565,12570,12572,12574,12578,12587,12590,12601,12602,12606,12607,12612,12615,12624,12639,12641,12645,12648,12652,12664,12665,12672,12682,12700,12707,12709,12715,12723,12724,12726,12728,12732,12734,12736,12741,12748,12750,12754,12756,12759,12761,12763,12766,12774,12783,12787,12789,12791,12794,12808,12826,12828,12842,12848,12849,12850,12855,12857,12863,12869,12871,12875,12876,12878,12881,12926,12928,12933,12936,12938,12940,12942,12944,12949,13098,13101,13106,13107,13108,13118,13124,13126,13144,13153,13264,13274,13401,13404,13412,13417,13423,13447,13586,13597,13600,13603,13607,13611,13613,13616,13620,13626,13728,13763,13770,13788,13789,13791,13795,13796,13797,13800,13970,13983,13993,13996,14004,14007,14011,14142,14153,14168,14171,14178,14180,14188,14193,14195,14197,14212,14229,14230, -chr19 47502899 47513582 m84039_230401_034725_s4/93523871/ccs 217,434,604,780,1188,1418,1577,1775,2228,2412,2593,2787,3056,3260,3455,3729,3970,4126,4347,4966,5216,5435,5651,5882,6100,6378,6555,6787,6910,7133,7335,7605,7761,7963,8157,8409,8607,8826,9017,9204,9383,9523,9713,9914,10198,10377, 145,125,119,134,139,108,111,112,129,129,119,109,119,115,110,80,103,130,119,110,106,100,110,98,96,119,77,122,141,103,87,111,106,135,96,118,113,78,126,112,111,130,121,119,123,92, 118,362,559,723,914,1327,1526,1688,1887,2357,2541,2712,2896,3175,3375,3565,3809,4073,4256,4466,5076,5322,5535,5761,5980,6196,6497,6632,6909,7051,7236,7422,7716,7867,8098,8253,8527,8720,8904,9143,9316,9494,9653,9834,10033,10321,10469, 99,72,45,57,274,91,51,87,341,55,52,75,160,85,80,164,161,53,91,500,140,113,116,121,120,182,58,155,1,82,99,183,45,96,59,156,80,106,113,61,67,29,60,80,165,56,49, 0,0,0,0,0,0,0,0,0,0,0,0,244,0,0,0,244,0,0,0,0,0,0,0,0,247,0,244,0,0,0,244,0,0,0,0,0,0,0,0,0,0,0,0,244,0,0, 0,4,5,8,118,129,132,136,137,156,158,160,163,166,169,172,182,183,192,196,198,199,202,206,216,248,362,365,369,379,381,384,395,396,397,401,402,408,410,415,433,559,561,569,577,580,581,584,587,601,603,723,733,738,740,743,749,762,765,766,771,775,777,779,914,925,927,931,943,946,954,955,956,964,966,968,971,973,976,978,980,987,988,993,995,1001,1003,1004,1007,1009,1013,1019,1021,1033,1105,1107,1123,1130,1139,1140,1144,1145,1148,1151,1158,1163,1165,1172,1173,1176,1180,1185,1187,1285,1327,1336,1346,1349,1353,1355,1357,1358,1361,1364,1369,1371,1372,1374,1377,1378,1381,1382,1389,1393,1395,1402,1408,1417,1526,1528,1532,1544,1546,1547,1550,1551,1553,1570,1576,1688,1690,1706,1714,1715,1718,1720,1723,1738,1751,1755,1758,1760,1774,1887,1890,1904,1906,1908,1909,1921,1933,1935,1941,1946,1950,1952,1953,1958,1959,1960,1963,1964,1973,1975,1980,1981,1988,2000,2006,2009,2013,2019,2023,2087,2090,2093,2095,2111,2114,2121,2122,2128,2133,2134,2139,2142,2151,2155,2159,2164,2168,2169,2171,2179,2182,2184,2187,2194,2204,2207,2209,2211,2212,2214,2216,2218,2224,2227,2357,2360,2375,2376,2385,2388,2393,2394,2398,2399,2411,2541,2549,2550,2554,2556,2562,2564,2565,2568,2570,2573,2581,2592,2712,2727,2729,2733,2736,2739,2747,2751,2754,2758,2759,2764,2766,2778,2786,2896,2898,2901,2908,2910,2921,2925,2927,2931,2932,2934,2940,2942,2945,2947,2948,2951,2953,2963,2965,2968,2970,2978,2979,2989,2993,2996,2998,2999,3001,3002,3010,3016,3019,3022,3024,3026,3028,3030,3031,3037,3041,3044,3049,3055,3175,3191,3195,3199,3201,3203,3206,3210,3212,3216,3219,3221,3223,3224,3227,3231,3234,3236,3238,3239,3243,3247,3248,3250,3252,3259,3375,3378,3382,3386,3398,3399,3404,3407,3412,3417,3418,3419,3422,3427,3428,3431,3433,3438,3454,3565,3572,3577,3579,3588,3591,3593,3597,3613,3615,3619,3621,3623,3626,3628,3631,3634,3638,3677,3680,3684,3689,3691,3693,3695,3701,3703,3712,3715,3719,3728,3809,3815,3816,3820,3839,3841,3849,3850,3851,3856,3868,3871,3874,3876,3883,3887,3888,3892,3895,3896,3898,3904,3907,3916,3918,3919,3925,3931,3936,3941,3942,3944,3946,3949,3951,3952,3954,3957,3961,3965,3966,3969,4073,4086,4090,4093,4103,4118,4122,4125,4256,4262,4273,4277,4278,4280,4283,4285,4290,4296,4300,4305,4307,4314,4322,4324,4327,4332,4334,4336,4346,4466,4469,4474,4476,4478,4492,4497,4500,4503,4504,4507,4510,4514,4516,4517,4520,4524,4528,4530,4540,4571,4579,4582,4651,4656,4658,4662,4664,4669,4670,4674,4675,4676,4679,4682,4684,4686,4688,4691,4697,4699,4705,4706,4708,4710,4713,4715,4717,4724,4726,4728,4733,4734,4737,4739,4742,4743,4753,4755,4756,4760,4762,4764,4766,4767,4780,4783,4786,4796,4804,4865,4875,4883,4885,4896,4899,4904,4905,4908,4913,4918,4921,4922,4925,4931,4933,4935,4937,4944,4949,4952,4956,4959,4965,5076,5077,5100,5107,5111,5118,5123,5126,5128,5129,5131,5136,5150,5152,5153,5155,5159,5160,5164,5165,5169,5171,5172,5174,5176,5179,5184,5188,5191,5193,5195,5198,5204,5208,5215,5322,5326,5333,5337,5339,5354,5357,5362,5365,5366,5368,5371,5373,5375,5377,5380,5382,5385,5388,5392,5395,5399,5401,5407,5410,5411,5414,5416,5417,5421,5427,5430,5432,5434,5460,5517,5535,5538,5543,5557,5560,5566,5568,5574,5578,5580,5585,5589,5591,5593,5595,5597,5603,5605,5610,5613,5615,5617,5618,5619,5620,5625,5627,5630,5634,5636,5643,5650,5761,5783,5785,5786,5791,5793,5797,5799,5801,5806,5807,5809,5811,5819,5820,5822,5825,5830,5833,5836,5838,5841,5844,5848,5850,5861,5864,5866,5868,5881,5980,5987,5993,5995,5997,5999,6001,6003,6011,6014,6028,6032,6040,6042,6047,6048,6050,6052,6056,6059,6060,6062,6063,6067,6068,6071,6073,6076,6078,6084,6086,6096,6099,6196,6201,6209,6211,6216,6220,6223,6225,6227,6231,6233,6236,6241,6244,6246,6248,6250,6252,6254,6257,6258,6261,6266,6268,6270,6275,6277,6278,6279,6285,6288,6291,6294,6295,6302,6303,6304,6312,6315,6318,6323,6328,6332,6337,6341,6345,6349,6352,6353,6360,6361,6364,6366,6368,6374,6377,6497,6503,6506,6518,6522,6526,6531,6532,6543,6548,6554,6632,6637,6644,6645,6660,6661,6670,6672,6681,6683,6686,6690,6691,6692,6703,6704,6708,6709,6711,6714,6716,6718,6722,6725,6726,6732,6735,6737,6740,6741,6745,6747,6753,6755,6757,6759,6760,6763,6766,6769,6770,6779,6781,6783,6786,6909,6940,7051,7053,7057,7059,7066,7067,7068,7073,7082,7084,7086,7087,7088,7091,7092,7094,7097,7103,7106,7107,7109,7111,7115,7117,7132,7161,7236,7243,7244,7255,7257,7259,7262,7266,7268,7271,7273,7276,7283,7285,7288,7290,7292,7295,7297,7300,7301,7304,7306,7307,7312,7317,7319,7321,7327,7334,7422,7436,7440,7450,7458,7464,7468,7471,7480,7483,7485,7486,7488,7489,7495,7497,7498,7501,7503,7505,7508,7509,7510,7513,7516,7522,7524,7525,7527,7529,7531,7533,7545,7547,7548,7553,7555,7559,7564,7567,7570,7574,7580,7584,7586,7588,7589,7592,7594,7597,7604,7624,7691,7716,7718,7723,7726,7739,7745,7746,7748,7751,7760,7839,7867,7875,7884,7887,7890,7894,7896,7898,7900,7903,7906,7908,7910,7913,7918,7931,7935,7937,7940,7943,7952,7961,7962,8098,8101,8105,8109,8114,8119,8121,8123,8125,8129,8130,8135,8136,8144,8154,8156,8253,8271,8273,8278,8285,8288,8289,8292,8293,8296,8302,8314,8316,8328,8330,8336,8338,8342,8344,8345,8347,8349,8351,8354,8357,8360,8366,8368,8370,8371,8384,8387,8390,8393,8401,8406,8408,8527,8530,8539,8541,8555,8557,8564,8579,8581,8585,8586,8590,8593,8606,8720,8723,8727,8736,8738,8740,8743,8745,8749,8750,8753,8754,8762,8764,8768,8774,8776,8781,8791,8793,8796,8798,8799,8801,8803,8815,8821,8825,8904,8926,8944,8950,8956,8959,8962,8964,8966,8968,8970,8975,8977,8980,8983,8986,8989,8994,8998,9016,9143,9145,9149,9151,9154,9157,9158,9166,9170,9171,9174,9177,9184,9188,9192,9203,9316,9333,9334,9336,9338,9340,9347,9348,9352,9355,9360,9362,9380,9382,9466,9494,9507,9509,9510,9520,9522,9653,9661,9684,9687,9690,9703,9712,9834,9836,9839,9844,9851,9854,9858,9861,9872,9875,9878,9880,9888,9891,9898,9905,9911,9913,10033,10046,10048,10056,10065,10069,10074,10080,10083,10084,10086,10088,10090,10095,10098,10100,10102,10106,10109,10111,10113,10114,10117,10122,10124,10127,10130,10132,10136,10139,10141,10144,10146,10148,10150,10152,10158,10161,10166,10173,10175,10180,10183,10187,10197,10321,10328,10337,10341,10345,10347,10349,10353,10355,10360,10365,10376,10469,10471,10473,10475,10485,10490,10494,10498,10503,10507,10510,10516,10517,10640,10643,10647,10650,10652,10659,10660,10661,10664, -chr19 47503064 47526556 m54329U_210810_004956/74187500/ccs 101,297,510,697,863,953,1062,1267,1448,1639,1809,2043,2247,2442,2622,2817,2996,3181,3309,3537,3752,3948,4143,4326,4519,4715,4914,5056,5249,5443,5630,5796,6004,6195,6351,6536,6715,6921,7106,7335,7496,7672,7871,8281,8460,8621,8857,9048,9211,9392,9571,9734,9917,10115,10611,10819,11408,11584,11741,12500,12734,12975,13146,13290,13653,13836,14072,14253,14412,14920,15385,15523,15653,15831,16183,16375,16552,16781,16938,17095,17332,17514,17734,17877,18075,18286,18443,18654,18853,19025,19172,19385,19553,19666,19833,20012,20219,20393,20627,20806,21017,21230,21421,21631,21803,22000,22232,22405,22620,22799,23161, 135,134,116,125,89,93,123,131,144,141,133,137,108,126,138,131,143,127,163,139,111,105,117,133,139,126,83,156,145,176,123,139,126,113,122,132,160,110,139,132,129,148,158,142,137,162,128,119,135,147,162,139,127,472,139,577,147,126,124,152,94,127,143,328,114,138,109,116,434,213,109,129,130,312,150,143,154,149,139,158,137,131,142,162,144,154,132,134,162,129,141,130,97,149,175,173,151,159,139,147,133,119,147,119,144,119,139,145,129,325,137, 236,431,626,822,952,1046,1185,1398,1592,1780,1942,2180,2355,2568,2760,2948,3139,3308,3472,3676,3863,4053,4260,4459,4658,4841,4997,5212,5394,5619,5753,5935,6130,6308,6473,6668,6875,7031,7245,7467,7625,7820,8029,8423,8597,8783,8985,9167,9346,9539,9733,9873,10044,10587,10750,11396,11555,11710,11865,12652,12828,13102,13289,13618,13767,13974,14181,14369,14846,15133,15494,15652,15783,16143,16333,16518,16706,16930,17077,17253,17469,17645,17876,18039,18219,18440,18575,18788,19015,19154,19313,19515,19650,19815,20008,20185,20370,20552,20766,20953,21150,21349,21568,21750,21947,22119,22371,22550,22749,23124,23298, 61,79,71,41,1,16,82,50,47,29,101,67,87,54,57,48,42,1,65,76,85,90,66,60,57,73,59,37,49,11,43,69,65,43,63,47,46,75,90,29,47,51,252,37,24,74,63,44,46,32,1,44,71,24,69,12,29,31,635,82,147,44,1,35,69,98,72,43,74,252,29,1,48,40,42,34,75,8,18,79,45,89,1,36,67,3,79,65,10,18,72,38,16,18,4,34,23,75,40,64,80,72,63,53,53,113,34,70,50,37,71, 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27,33,34,37,38,41,45,48,49,51,56,59,60,61,64,66,69,83,86,88,97,100,236,243,250,258,269,278,283,289,296,431,437,439,464,466,470,473,475,482,485,488,490,492,500,503,506,509,626,634,638,644,647,649,657,658,659,661,665,668,672,680,696,822,836,838,858,862,952,1046,1050,1055,1061,1185,1193,1194,1197,1200,1214,1217,1221,1223,1225,1231,1234,1238,1241,1244,1246,1253,1257,1261,1263,1266,1398,1406,1407,1408,1410,1419,1421,1433,1435,1440,1445,1447,1592,1603,1605,1607,1623,1624,1626,1634,1636,1638,1780,1785,1790,1793,1795,1808,1942,1954,1969,1977,1981,1988,1994,1996,2004,2006,2022,2025,2039,2042,2180,2181,2183,2188,2197,2201,2202,2204,2210,2211,2220,2223,2229,2234,2246,2355,2370,2376,2384,2385,2389,2391,2393,2397,2399,2403,2411,2416,2420,2423,2425,2427,2431,2433,2437,2439,2441,2568,2570,2582,2586,2589,2593,2594,2599,2621,2760,2777,2782,2783,2794,2798,2800,2803,2805,2809,2816,2948,2950,2962,2973,2977,2980,2982,2985,2987,2991,2995,3139,3152,3159,3162,3165,3167,3170,3173,3175,3180,3308,3472,3491,3493,3499,3502,3503,3508,3512,3515,3519,3522,3524,3528,3530,3536,3676,3691,3697,3709,3711,3718,3722,3742,3751,3863,3868,3869,3871,3878,3885,3891,3895,3898,3902,3903,3908,3914,3916,3921,3925,3947,4053,4060,4062,4068,4070,4073,4077,4078,4082,4087,4089,4091,4095,4097,4103,4108,4112,4113,4115,4120,4125,4131,4140,4142,4260,4266,4270,4272,4273,4277,4279,4280,4284,4299,4305,4310,4314,4325,4459,4461,4463,4468,4473,4475,4476,4480,4482,4484,4487,4488,4492,4494,4498,4500,4505,4515,4518,4658,4664,4665,4670,4675,4679,4683,4689,4694,4701,4706,4711,4714,4841,4846,4847,4850,4852,4855,4860,4865,4867,4871,4875,4878,4880,4884,4898,4899,4904,4913,4997,5006,5011,5016,5021,5028,5030,5038,5048,5055,5156,5212,5217,5219,5222,5223,5225,5229,5232,5238,5242,5247,5248,5394,5397,5403,5405,5411,5442,5619,5621,5622,5627,5629,5753,5767,5784,5788,5791,5795,5935,5941,5943,5949,5952,5957,5960,5967,5969,5974,5977,5981,6001,6003,6130,6138,6151,6152,6154,6164,6173,6194,6308,6319,6342,6345,6350,6473,6481,6496,6503,6505,6506,6517,6519,6522,6526,6531,6535,6668,6676,6684,6687,6689,6695,6707,6714,6875,6887,6889,6893,6895,6920,7031,7039,7042,7046,7051,7061,7064,7068,7073,7075,7081,7096,7103,7105,7184,7245,7249,7256,7257,7259,7272,7277,7281,7287,7299,7301,7314,7317,7320,7329,7332,7334,7467,7470,7495,7625,7628,7646,7650,7652,7654,7657,7658,7659,7664,7667,7669,7671,7820,7841,7845,7848,7853,7858,7863,7870,7996,8029,8031,8036,8041,8044,8048,8053,8060,8065,8066,8070,8072,8076,8089,8091,8098,8109,8114,8146,8202,8206,8220,8226,8229,8234,8237,8242,8244,8248,8250,8253,8257,8260,8267,8269,8275,8280,8423,8424,8428,8431,8440,8444,8448,8451,8457,8459,8503,8541,8597,8614,8620,8783,8789,8795,8798,8803,8805,8807,8809,8815,8820,8823,8826,8829,8831,8834,8836,8850,8856,8985,8991,8993,8997,8998,9004,9010,9011,9014,9017,9024,9027,9028,9032,9035,9043,9047,9167,9185,9193,9196,9203,9210,9346,9348,9351,9356,9361,9373,9378,9384,9387,9391,9539,9549,9556,9562,9563,9565,9570,9733,9873,9883,9885,9890,9898,9907,9916,10044,10047,10054,10056,10059,10074,10080,10081,10083,10086,10087,10090,10092,10097,10099,10103,10105,10106,10109,10112,10114,10587,10591,10593,10594,10600,10607,10610,10750,10794,10796,10798,10800,10802,10804,10808,10818,11396,11400,11407,11555,11566,11568,11581,11583,11710,11716,11718,11722,11725,11730,11732,11740,11865,11866,11939,11940,11942,11944,11946,11947,11951,11957,11966,11970,11971,11973,11976,11980,11991,11995,11996,12010,12015,12017,12018,12023,12029,12032,12039,12042,12043,12044,12065,12067,12075,12078,12087,12097,12099,12101,12104,12106,12114,12121,12124,12126,12128,12131,12134,12138,12139,12144,12146,12155,12156,12163,12166,12168,12170,12172,12177,12182,12184,12186,12187,12190,12192,12195,12199,12202,12204,12208,12210,12213,12214,12218,12219,12220,12224,12226,12227,12238,12250,12254,12256,12260,12263,12266,12267,12270,12273,12276,12280,12281,12283,12286,12289,12294,12299,12305,12317,12325,12331,12340,12341,12343,12345,12349,12351,12353,12355,12358,12360,12365,12367,12369,12371,12373,12376,12378,12383,12392,12401,12405,12407,12409,12417,12426,12441,12444,12446,12453,12455,12457,12458,12460,12462,12466,12473,12477,12481,12483,12484,12489,12493,12496,12499,12652,12655,12679,12682,12684,12687,12690,12692,12693,12695,12697,12699,12701,12703,12706,12716,12718,12719,12724,12733,12828,12831,12837,12842,12850,12852,12853,12856,12860,12862,12865,12867,12870,12874,12880,12882,12884,12886,12888,12890,12892,12896,12898,12920,12922,12923,12925,12927,12944,12949,12950,12951,12954,12957,12958,12967,12969,12971,12974,13102,13104,13107,13110,13113,13115,13128,13130,13134,13137,13145,13289,13618,13624,13629,13636,13643,13644,13649,13650,13652,13767,13776,13794,13797,13800,13802,13804,13806,13807,13810,13814,13817,13825,13827,13828,13833,13835,13974,13979,13982,13983,13987,13993,13997,14000,14003,14004,14006,14008,14016,14019,14022,14025,14028,14032,14036,14041,14043,14051,14056,14061,14065,14071,14181,14189,14193,14194,14197,14201,14205,14206,14211,14212,14243,14248,14252,14369,14374,14380,14383,14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-chr19 47503211 47517758 m84039_230401_034725_s4/253104323/ccs 78,293,474,633,821,998,1184,1376,1713,1908,2076,2252,2454,2619,2771,2970,3145,3351,3482,3703,3895,4093,4274,4477,4625,4814,5008,5182,5341,5509,5648,5860,6069,6242,6436,6625,6850,7001,7248,7435,7607,7778,7967,8157,8329,8519,8736,8936,9107,9599,9807,10025,10185,10322,10520,10834,10934,11138,11328,11689,12432,12515,12858,13091,13259,13418,13549,13724,13878,14044,14259, 156,119,132,139,130,151,140,311,168,136,131,147,143,137,137,139,158,130,161,126,113,133,121,131,156,159,151,109,108,131,139,156,136,136,142,155,126,161,126,128,138,144,155,138,164,147,126,118,391,150,141,136,123,144,233,99,147,106,226,79,82,164,211,165,151,113,174,118,148,122,142, 234,412,606,772,951,1149,1324,1687,1881,2044,2207,2399,2597,2756,2908,3109,3303,3481,3643,3829,4008,4226,4395,4608,4781,4973,5159,5291,5449,5640,5787,6016,6205,6378,6578,6780,6976,7162,7374,7563,7745,7922,8122,8295,8493,8666,8862,9054,9498,9749,9948,10161,10308,10466,10753,10933,11081,11244,11554,11768,12514,12679,13069,13256,13410,13531,13723,13842,14026,14166, 59,62,27,49,47,35,52,26,27,32,45,55,22,15,62,36,48,1,60,66,85,48,82,17,33,35,23,50,60,8,73,53,37,58,47,70,25,86,61,44,33,45,35,34,26,70,74,53,101,58,77,24,14,54,81,1,57,84,135,664,1,179,22,3,8,18,1,36,18,93, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,250,0,245,0,0,0,0,0,0,0,0, 2,4,6,26,57,65,77,234,237,258,265,270,273,276,283,286,290,292,354,412,422,429,432,438,451,466,473,606,614,616,620,624,632,772,776,778,782,789,794,796,801,819,820,951,958,963,966,969,974,977,980,982,985,989,995,997,1149,1152,1159,1165,1169,1173,1175,1181,1183,1324,1330,1339,1343,1345,1353,1358,1360,1372,1375,1687,1693,1696,1700,1701,1702,1704,1706,1712,1881,1891,1894,1899,1903,1907,2044,2047,2075,2207,2214,2222,2224,2228,2231,2243,2249,2251,2399,2414,2416,2420,2422,2426,2438,2441,2446,2453,2500,2597,2612,2614,2618,2756,2770,2908,2911,2918,2925,2926,2928,2930,2934,2937,2939,2944,2956,2964,2965,2969,3109,3133,3142,3144,3235,3303,3309,3314,3320,3323,3329,3331,3342,3350,3381,3481,3562,3602,3643,3651,3668,3673,3675,3680,3702,3829,3835,3838,3840,3845,3851,3855,3859,3864,3869,3871,3876,3880,3894,4008,4010,4018,4020,4022,4038,4041,4042,4045,4047,4049,4051,4054,4056,4064,4070,4074,4077,4083,4085,4090,4092,4226,4232,4234,4236,4240,4243,4246,4249,4252,4257,4261,4264,4273,4395,4397,4400,4404,4407,4411,4415,4424,4426,4429,4476,4608,4609,4612,4618,4624,4781,4784,4786,4787,4790,4794,4798,4805,4810,4813,4973,4981,4983,4998,5002,5004,5007,5159,5166,5181,5291,5298,5308,5313,5315,5318,5322,5331,5338,5340,5449,5466,5471,5473,5474,5479,5481,5485,5487,5502,5504,5508,5640,5647,5761,5787,5795,5801,5804,5807,5809,5811,5812,5819,5826,5829,5833,5838,5839,5841,5843,5844,5847,5849,5853,5855,5857,5859,6016,6029,6040,6041,6052,6054,6056,6065,6068,6205,6215,6220,6221,6223,6227,6235,6239,6241,6378,6379,6405,6409,6412,6413,6422,6424,6427,6428,6435,6578,6588,6596,6618,6624,6780,6799,6810,6822,6849,6976,6992,6995,7000,7162,7165,7168,7171,7174,7180,7183,7185,7190,7191,7193,7197,7201,7204,7213,7215,7217,7219,7221,7226,7236,7247,7374,7404,7406,7411,7414,7418,7434,7563,7584,7586,7588,7591,7593,7601,7604,7606,7745,7769,7777,7818,7922,7924,7932,7935,7937,7938,7941,7943,7950,7954,7958,7959,7961,7966,8122,8128,8133,8135,8140,8148,8149,8152,8156,8295,8308,8310,8312,8318,8324,8325,8328,8493,8503,8518,8666,8668,8671,8674,8677,8680,8689,8707,8712,8715,8716,8722,8726,8732,8735,8862,8868,8879,8883,8886,8888,8891,8894,8898,8902,8904,8906,8909,8914,8917,8919,8922,8924,8928,8935,9054,9057,9061,9072,9074,9079,9082,9085,9088,9093,9094,9098,9106,9498,9501,9503,9506,9507,9509,9517,9520,9521,9522,9524,9527,9529,9532,9537,9538,9539,9544,9545,9547,9548,9551,9553,9554,9556,9557,9574,9577,9581,9598,9749,9755,9758,9762,9767,9771,9773,9776,9783,9788,9791,9793,9795,9797,9799,9802,9804,9806,9948,9950,9954,9956,9957,9960,9965,9972,9973,9975,9979,9981,9982,9985,9988,9989,10000,10009,10012,10015,10022,10024,10075,10161,10163,10176,10184,10308,10321,10466,10468,10471,10481,10488,10494,10501,10503,10519,10753,10763,10771,10782,10788,10809,10833,10933,11081,11083,11107,11109,11112,11115,11137,11244,11252,11266,11271,11285,11291,11295,11302,11308,11320,11327,11554,11567,11572,11579,11581,11583,11588,11591,11600,11605,11607,11614,11615,11617,11619,11623,11624,11625,11627,11632,11634,11637,11639,11640,11643,11645,11649,11651,11666,11688,11768,11778,11791,11792,11794,11796,11798,11799,11807,11818,11822,11825,11828,11832,11843,11847,11881,11884,11891,11894,11896,11909,11917,11919,11927,11930,11939,11949,11951,11953,11956,11958,11965,11966,11967,11976,11983,12007,12008,12015,12018,12020,12022,12024,12028,12033,12035,12037,12038,12041,12043,12046,12050,12053,12055,12059,12061,12064,12065,12069,12070,12071,12075,12077,12078,12089,12101,12105,12107,12111,12114,12117,12118,12121,12124,12127,12130,12131,12132,12134,12137,12140,12145,12150,12156,12168,12174,12176,12182,12191,12192,12194,12196,12200,12202,12204,12206,12209,12211,12216,12218,12220,12222,12224,12227,12229,12231,12234,12243,12252,12256,12258,12260,12263,12268,12271,12277,12292,12295,12297,12304,12311,12313,12317,12318,12319,12325,12326,12328,12332,12335,12338,12340,12344,12345,12347,12350,12356,12360,12364,12366,12368,12374,12376,12377,12379,12382,12383,12385,12388,12389,12390,12397,12402,12404,12405,12407,12409,12411,12413,12418,12431,12514,12679,12685,12688,12693,12701,12703,12704,12707,12711,12713,12716,12718,12721,12725,12731,12733,12735,12737,12739,12741,12743,12747,12749,12766,12769,12771,12772,12774,12776,12780,12806,12807,12816,12818,12857,13069,13080,13085,13087,13090,13256,13258,13410,13412,13414,13417,13531,13537,13548,13723,13842,13852,13855,13857,13860,13861,13865,13868,13874,13877,14026,14034,14038,14043,14166,14168,14171,14175,14184,14187,14197,14199,14201,14202,14211,14215,14223,14235,14246,14248,14258,14401,14405,14407,14412,14424,14428,14429,14430,14432,14435,14436,14439,14443,14446,14452,14460,14472,14479,14527,14529,14530,14531,14532,14533, -chr19 47503318 47514068 m54329U_210326_192251/32048678/ccs 160,367,510,757,947,1077,1265,1488,1666,1865,2058,2247,2446,2665,2869,3104,3298,3565,3736,3855,4119,4332,4498,4710,4885,5107,5294,5505,5672,5906,6083,6271,6463,6626,6802,7032,7206,7382,7589,7759,8022,8212,8389,8674,8809,9004,9204,9419,9603,9756,9966,10128,10362,10516, 141,85,142,125,98,119,145,151,127,154,118,145,147,133,148,112,120,75,118,134,86,101,135,144,173,108,127,111,132,173,140,134,146,126,136,139,136,157,134,123,112,120,108,134,159,123,150,142,106,114,115,146,141,117, 105,301,452,652,882,1045,1196,1410,1639,1793,2019,2176,2392,2593,2798,3017,3216,3418,3640,3854,3989,4205,4433,4633,4854,5058,5215,5421,5616,5804,6079,6223,6405,6609,6752,6938,7171,7342,7539,7723,7882,8134,8332,8497,8808,8968,9127,9354,9561,9709,9870,10081,10274,10503,10633, 55,66,58,105,65,32,69,78,27,72,39,71,54,72,71,87,82,147,96,1,130,127,65,77,31,49,79,84,56,102,4,48,58,17,50,94,35,40,50,36,140,78,57,177,1,36,77,65,42,47,96,47,88,13,57, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,246,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,242,0,0,250,0,0,0,0,0,0,0,0,0,0,0, 79,105,110,121,127,128,130,131,134,135,138,141,143,148,151,158,159,301,305,315,320,322,323,325,327,329,331,344,347,348,351,352,353,357,359,365,366,452,454,494,509,536,652,655,656,659,664,673,675,676,681,684,686,689,691,696,705,707,709,713,714,717,718,723,728,729,736,741,743,746,748,750,753,755,756,882,905,910,935,937,940,946,1045,1049,1052,1055,1062,1068,1071,1072,1074,1076,1196,1198,1231,1235,1239,1241,1245,1249,1251,1254,1256,1257,1262,1263,1264,1410,1417,1421,1423,1425,1427,1429,1431,1464,1466,1469,1471,1475,1487,1639,1648,1654,1662,1663,1665,1750,1793,1828,1829,1831,1832,1846,1857,1859,1864,2019,2024,2026,2029,2046,2048,2051,2057,2113,2176,2186,2188,2190,2192,2194,2198,2204,2206,2209,2213,2215,2218,2219,2226,2230,2231,2236,2245,2246,2392,2396,2415,2419,2420,2423,2429,2432,2434,2435,2436,2439,2441,2442,2443,2445,2593,2607,2616,2621,2623,2627,2632,2635,2637,2641,2646,2647,2651,2654,2661,2662,2664,2798,2802,2810,2817,2824,2825,2827,2829,2833,2836,2838,2843,2854,2861,2863,2864,2866,2868,2905,3017,3019,3024,3041,3043,3047,3049,3053,3056,3063,3066,3067,3068,3075,3079,3091,3093,3095,3096,3099,3103,3216,3222,3223,3228,3241,3243,3245,3249,3252,3253,3258,3260,3261,3262,3265,3269,3272,3276,3278,3297,3418,3423,3425,3427,3432,3442,3444,3448,3452,3454,3457,3460,3462,3469,3473,3474,3478,3481,3482,3483,3485,3486,3491,3503,3519,3525,3531,3533,3538,3541,3543,3554,3555,3558,3560,3561,3563,3564,3640,3643,3645,3646,3649,3662,3667,3668,3670,3679,3699,3702,3704,3707,3709,3710,3712,3714,3735,3854,3989,3995,3998,4006,4017,4020,4021,4023,4025,4027,4029,4030,4034,4036,4037,4041,4045,4051,4057,4060,4063,4068,4070,4072,4074,4083,4086,4087,4090,4091,4094,4098,4101,4108,4118,4205,4215,4218,4220,4222,4227,4228,4230,4232,4234,4235,4239,4241,4243,4246,4247,4251,4253,4257,4259,4264,4265,4269,4271,4281,4283,4287,4288,4294,4296,4302,4303,4305,4307,4310,4312,4314,4317,4321,4325,4331,4433,4437,4441,4445,4449,4451,4456,4459,4460,4463,4468,4470,4473,4476,4481,4483,4488,4494,4497,4633,4637,4651,4654,4661,4666,4667,4671,4674,4675,4683,4688,4692,4695,4697,4698,4705,4709,4854,4858,4862,4866,4868,4873,4878,4880,4884,5058,5061,5066,5073,5077,5080,5082,5088,5106,5215,5229,5232,5252,5254,5263,5266,5274,5275,5276,5278,5281,5284,5286,5288,5293,5421,5440,5443,5446,5450,5452,5463,5466,5468,5475,5496,5504,5616,5630,5634,5635,5638,5642,5644,5650,5652,5659,5665,5671,5804,5812,5814,5819,5823,5826,5828,5830,5831,5834,5836,5839,5842,5846,5849,5851,5853,5854,5855,5857,5861,5869,5871,5873,5878,5882,5891,5894,5897,5905,6079,6082,6223,6235,6237,6240,6247,6248,6258,6260,6263,6264,6268,6270,6405,6414,6417,6421,6450,6451,6454,6456,6462,6609,6611,6612,6614,6625,6752,6759,6767,6772,6773,6775,6777,6801,6938,6943,6951,6962,6968,6972,6976,7014,7031,7171,7174,7178,7205,7342,7345,7350,7369,7373,7381,7539,7541,7544,7546,7547,7549,7556,7565,7588,7723,7725,7727,7729,7733,7734,7739,7740,7744,7748,7751,7758,7882,7893,7896,7897,7900,7903,7906,7907,7909,7911,7914,7918,7920,7921,7928,7932,7934,7936,7937,7942,7946,7948,7949,7951,7953,7955,7958,7961,7964,7968,7972,7994,7997,8005,8010,8012,8021,8134,8139,8143,8145,8148,8149,8151,8153,8156,8159,8161,8169,8190,8191,8195,8198,8211,8332,8339,8343,8345,8348,8350,8354,8359,8360,8364,8366,8367,8369,8374,8382,8388,8497,8505,8509,8511,8515,8526,8529,8532,8533,8535,8538,8539,8541,8545,8551,8557,8559,8563,8566,8569,8571,8573,8577,8583,8585,8588,8591,8594,8597,8599,8602,8603,8604,8606,8607,8609,8610,8616,8618,8621,8624,8629,8632,8633,8639,8643,8649,8652,8656,8658,8659,8666,8670,8673,8808,8968,8970,8973,8987,8994,8998,9000,9003,9127,9149,9175,9180,9181,9189,9196,9199,9203,9328,9354,9358,9360,9362,9368,9370,9372,9375,9379,9386,9418,9561,9565,9568,9577,9581,9583,9591,9602,9709,9711,9725,9726,9731,9736,9739,9741,9748,9750,9753,9755,9870,9873,9888,9891,9895,9897,9898,9901,9914,9916,9921,9925,9928,9931,9933,9934,9938,9955,9959,9963,9965,10081,10100,10113,10115,10117,10119,10120,10127,10274,10290,10291,10295,10298,10300,10302,10311,10316,10318,10334,10335,10339,10341,10344,10346,10349,10350,10352,10354,10361,10447,10503,10507,10512,10515,10633,10636,10643,10644,10648,10650,10652,10656,10662,10671,10674,10677,10681,10684,10690, -chr19 47503416 47522747 m84008_230107_003043_s1/199754789/ccs 182,371,590,765,977,1157,1348,1568,1762,1946,2134,2369,2632,2772,2957,3196,3396,3534,3754,3953,4174,4508,4758,4973,5128,5308,5491,5635,5979,6161,6337,6546,6760,6956,7148,7862,8051,8245,8394,8608,8828,9586,9724,9981,10181,10338,10523,10717,10900,11039,11203,11589,12167,12394,12721,12914,13082,13254,13470,13682,13796,14033,14253,14478,14742,14979,15143,15305,15772,16015,16145,16456,16634,16807,16968,17176,17366,17583,17781,17969,18142,18359,18552,18797,18984, 184,162,137,182,173,166,152,159,167,163,155,130,94,179,208,143,134,166,157,152,273,113,137,127,153,146,141,324,160,129,161,117,174,140,705,153,126,116,142,148,377,111,144,170,134,140,176,144,138,151,310,76,139,276,160,167,154,147,131,113,178,146,127,144,138,149,141,466,136,120,269,136,147,130,155,158,170,131,146,159,169,128,125,123,147, 154,366,533,727,947,1150,1323,1500,1727,1929,2109,2289,2499,2726,2951,3165,3339,3530,3700,3911,4105,4447,4621,4895,5100,5281,5454,5632,5959,6139,6290,6498,6663,6934,7096,7853,8015,8177,8361,8536,8756,9205,9697,9868,10151,10315,10478,10699,10861,11038,11190,11513,11665,12306,12670,12881,13081,13236,13401,13601,13795,13974,14179,14380,14622,14880,15128,15284,15771,15908,16135,16414,16592,16781,16937,17123,17334,17536,17714,17927,18128,18311,18487,18677,18920,19131, 28,5,57,38,30,7,25,68,35,17,25,80,133,46,6,31,57,4,54,42,69,61,137,78,28,27,37,3,20,22,47,48,97,22,52,9,36,68,33,72,72,381,27,113,30,23,45,18,39,1,13,76,502,88,51,33,1,18,69,81,1,59,74,98,120,99,15,21,1,107,10,42,42,26,31,53,32,47,67,42,14,48,65,120,64,16, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,248,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,243,0,0,0,0,0,0,0,0,0,0,250,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,243,0,0, 7,9,154,157,171,174,180,181,366,370,533,535,537,540,544,556,557,560,568,577,582,585,589,727,729,737,743,746,761,764,947,951,954,960,964,970,976,1150,1156,1323,1327,1341,1347,1500,1510,1547,1555,1557,1561,1562,1567,1692,1727,1728,1733,1735,1750,1754,1756,1761,1929,1931,1935,1943,1945,2109,2111,2127,2130,2133,2181,2289,2305,2316,2317,2332,2337,2338,2340,2368,2499,2517,2521,2526,2540,2545,2548,2549,2555,2556,2558,2559,2560,2565,2567,2592,2601,2602,2606,2608,2611,2617,2621,2631,2726,2735,2756,2757,2759,2761,2771,2951,2952,2956,3165,3177,3195,3339,3345,3360,3364,3393,3395,3530,3533,3700,3717,3722,3753,3911,3917,3943,3948,3950,3952,4105,4124,4125,4129,4131,4153,4173,4447,4450,4453,4469,4485,4488,4507,4621,4625,4646,4651,4657,4659,4663,4666,4668,4670,4673,4679,4683,4686,4689,4690,4693,4701,4702,4705,4708,4713,4731,4739,4751,4753,4757,4895,4901,4904,4946,4950,4953,4955,4968,4972,5100,5102,5116,5118,5125,5127,5281,5283,5285,5288,5290,5296,5299,5304,5307,5454,5466,5471,5473,5475,5477,5482,5483,5488,5490,5632,5634,5959,5972,5975,5978,6139,6160,6195,6290,6320,6322,6325,6328,6336,6498,6501,6507,6508,6519,6521,6527,6545,6663,6683,6693,6731,6740,6742,6745,6752,6754,6759,6934,6943,6955,7096,7097,7099,7132,7145,7147,7853,7861,8015,8050,8177,8201,8203,8208,8224,8231,8244,8361,8386,8393,8427,8536,8547,8550,8552,8559,8571,8591,8594,8601,8607,8637,8756,8775,8778,8788,8796,8798,8809,8810,8822,8824,8827,9205,9207,9211,9213,9230,9253,9258,9259,9262,9266,9292,9294,9297,9303,9304,9309,9310,9312,9313,9315,9318,9319,9336,9382,9384,9388,9389,9392,9394,9427,9441,9448,9450,9480,9488,9489,9491,9494,9504,9506,9532,9541,9544,9548,9556,9560,9569,9582,9585,9697,9713,9717,9719,9720,9723,9821,9868,9898,9899,9903,9905,9912,9917,9919,9929,9931,9935,9936,9941,9965,9966,9980,10151,10164,10180,10315,10326,10330,10335,10337,10478,10482,10483,10488,10503,10515,10522,10699,10716,10834,10861,10864,10866,10869,10899,11038,11190,11191,11202,11513,11521,11522,11524,11548,11550,11574,11588,11665,11673,11675,11683,11686,11695,11714,11721,11729,11731,11732,11734,11736,11746,11763,11764,11771,11774,11776,11778,11784,11791,11793,11802,11809,11815,11817,11820,11821,11825,11826,11873,11874,11877,11880,11883,11887,11890,11893,11896,11901,11906,11924,11932,11947,11948,11952,11956,11958,11960,12014,12024,12027,12031,12052,12072,12074,12087,12090,12093,12095,12099,12100,12102,12152,12157,12159,12160,12162,12164,12166,12306,12308,12311,12324,12329,12338,12340,12341,12349,12365,12370,12374,12376,12386,12390,12393,12670,12678,12680,12718,12720,12881,12883,12903,12913,13081,13236,13244,13246,13253,13305,13401,13402,13435,13462,13469,13601,13623,13629,13635,13637,13642,13652,13666,13681,13795,13974,13980,14003,14011,14032,14179,14180,14183,14189,14243,14248,14250,14252,14380,14382,14385,14386,14387,14389,14405,14407,14408,14412,14424,14428,14432,14437,14446,14456,14467,14473,14477,14622,14626,14630,14633,14635,14637,14643,14648,14658,14661,14663,14669,14671,14675,14677,14679,14682,14684,14704,14707,14710,14711,14714,14720,14726,14729,14733,14740,14741,14880,14887,14893,14895,14896,14912,14922,14926,14930,14931,14932,14934,14938,14942,14944,14946,14950,14953,14955,14959,14960,14964,14975,14978,15128,15131,15142,15284,15289,15292,15295,15304,15771,15908,15939,15941,15943,15951,15958,15962,15982,15989,15990,15999,16001,16005,16008,16014,16135,16142,16144,16414,16423,16426,16438,16442,16445,16448,16455,16592,16605,16612,16615,16628,16630,16633,16781,16806,16937,16941,16945,16948,16952,16967,17123,17125,17132,17140,17161,17162,17165,17175,17334,17340,17344,17346,17352,17365,17536,17542,17563,17565,17579,17582,17714,17720,17728,17736,17741,17748,17753,17765,17767,17770,17777,17780,17927,17930,17934,17937,17943,17945,17947,17953,17955,17959,17963,17968,18128,18134,18136,18140,18141,18311,18312,18314,18323,18326,18330,18336,18354,18358,18487,18491,18495,18499,18511,18515,18532,18535,18551,18677,18680,18684,18687,18693,18698,18703,18707,18709,18710,18713,18729,18736,18738,18740,18742,18744,18752,18756,18759,18769,18770,18779,18796,18920,18922,18923,18929,18947,18949,18951,18953,18956,18959,18965,18983,19131,19137,19145,19147, -chr19 47503536 47521676 m64076_221119_202646/134220289/ccs 64,213,406,579,817,1097,1294,1546,1700,1925,2087,2272,2461,2729,2889,3053,3259,3425,3618,3839,4010,4209,4418,4598,4796,4982,5091,5254,5446,5736,5907,6114,6299,6503,6659,6868,7023,7353,7519,7699,7864,8044,8210,8377,8566,8773,8902,9090,9278,9466,9633,9816,9984,10138,10291,10419,10742,10879,11009,11200,11346,12154,12291,12430,12758,12968,13150,13340,13487,13667,13866,14133,14565,14839,15307,15467,15586,15976,16177,16384,16540,16744,16918,17117,17323,17515,17701,17874, 78,135,107,140,211,124,133,80,109,142,99,109,144,87,105,124,114,102,100,95,89,104,113,120,123,98,155,146,289,124,127,83,142,101,138,117,270,120,139,121,130,121,113,123,115,93,141,97,128,105,108,151,129,127,127,267,125,110,141,83,111,116,129,324,136,181,149,146,118,114,107,118,101,135,112,112,158,104,78,86,152,116,121,140,123,96,112,104, 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-chr19 47504354 47515136 m54329U_210326_192251/85918147/ccs 73,241,456,669,861,1062,1280,1407,1634,1803,2018,2177,2366,2511,2711,2880,3044,3238,3376,3544,3736,3921,4097,4259,4459,4616,4809,5274,5426,5588,5793,5977,6135,6318,6467,6654,6845,7013,7179,7376,7568,7736,7889,8115,8275,8438,8640,8771,8976,9095,9279,9460,9640,9888,10032,10169,10344, 144,195,164,145,140,106,75,147,132,160,138,161,144,162,156,129,134,112,135,133,125,123,126,141,116,127,460,146,136,169,127,124,151,148,118,156,140,138,138,106,128,132,139,135,129,102,118,128,95,160,124,116,124,115,127,141,254, 68,217,436,620,814,1001,1168,1355,1554,1766,1963,2156,2338,2510,2673,2867,3009,3178,3350,3511,3677,3861,4044,4223,4400,4575,4743,5269,5420,5562,5757,5920,6101,6286,6466,6585,6810,6985,7151,7317,7482,7696,7868,8028,8250,8404,8540,8758,8899,9071,9255,9403,9576,9764,10003,10159,10310, 5,24,20,49,47,61,112,52,80,37,55,21,28,1,38,13,35,60,26,33,59,60,53,36,59,41,66,5,6,26,36,57,34,32,1,69,35,28,28,59,86,40,21,87,25,34,100,13,77,24,24,57,64,124,29,10,34, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,243,0,0,0, 68,72,217,219,232,240,436,455,620,634,640,642,645,654,658,661,666,668,814,816,822,827,831,834,837,843,851,853,855,856,860,1001,1006,1011,1014,1019,1036,1039,1043,1051,1056,1061,1168,1180,1209,1215,1216,1217,1275,1279,1355,1371,1378,1382,1383,1386,1391,1394,1396,1397,1398,1401,1403,1404,1406,1554,1556,1562,1568,1570,1572,1574,1576,1577,1583,1587,1592,1595,1597,1601,1606,1607,1609,1611,1614,1615,1621,1624,1633,1766,1769,1776,1779,1781,1783,1784,1786,1788,1792,1793,1795,1797,1802,1963,1967,1976,1978,2000,2002,2006,2008,2011,2017,2156,2162,2173,2176,2338,2340,2341,2345,2354,2356,2360,2361,2365,2510,2673,2674,2675,2682,2684,2688,2694,2697,2699,2702,2710,2867,2873,2877,2879,3009,3012,3020,3022,3024,3026,3035,3038,3039,3042,3043,3178,3181,3183,3190,3192,3194,3198,3202,3204,3208,3210,3215,3216,3225,3228,3230,3232,3237,3350,3368,3375,3511,3515,3518,3519,3522,3525,3530,3543,3677,3682,3684,3685,3689,3693,3697,3699,3702,3706,3707,3711,3712,3716,3719,3721,3726,3729,3735,3861,3863,3866,3869,3873,3876,3880,3886,3890,3901,3904,3909,3915,3920,4044,4047,4049,4055,4057,4061,4064,4075,4077,4082,4085,4096,4223,4243,4245,4248,4253,4255,4258,4400,4411,4416,4421,4447,4449,4458,4575,4579,4599,4603,4615,4743,4746,4748,4750,4751,4756,4758,4763,4767,4770,4772,4774,4776,4778,4780,4783,4786,4790,4793,4795,4797,4798,4801,4805,4808,5269,5273,5420,5425,5562,5573,5575,5577,5587,5757,5762,5768,5775,5779,5784,5792,5920,5950,5952,5955,5956,5958,5960,5965,5971,5973,5976,6101,6103,6107,6115,6118,6122,6125,6132,6134,6286,6287,6289,6293,6294,6296,6317,6466,6585,6600,6605,6607,6611,6616,6624,6627,6629,6633,6637,6642,6644,6649,6653,6810,6814,6818,6819,6821,6824,6826,6833,6837,6841,6844,6985,6993,6995,7000,7004,7008,7009,7012,7151,7155,7159,7167,7168,7170,7172,7175,7178,7317,7325,7331,7341,7343,7348,7349,7351,7353,7363,7371,7375,7482,7494,7499,7500,7502,7506,7509,7514,7516,7518,7520,7526,7528,7531,7534,7537,7540,7542,7545,7547,7567,7696,7702,7708,7709,7711,7712,7715,7721,7722,7725,7728,7729,7730,7735,7795,7868,7876,7886,7888,8028,8037,8046,8052,8059,8062,8065,8067,8072,8077,8082,8084,8089,8095,8098,8102,8103,8109,8114,8250,8265,8273,8274,8404,8407,8416,8417,8437,8540,8545,8556,8557,8562,8568,8571,8575,8576,8577,8583,8584,8586,8589,8593,8594,8596,8599,8601,8602,8604,8609,8611,8615,8618,8627,8633,8636,8639,8758,8765,8767,8770,8899,8903,8923,8925,8928,8930,8935,8945,8951,8952,8958,8959,8964,8966,8968,8975,9071,9093,9094,9255,9260,9262,9266,9278,9403,9404,9408,9411,9414,9418,9419,9426,9430,9433,9435,9437,9444,9451,9456,9459,9576,9587,9589,9591,9595,9598,9604,9613,9616,9619,9623,9628,9639,9764,9768,9773,9778,9782,9789,9790,9793,9798,9800,9803,9805,9808,9812,9814,9815,9817,9826,9829,9836,9837,9839,9841,9846,9847,9850,9857,9859,9861,9864,9866,9873,9875,9880,9883,9887,10003,10008,10011,10013,10026,10027,10031,10159,10162,10166,10168,10310,10343,10598,10609,10611,10615,10617,10625,10626,10628,10630,10632,10638,10651,10652,10654,10656,10659,10669,10678,10682,10735,10741,10744,10751,10756, -chr19 47504438 47519753 m84039_230404_003541_s3/35456981/ccs 138,310,513,678,899,1056,1223,1360,1551,1712,1910,2057,2264,2473,2642,2810,3018,3207,3390,3541,3767,3970,4145,4282,4611,4807,5006,5211,5359,5555,5735,5907,6088,6244,6410,6623,6827,7001,7182,7314,7535,7907,8142,8446,8615,8802,8989,9119,9289,9546,9700,9859,9975,10068,10394,11293,11461,11635,11775,11939,12110,12285,12473,12741,12900,13040,13218,13396,13570,14035,14152,14344,14466,14660,14795,14965, 126,150,92,147,84,102,134,125,118,126,120,141,129,127,145,105,97,108,122,154,109,120,127,321,142,130,103,94,94,120,138,138,143,140,137,153,134,136,131,146,359,114,117,114,112,140,125,138,134,122,118,115,92,103,108,121,118,104,131,151,150,113,231,135,114,142,152,116,252,110,118,104,126,123,131,111, 91,264,460,605,825,983,1158,1357,1485,1669,1838,2030,2198,2393,2600,2787,2915,3115,3315,3512,3695,3876,4090,4272,4603,4753,4937,5109,5305,5453,5675,5873,6045,6231,6384,6547,6776,6961,7137,7313,7460,7894,8021,8259,8560,8727,8942,9114,9257,9423,9668,9818,9974,10067,10171,10502,11414,11579,11739,11906,12090,12260,12398,12704,12876,13014,13182,13370,13512,13822,14145,14270,14448,14592,14783,14926,15076, 47,46,53,73,74,73,65,3,66,43,72,27,66,80,42,23,103,92,75,29,72,94,55,10,8,54,69,102,54,102,60,34,43,13,26,76,51,40,45,1,75,13,121,187,55,75,47,5,32,123,32,41,1,1,223,791,47,56,36,33,20,25,75,37,24,26,36,26,58,213,7,74,18,68,12,39,36, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,248,0,0,0,0,0,0,0,0,0,0,248,251,0,0,0,0,0,0,0,0,0,0,0,0,0,249,0,0,0,0,0,0,0, 0,1,2,3,5,6,91,94,106,109,111,119,137,264,266,305,307,309,460,463,467,469,471,472,477,480,494,511,512,605,622,627,632,634,650,653,657,667,670,674,675,677,825,834,847,856,861,862,866,872,874,876,881,898,983,985,996,998,1000,1004,1007,1012,1021,1025,1027,1028,1031,1033,1036,1039,1044,1055,1158,1161,1186,1188,1190,1192,1196,1202,1222,1357,1359,1485,1487,1500,1504,1507,1512,1514,1523,1524,1526,1546,1550,1669,1673,1675,1679,1682,1684,1687,1690,1694,1702,1704,1706,1711,1838,1839,1841,1845,1849,1854,1861,1862,1863,1865,1868,1870,1873,1881,1885,1909,2030,2035,2040,2042,2045,2051,2054,2056,2198,2220,2222,2226,2234,2237,2256,2263,2393,2394,2399,2404,2407,2415,2417,2420,2424,2428,2429,2432,2434,2437,2452,2457,2472,2600,2606,2612,2615,2617,2620,2622,2628,2632,2636,2641,2787,2795,2797,2799,2809,2915,2938,2953,2956,2957,2960,2961,2964,2967,2968,2971,2974,2978,2981,2984,2988,3004,3017,3115,3120,3126,3134,3140,3143,3146,3148,3152,3169,3170,3172,3174,3177,3179,3184,3188,3192,3206,3315,3317,3322,3329,3334,3336,3339,3342,3344,3347,3349,3360,3363,3368,3389,3512,3520,3527,3532,3533,3537,3540,3571,3695,3699,3710,3722,3730,3737,3742,3748,3750,3758,3766,3876,3892,3895,3901,3908,3914,3919,3922,3925,3929,3936,3938,3940,3945,3962,3969,4090,4092,4108,4115,4117,4126,4144,4272,4279,4281,4603,4606,4610,4753,4756,4759,4760,4763,4767,4783,4793,4802,4806,4937,4944,4948,4955,4960,4962,4968,4971,4974,4977,4979,4983,5005,5109,5110,5125,5126,5130,5132,5134,5135,5137,5146,5148,5151,5155,5160,5164,5168,5173,5174,5187,5190,5191,5200,5210,5305,5316,5318,5324,5326,5328,5332,5335,5336,5338,5340,5343,5354,5356,5358,5453,5454,5516,5518,5524,5531,5533,5542,5549,5554,5675,5680,5693,5697,5702,5704,5710,5732,5734,5873,5876,5888,5893,5894,5902,5903,5906,6045,6054,6070,6081,6083,6087,6231,6235,6243,6384,6406,6409,6547,6555,6571,6575,6580,6585,6587,6596,6601,6602,6606,6610,6613,6620,6622,6776,6782,6799,6808,6811,6815,6817,6820,6826,6874,6961,6965,6967,6970,6973,6976,6978,6981,6984,6986,6990,6993,6996,7000,7137,7147,7150,7161,7164,7168,7181,7313,7460,7482,7485,7493,7494,7500,7510,7513,7534,7894,7906,8021,8025,8027,8032,8036,8043,8044,8059,8062,8065,8068,8069,8072,8074,8076,8078,8082,8084,8089,8094,8098,8106,8121,8123,8131,8134,8141,8259,8265,8268,8270,8271,8275,8280,8283,8284,8286,8301,8304,8306,8309,8314,8315,8316,8321,8322,8324,8325,8327,8328,8331,8345,8354,8358,8361,8375,8380,8381,8383,8388,8391,8394,8396,8400,8401,8404,8406,8408,8414,8416,8421,8427,8430,8432,8443,8445,8560,8568,8572,8576,8579,8581,8583,8592,8594,8597,8614,8727,8731,8734,8742,8756,8759,8762,8765,8766,8775,8786,8801,8942,8944,8953,8956,8961,8981,8988,9114,9118,9257,9258,9276,9278,9280,9286,9288,9423,9425,9427,9429,9431,9433,9437,9441,9447,9453,9454,9456,9459,9461,9465,9468,9469,9471,9476,9478,9484,9487,9489,9490,9493,9496,9500,9501,9506,9508,9509,9510,9512,9521,9525,9530,9532,9533,9536,9540,9541,9545,9668,9671,9678,9681,9683,9695,9696,9699,9818,9835,9837,9858,9974,10067,10125,10163,10171,10175,10176,10183,10193,10195,10210,10222,10226,10229,10237,10241,10245,10250,10252,10267,10269,10274,10275,10277,10281,10284,10285,10288,10290,10294,10299,10307,10310,10312,10316,10323,10330,10333,10337,10341,10343,10345,10348,10349,10352,10355,10357,10359,10363,10367,10376,10381,10383,10393,10502,10506,10510,10512,10527,10531,10533,10537,10541,10548,10567,10568,10570,10572,10574,10575,10583,10585,10594,10598,10601,10604,10608,10619,10623,10624,10631,10634,10641,10643,10645,10646,10651,10657,10660,10667,10670,10672,10685,10693,10695,10703,10706,10715,10725,10727,10729,10732,10734,10741,10742,10743,10749,10752,10754,10756,10759,10762,10766,10767,10772,10774,10783,10784,10791,10794,10796,10798,10800,10805,10810,10812,10814,10815,10818,10820,10823,10832,10836,10838,10841,10842,10846,10847,10848,10852,10855,10866,10878,10882,10884,10888,10891,10894,10895,10898,10901,10904,10908,10909,10911,10914,10917,10922,10927,10945,10953,10959,10968,10969,10971,10973,10977,10979,10981,10983,10986,10988,10993,10995,10997,10999,11001,11004,11006,11008,11033,11035,11037,11038,11040,11047,11050,11054,11069,11072,11074,11089,11091,11092,11102,11104,11106,11110,11113,11116,11118,11122,11123,11125,11128,11161,11173,11175,11180,11182,11183,11185,11187,11189,11191,11212,11213,11215,11221,11223,11228,11230,11238,11242,11244,11245,11247,11257,11261,11265,11281,11284,11292,11414,11417,11418,11422,11425,11431,11433,11435,11438,11441,11442,11446,11460,11579,11580,11587,11598,11600,11603,11616,11619,11622,11632,11634,11739,11742,11744,11748,11760,11763,11774,11906,11916,11927,11930,11938,12090,12109,12260,12264,12269,12271,12272,12284,12398,12417,12419,12422,12425,12435,12438,12442,12472,12704,12716,12718,12731,12733,12735,12740,12876,12880,12883,12887,12892,12899,13014,13035,13039,13182,13183,13185,13200,13202,13206,13210,13213,13217,13370,13371,13375,13379,13383,13395,13512,13515,13520,13523,13528,13531,13533,13543,13555,13559,13561,13562,13565,13567,13569,13822,13833,13836,13852,13857,13860,13863,13866,13869,13872,13880,13884,13886,13889,13891,13896,13898,13901,13904,13912,13916,13919,13920,13925,13927,13928,13939,13943,13944,13946,13948,13950,13954,13957,13958,13960,13963,13970,13976,13978,13982,13985,13991,13994,13996,14003,14007,14013,14019,14021,14025,14034,14145,14151,14270,14279,14281,14285,14295,14298,14303,14306,14310,14316,14321,14323,14324,14327,14331,14338,14341,14343,14448,14451,14465,14592,14594,14604,14606,14613,14621,14631,14634,14638,14641,14642,14647,14659,14687,14783,14785,14789,14794,14926,14931,14934,14942,14945,14950,14951,14952,14955,14958,14964,15076,15083,15085,15089,15095,15097,15098,15103,15105,15106,15111,15304, -chr19 47504443 47525656 m84039_230401_031619_s3/32769141/ccs 130,486,664,854,1094,1542,1809,2025,2254,2449,2748,3045,3165,3562,3713,3835,4063,4179,4259,4358,4584,4806,5206,5285,5453,5648,5874,6079,6276,6587,6698,6811,7053,7372,7782,7911,8025,8174,8262,8339,8446,9158,9347,9543,9751,9901,10049,10202,10418,10634,10921,11087,11207,11454,11686,11841,12047,12177,12314,12496,12589,12763,12930,13180,13394,13530,13641,13754,13860,14113,14372,14704,14959,15199,15364,15619,15703,15945,16107,16402,16600,16795,16936,17073,17212,17371,17546,17754,17868,18018,18163,18262,18537,18819,18998,19321,19478,19644,20036,20181,20371,20488,20571,20771,20997, 355,132,189,219,447,266,215,199,190,298,184,119,298,150,121,227,115,79,98,142,146,301,78,146,123,221,146,196,310,108,105,160,270,263,128,113,146,87,76,106,711,166,171,169,127,147,152,126,150,179,151,101,168,170,154,205,129,131,181,83,146,148,175,213,103,110,99,102,138,174,246,195,238,145,184,83,234,161,123,142,104,129,95,135,131,142,129,100,135,134,98,272,266,141,238,156,134,124,125,136,116,82,186,211,135, 129,485,618,853,1073,1541,1808,2024,2224,2444,2747,2932,3164,3463,3712,3834,4062,4178,4258,4357,4500,4730,5107,5284,5431,5576,5869,6020,6275,6586,6695,6803,6971,7323,7635,7910,8024,8171,8261,8338,8445,9157,9324,9518,9712,9878,10048,10201,10328,10568,10813,11072,11188,11375,11624,11840,12046,12176,12308,12495,12579,12735,12911,13105,13393,13497,13640,13740,13856,13998,14287,14618,14899,15197,15344,15548,15702,15937,16106,16230,16544,16704,16924,17031,17208,17343,17513,17675,17854,18003,18152,18261,18534,18803,18960,19236,19477,19612,19768,20161,20317,20487,20570,20757,20982, 1,1,46,1,21,1,1,1,30,5,1,113,1,99,1,1,1,1,1,1,84,76,99,1,22,72,5,59,1,1,3,8,82,49,147,1,1,3,1,1,1,1,23,25,39,23,1,1,90,66,108,15,19,79,62,1,1,1,6,1,10,28,19,75,1,33,1,14,4,115,85,86,60,2,20,71,1,8,1,172,56,91,12,42,4,28,33,79,14,15,11,1,3,16,38,85,1,32,268,20,54,1,1,14,15, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,242,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,248,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,244,0,0,0,0,0,0, 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-chr19 47504450 47522937 m84008_230107_003043_s1/117770546/ccs 142,373,534,708,852,1042,1210,1379,1708,1926,2116,2321,2489,2655,2810,3014,3213,3384,3598,3776,3927,4091,4271,4482,4663,5019,5254,5386,5608,5766,5976,6115,6343,6536,6693,6857,7060,7214,7482,7612,7953,8368,8578,8704,9031,9188,10040,10227,10583,11086,11323,11485,11702,11874,12241,12429,12602,12761,12983,13369,13969,14068,14290,14466,14647,14733,14850,15053,15211,15370,15548,15883,16070,16209,16460,16649,17251,17431,17653,17856,18233, 173,152,173,138,140,167,149,326,173,189,150,161,161,154,191,177,120,153,136,150,163,179,175,180,334,158,131,187,143,158,133,188,151,156,136,166,141,146,126,340,296,158,123,318,156,803,152,299,110,201,155,144,148,349,154,138,158,153,303,323,93,221,160,146,85,88,153,157,158,169,307,186,137,247,178,531,138,217,142,305,133, 125,315,525,707,846,992,1209,1359,1705,1881,2115,2266,2482,2650,2809,3001,3191,3333,3537,3734,3926,4090,4270,4446,4662,4997,5177,5385,5573,5751,5924,6109,6303,6494,6692,6829,7023,7201,7360,7608,7952,8249,8526,8701,9022,9187,9991,10192,10526,10693,11287,11478,11629,11850,12223,12395,12567,12760,12914,13286,13692,14062,14289,14450,14612,14732,14821,15003,15210,15369,15539,15855,16069,16207,16456,16638,17180,17389,17648,17795,18161, 17,58,9,1,6,50,1,20,3,45,1,55,7,5,1,13,22,51,61,42,1,1,1,36,1,22,77,1,35,15,52,6,40,42,1,28,37,13,122,4,1,119,52,3,9,1,49,35,57,393,36,7,73,24,18,34,35,1,69,83,277,6,1,16,35,1,29,50,1,1,9,28,1,2,4,11,71,42,5,61,72, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,251,0,0,0,0,0,0,0,0,0,0,251,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 125,139,141,315,341,355,357,359,369,372,525,533,648,707,846,850,851,887,992,1041,1209,1359,1361,1376,1378,1705,1707,1881,1894,1925,2115,2266,2281,2320,2482,2488,2650,2654,2809,2880,3001,3004,3013,3191,3212,3333,3347,3352,3359,3361,3366,3369,3373,3381,3383,3537,3540,3543,3545,3546,3557,3593,3597,3734,3735,3759,3763,3765,3768,3775,3926,4090,4270,4446,4448,4453,4454,4459,4466,4473,4477,4478,4481,4662,4997,5002,5018,5177,5201,5218,5225,5228,5233,5253,5385,5573,5594,5599,5601,5607,5751,5756,5763,5765,5924,5936,5975,6109,6114,6303,6318,6323,6324,6342,6494,6499,6501,6535,6692,6732,6829,6853,6856,6898,7023,7024,7028,7040,7048,7057,7059,7201,7205,7213,7360,7364,7399,7420,7435,7450,7453,7478,7481,7608,7611,7952,8249,8280,8286,8289,8291,8292,8294,8315,8318,8344,8346,8351,8352,8354,8357,8359,8363,8364,8367,8526,8531,8535,8537,8540,8542,8558,8561,8563,8572,8575,8577,8701,8703,9022,9030,9187,9991,9998,10003,10028,10032,10038,10039,10192,10198,10202,10207,10209,10216,10226,10526,10527,10529,10531,10533,10534,10538,10542,10544,10553,10557,10563,10578,10582,10652,10693,10701,10702,10708,10718,10750,10755,10757,10769,10771,10773,10777,10779,10782,10786,10789,10795,10797,10800,10801,10805,10806,10807,10811,10813,10846,10850,10854,10857,10860,10870,10873,10876,10912,10928,10936,10940,10945,10954,10958,10960,10963,10970,10979,11027,11032,11039,11043,11046,11048,11052,11053,11054,11070,11075,11079,11080,11082,11085,11287,11304,11310,11311,11312,11322,11478,11482,11484,11629,11636,11646,11653,11655,11657,11659,11661,11675,11676,11682,11688,11693,11699,11701,11850,11851,11870,11873,12223,12228,12229,12234,12240,12395,12399,12405,12411,12413,12414,12422,12425,12428,12567,12578,12593,12596,12601,12760,12914,12919,12922,12930,12932,12934,12953,12957,12963,12966,12982,13286,13336,13351,13366,13368,13692,13734,13736,13739,13741,13748,13774,13778,13779,13785,13786,13788,13790,13792,13797,13809,13810,13814,13822,13825,13828,13831,13840,13842,13845,13847,13850,13854,13860,13865,13889,13901,13903,13905,13908,13916,13918,13920,13922,13934,13936,13937,13943,13951,13953,13968,14062,14067,14289,14450,14465,14612,14619,14638,14644,14646,14732,14821,14823,14826,14828,14839,14841,14846,14849,15003,15018,15019,15022,15025,15029,15035,15038,15046,15052,15210,15369,15539,15547,15855,15861,15863,15882,15994,16069,16207,16208,16456,16459,16638,16648,17180,17185,17204,17222,17226,17228,17230,17233,17247,17250,17291,17389,17417,17419,17425,17430,17648,17652,17795,17797,17798,17813,17814,17817,17819,17821,17828,17831,17836,17838,17840,17842,17844,17855,18161,18165,18167,18170,18174,18178,18185,18186,18189,18191,18196,18202,18209,18214,18232,18366,18376,18389,18393,18396, -chr19 47504613 47515474 m54329U_210323_190418/128584032/ccs 202,432,615,763,1024,1156,1378,1548,1768,1955,2137,2349,2500,2634,2858,3192,3328,3482,3689,3860,4055,4222,4549,4785,4932,5091,5266,5490,5603,5827,6035,6202,6360,6576,6743,6943,7082,7288,7390,7582,7739,7932,8133,8319,8516,8847,9003,9400,9545,9680,9975,10120, 140,126,109,128,75,133,115,120,110,106,110,115,113,99,90,105,115,125,75,109,92,80,115,80,87,100,121,82,112,92,100,106,96,104,99,115,108,87,134,107,106,115,106,106,103,121,109,85,90,251,119,118, 127,342,558,724,891,1099,1289,1493,1668,1878,2061,2247,2464,2613,2733,2948,3297,3443,3607,3764,3969,4147,4302,4664,4865,5019,5191,5387,5572,5715,5919,6135,6308,6456,6680,6842,7058,7190,7375,7524,7689,7845,8047,8239,8425,8619,8968,9112,9485,9635,9931,10094, 75,90,57,39,133,57,89,55,100,77,76,102,36,21,125,244,31,39,82,96,86,75,247,121,67,72,75,103,31,112,116,67,52,120,63,101,24,98,15,58,50,87,86,80,91,228,35,288,60,45,44,26, 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-chr19 47504774 47527496 m54329U_210814_130637/56492117/ccs 82,300,513,684,833,996,1215,1375,1549,1771,2002,2185,2353,2493,2707,2911,3125,3313,3491,3707,3840,4045,4125,4337,4496,4646,4827,5037,5168,5373,5620,5811,6015,6187,6383,6596,6958,7124,7345,7545,7727,7942,8149,8272,8450,8626,8857,9037,9201,9395,9591,9742,9930,10057,10980,11188,11379,11543,11709,11879,12058,12250,12465,12691,13055,13232,13420,13596,13738,14155,14421,14572,14718,14891,15185,15349,15526,15744,15872,16042,16247,16414,16577,16759,16933,17631,17799,17955,18116,18282,18462,18641,18796,18940,19135,19305,19485,19706,19885,20081,20247,20440,20805,21020,21383,21551,21686,21903,22085,22211,22417, 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-chr19 47505225 47524765 m54329U_210814_130637/53151002/ccs 141,318,501,726,909,1080,1271,1431,1619,1750,1954,2144,2302,2487,2683,2842,3016,3191,3337,3512,3855,4024,4205,4394,4557,4740,4917,5087,5260,5436,5630,5830,6050,6245,6419,6661,6846,7057,7202,7386,7569,7745,7959,8120,8294,8450,8924,9504,9649,10467,10682,10892,11083,11248,11447,11835,12016,12181,12386,12524,12717,12862,13284,13504,13670,13982,14231,14416,14607,14782,15168,15334,15539,15735,15871,16088,16321,16471,16644,16816,17038,17218,17404,17723,17927,18124,18355,18521,18699,18855,19094,19260, 130,182,121,134,146,148,127,162,130,169,141,143,163,142,120,147,141,120,174,320,146,145,138,151,151,150,140,172,155,188,168,151,138,152,161,142,137,144,183,123,157,190,129,167,150,473,486,135,105,128,145,143,126,130,384,144,153,133,130,175,127,128,153,135,279,136,134,124,127,329,147,165,165,135,169,147,112,146,150,124,143,159,306,169,171,114,103,147,117,139,139,134, 75,271,500,622,860,1055,1228,1398,1593,1749,1919,2095,2287,2465,2629,2803,2989,3157,3311,3511,3832,4001,4169,4343,4545,4708,4890,5057,5259,5415,5624,5798,5981,6188,6397,6580,6803,6983,7201,7385,7509,7726,7935,8088,8287,8444,8923,9410,9639,9754,10595,10827,11035,11209,11378,11831,11979,12169,12314,12516,12699,12844,12990,13437,13639,13949,14118,14365,14540,14734,15111,15315,15499,15704,15870,16040,16235,16433,16617,16794,16940,17181,17377,17710,17892,18098,18238,18458,18668,18816,18994,19233,19394, 66,47,1,104,49,25,43,33,26,1,35,49,15,22,54,39,27,34,26,1,23,23,36,51,12,32,27,30,1,21,6,32,69,57,22,81,43,74,1,1,60,19,24,32,7,6,1,94,10,713,87,65,48,39,69,4,37,12,72,8,18,18,294,67,31,33,113,51,67,48,57,19,40,31,1,48,86,38,27,22,98,37,27,13,35,26,117,63,31,39,100,27,63, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,243,0,248,0,0,0,0,0,0,0,0,0,0,0,0,251,0,0,0,243,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 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-chr19 47505293 47522617 m54329U_210323_190418/102761996/ccs 55,245,435,853,1090,1255,1457,1635,1841,2025,2212,2420,2618,2796,2982,3166,3349,3579,3718,3904,4106,4286,4475,4656,4861,5030,5237,5424,5596,5779,5977,6144,6336,6519,6705,6857,7057,7250,7393,7640,7820,8037,8203,8367,8528,8719,8854,9369,9561,10374,10566,10737,10902,11074,11442,11605,11805,11963,12185,12299,12488,12706,12872,13124,13510,13770,14026,14310,14456,14635,14835,15028,15220,15335,15556,15750,15943,16157,16317,16528,16705,16877,17132, 146,122,133,131,91,150,105,140,124,118,91,117,117,139,109,129,139,86,117,178,121,124,146,169,165,117,95,108,118,147,134,143,142,116,127,125,131,125,175,117,132,124,143,131,137,134,500,125,121,92,95,148,137,340,110,133,122,144,79,159,130,107,148,249,209,121,194,133,150,138,123,125,114,153,141,139,146,92,130,137,139,119,130, 201,367,568,984,1181,1405,1562,1775,1965,2143,2303,2537,2735,2935,3091,3295,3488,3665,3835,4082,4227,4410,4621,4825,5026,5147,5332,5532,5714,5926,6111,6287,6478,6635,6832,6982,7188,7375,7568,7757,7952,8161,8346,8498,8665,8853,9354,9494,9682,10466,10661,10885,11039,11414,11552,11738,11927,12107,12264,12458,12618,12813,13020,13373,13719,13891,14220,14443,14606,14773,14958,15153,15334,15488,15697,15889,16089,16249,16447,16665,16844,16996, 44,68,285,106,74,52,73,66,60,69,117,81,61,47,75,54,91,53,69,24,59,65,35,36,4,90,92,64,65,51,33,49,41,70,25,75,62,18,72,63,85,42,21,30,54,1,15,67,692,100,76,17,35,28,53,67,36,78,35,30,88,59,104,137,51,135,90,13,29,62,70,67,1,68,53,54,68,68,81,40,33,136, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,248,0,0,0,0,0,0,0,0,0,0,0,0,0,0,242,0,242,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 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-chr19 47505522 47515592 m54329U_210323_190418/71500016/ccs 167,368,552,720,932,1103,1303,1413,1676,1865,2053,2265,2463,2607,2853,3110,3244,3405,3772,3952,4105,4303,4529,4706,4902,5080,5446,5617,5809,5950,6177,6340,6505,6654,6812,6966,7155,7349,7561,7761,8130,8279,8467,8642,8855,9012,9180, 134,128,78,148,104,136,109,176,145,133,116,122,94,104,204,133,147,303,89,97,135,141,131,96,112,125,114,126,120,136,81,97,103,123,136,188,151,101,118,358,129,142,110,102,90,115,259, 103,301,496,630,868,1036,1239,1412,1589,1821,1998,2169,2387,2557,2711,3057,3243,3391,3708,3861,4049,4240,4444,4660,4802,5014,5205,5560,5743,5929,6086,6258,6437,6608,6777,6948,7154,7306,7450,7679,8119,8259,8421,8577,8744,8945,9127, 64,67,56,90,64,67,64,1,87,44,55,96,76,50,142,53,1,14,64,91,56,63,85,46,100,66,241,57,66,21,91,82,68,46,35,18,1,43,111,82,11,20,46,65,111,67,53, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 61,103,107,109,113,116,122,123,124,127,131,134,138,139,141,144,146,166,301,306,312,315,320,322,325,328,339,343,345,348,350,354,367,421,496,500,518,525,530,532,544,547,548,551,630,637,672,675,683,687,690,692,695,698,706,711,714,719,786,868,872,886,888,889,892,895,896,898,900,905,907,911,913,931,1036,1038,1040,1044,1047,1048,1096,1102,1239,1245,1254,1257,1266,1271,1275,1278,1299,1302,1412,1589,1620,1623,1627,1632,1637,1639,1641,1653,1656,1658,1662,1663,1675,1821,1823,1830,1831,1835,1838,1857,1862,1864,1998,2017,2022,2025,2027,2029,2030,2034,2036,2038,2046,2048,2052,2169,2172,2175,2183,2185,2190,2193,2194,2196,2200,2203,2206,2211,2217,2218,2223,2236,2240,2242,2247,2264,2387,2400,2401,2404,2406,2418,2420,2424,2428,2431,2441,2442,2445,2446,2451,2452,2457,2458,2462,2557,2560,2562,2567,2570,2576,2579,2581,2583,2588,2591,2595,2598,2601,2602,2606,2711,2718,2722,2726,2728,2732,2746,2751,2755,2757,2760,2762,2764,2766,2769,2771,2774,2777,2781,2784,2788,2790,2794,2796,2799,2800,2803,2810,2816,2848,2852,3057,3064,3066,3067,3070,3086,3088,3109,3212,3243,3391,3398,3399,3404,3708,3710,3728,3736,3740,3743,3744,3750,3757,3759,3765,3766,3768,3771,3861,3865,3867,3868,3870,3872,3874,3876,3888,3894,3897,3899,3900,3903,3905,3909,3928,3951,4049,4052,4057,4059,4073,4079,4085,4090,4094,4104,4240,4241,4244,4246,4247,4249,4252,4254,4256,4260,4263,4266,4268,4271,4277,4282,4284,4286,4290,4302,4444,4446,4452,4459,4460,4461,4466,4470,4473,4475,4477,4480,4481,4482,4485,4486,4500,4503,4505,4516,4519,4526,4528,4660,4662,4665,4667,4670,4677,4679,4682,4684,4691,4697,4699,4700,4705,4802,4814,4815,4820,4828,4829,4833,4841,4849,4851,4855,4857,4861,4873,4876,4881,4885,4887,4889,4894,4897,4901,5014,5016,5020,5023,5026,5042,5049,5058,5072,5073,5075,5078,5079,5145,5205,5214,5220,5223,5225,5227,5231,5234,5241,5244,5245,5250,5252,5256,5261,5263,5267,5268,5273,5274,5276,5279,5282,5286,5290,5292,5295,5297,5316,5323,5390,5397,5401,5404,5407,5409,5415,5419,5423,5426,5429,5433,5437,5445,5560,5572,5581,5587,5591,5592,5597,5599,5600,5604,5609,5610,5614,5616,5743,5746,5749,5752,5778,5789,5797,5799,5805,5808,5929,5935,5937,5939,5942,5945,5949,5978,6086,6090,6093,6095,6099,6100,6107,6109,6113,6115,6116,6120,6122,6125,6129,6131,6133,6136,6138,6142,6143,6147,6148,6149,6153,6155,6158,6170,6176,6258,6261,6280,6285,6289,6291,6293,6299,6303,6306,6317,6320,6321,6323,6326,6327,6339,6437,6440,6444,6452,6454,6458,6461,6464,6470,6481,6485,6487,6490,6491,6495,6497,6499,6504,6608,6610,6620,6628,6630,6631,6634,6641,6653,6777,6784,6811,6948,6953,6954,6959,6965,7154,7306,7308,7326,7329,7331,7342,7348,7450,7456,7459,7463,7468,7474,7477,7478,7480,7484,7489,7492,7494,7496,7498,7500,7501,7503,7505,7510,7511,7516,7518,7519,7521,7524,7530,7535,7538,7540,7555,7560,7679,7681,7682,7744,7750,7755,7760,8119,8120,8126,8129,8259,8267,8271,8274,8276,8278,8421,8425,8426,8431,8434,8435,8437,8440,8446,8450,8455,8458,8461,8465,8466,8577,8594,8597,8599,8601,8604,8607,8609,8611,8613,8616,8618,8621,8622,8625,8632,8633,8636,8641,8689,8744,8750,8752,8756,8761,8763,8771,8773,8780,8784,8786,8804,8807,8810,8812,8815,8818,8832,8854,8945,8947,8962,8969,8974,8978,8982,8985,8988,8991,8992,8994,8998,9002,9008,9011,9127,9149,9162,9177,9179,9439,9468,9490,9491,9493,9495,9497,9498,9502,9506,9508,9517,9521,9524,9527,9531,9542,9546,9547,9574,9580,9583,9593,9595,9608,9616,9618,9638,9648,9650,9652,9655,9657,9664,9665,9673,9680,9686,9690,9696,9707,9715,9718,9720,9722,9724,9734,9736,9738,9739,9742,9744,9747,9751,9754,9756,9760,9762,9765,9766,9770,9771,9772,9776,9778,9779,9802,9806,9808,9809,9812,9815,9819,9822,9825,9828,9831,9832,9833,9835,9838,9841,9851,9857,9876,9884,9893,9894,9896,9898,9902,9904,9906,9908,9911,9913,9920,9922,9926,9929,9933,9936,9945,9958,9960,9962,9963,9965,9970,9973,9977,9994,9997,9999,10009,10011,10012,10014,10016,10021,10026,10028,10030,10034,10036,10037,10040,10046,10047,10049,10052,10053,10054,10055,10056,10058,10062,10066, -chr19 47506015 47516286 m54329U_210323_190418/26544028/ccs 140,345,516,681,904,1113,1291,1479,1679,1855,2033,2234,2377,2567,2744,2927,3122,3271,3465,3628,3835,4005,4198,4399,4633,4801,5040,5220,5423,5646,5857,6031,6209,6422,6608,6755,7008,7195,7376,7558,7738,7919,8092,8244,8482,8681,8863,9766,10071, 138,130,158,171,132,120,131,133,135,128,142,134,138,139,124,128,132,155,120,132,160,159,157,135,88,146,131,162,135,136,143,156,145,139,136,135,125,147,138,145,124,133,114,135,115,130,113,260,108, 109,278,475,674,852,1036,1233,1422,1612,1814,1983,2175,2368,2515,2706,2868,3055,3254,3426,3585,3760,3995,4164,4355,4534,4721,4947,5171,5382,5558,5782,6000,6187,6354,6561,6744,6890,7133,7342,7514,7703,7862,8052,8206,8379,8597,8811,8976,10026,10179, 31,67,41,7,52,77,58,57,67,41,50,59,9,52,38,59,67,17,39,43,75,10,34,44,99,80,93,49,41,88,75,31,22,68,47,11,118,62,34,44,35,57,40,38,103,84,52,790,45,56, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,243,0,0,0,0,0,0,0,0,0,0,248,0,0, 108,111,114,118,125,128,130,135,139,278,285,286,289,305,309,318,320,333,342,344,475,498,504,513,515,674,680,852,867,874,876,881,903,1036,1041,1052,1056,1060,1065,1068,1070,1072,1075,1077,1079,1081,1085,1098,1112,1233,1239,1242,1243,1246,1248,1250,1252,1255,1257,1265,1271,1275,1278,1284,1286,1290,1422,1424,1427,1435,1437,1441,1444,1447,1453,1458,1462,1465,1478,1612,1616,1631,1632,1640,1644,1645,1649,1651,1653,1669,1672,1675,1678,1814,1820,1824,1826,1833,1838,1841,1854,1983,1986,1988,1989,2007,2012,2015,2032,2059,2175,2185,2191,2204,2206,2209,2212,2216,2219,2223,2227,2229,2233,2368,2370,2376,2515,2517,2520,2526,2529,2531,2533,2534,2540,2542,2549,2551,2554,2559,2566,2706,2715,2723,2726,2727,2728,2731,2734,2743,2868,2870,2877,2883,2885,2887,2889,2893,2899,2901,2903,2904,2906,2926,3055,3057,3059,3061,3085,3086,3089,3091,3093,3094,3099,3101,3106,3110,3113,3115,3121,3254,3256,3258,3260,3267,3270,3426,3432,3438,3440,3442,3444,3447,3449,3452,3456,3464,3585,3598,3601,3602,3608,3612,3616,3621,3622,3625,3627,3760,3768,3779,3787,3823,3828,3831,3834,3995,4004,4164,4176,4178,4188,4190,4197,4355,4361,4370,4373,4376,4385,4388,4390,4395,4398,4534,4552,4556,4558,4559,4568,4570,4576,4579,4580,4584,4609,4611,4616,4632,4721,4724,4735,4739,4742,4746,4747,4752,4754,4758,4761,4764,4766,4770,4771,4776,4777,4779,4782,4785,4789,4791,4793,4795,4798,4800,4947,4954,4958,4963,4976,4980,4984,4989,4991,4993,4996,4999,5000,5004,5009,5018,5024,5025,5039,5171,5180,5187,5188,5191,5205,5209,5210,5212,5219,5382,5387,5388,5390,5394,5396,5399,5402,5407,5410,5413,5415,5419,5422,5558,5561,5564,5566,5567,5576,5579,5581,5590,5593,5597,5599,5602,5603,5604,5614,5616,5618,5619,5623,5625,5630,5636,5638,5639,5641,5645,5782,5787,5795,5801,5805,5808,5815,5816,5819,5822,5823,5825,5828,5843,5853,5856,6000,6005,6010,6016,6020,6027,6030,6187,6188,6190,6192,6194,6195,6199,6201,6203,6204,6205,6208,6354,6355,6358,6360,6362,6365,6373,6387,6390,6393,6408,6412,6415,6416,6421,6561,6584,6587,6590,6607,6744,6751,6754,6890,6892,6901,6907,6913,6916,6920,6922,6928,6929,6931,6934,6938,6941,6944,6946,6949,6954,6960,6963,6967,6972,6976,6978,6981,6982,6984,6986,6988,6993,6996,7002,7007,7133,7137,7138,7143,7144,7149,7154,7156,7160,7162,7163,7166,7169,7171,7173,7174,7178,7179,7181,7185,7187,7188,7191,7194,7342,7343,7349,7361,7365,7367,7369,7371,7375,7514,7525,7528,7536,7538,7540,7543,7547,7550,7552,7557,7703,7705,7707,7709,7715,7717,7719,7721,7725,7727,7728,7737,7862,7876,7883,7888,7890,7894,7897,7898,7900,7905,7909,7916,7918,8052,8058,8066,8068,8076,8081,8091,8206,8224,8229,8232,8236,8237,8239,8240,8242,8243,8379,8390,8400,8401,8403,8405,8407,8412,8413,8415,8418,8422,8425,8429,8431,8434,8437,8441,8442,8444,8446,8452,8454,8458,8469,8476,8481,8597,8602,8603,8605,8610,8616,8621,8623,8627,8629,8631,8634,8636,8638,8642,8644,8645,8657,8661,8663,8664,8670,8672,8676,8680,8811,8816,8818,8825,8828,8830,8836,8838,8843,8845,8847,8848,8850,8856,8862,8976,8979,9002,9003,9005,9007,9009,9010,9014,9015,9019,9021,9030,9034,9037,9040,9044,9055,9059,9060,9092,9093,9096,9103,9106,9108,9121,9129,9131,9139,9142,9161,9163,9165,9168,9170,9179,9180,9186,9188,9189,9191,9193,9220,9221,9228,9231,9233,9235,9237,9243,9248,9250,9252,9253,9257,9259,9262,9266,9269,9271,9275,9277,9280,9281,9285,9286,9287,9291,9293,9294,9318,9322,9324,9325,9328,9331,9334,9335,9338,9341,9344,9347,9348,9351,9354,9357,9363,9368,9374,9386,9409,9410,9412,9414,9418,9420,9422,9424,9429,9434,9436,9438,9440,9442,9445,9447,9449,9452,9461,9470,9471,9474,9476,9478,9479,9481,9486,9489,9511,9514,9516,9525,9527,9528,9531,9532,9534,9540,9541,9542,9551,9555,9556,9557,9558,9561,9563,9567,9568,9570,9573,9574,9575,9605,9606,9618,9620,9625,9627,9628,9630,9632,9634,9639,9640,9641,9643,9644,9645,9646,9647,9651,9652,9654,9657,9658,9660,9662,9664,9666,9668,9671,9672,9673,9684,9688,9690,9691,9693,9703,9707,9711,9712,9713,9718,9720,9723,9727,9730,9732,9734,9738,9744,9754,9757,9759,9765,10026,10028,10031,10032,10034,10035,10046,10048,10051,10070,10179,10196,10222,10228,10230,10234, -chr19 47506215 47513023 m64076_221119_202646/55771763/ccs 170,333,562,725,915,1132,1341,1496,1641,1820,2029,2228,2401,2588,2742,2940,3067,3256,3460,3633,3841,4030,4168,4356,4524,4835,4991,5166,5328,5680,5852,5997,6156,6393, 134,141,112,99,124,92,98,117,123,162,117,137,141,109,108,126,140,128,130,148,120,100,134,103,103,89,86,111,96,87,85,111,100,95, 106,304,474,674,824,1039,1224,1439,1613,1764,1982,2146,2365,2542,2697,2850,3066,3207,3384,3590,3781,3961,4130,4302,4459,4627,4924,5077,5277,5424,5767,5937,6108,6256, 64,29,88,51,91,93,117,57,28,56,47,82,36,46,45,90,1,49,76,43,60,69,38,54,65,208,67,89,51,256,85,60,48,137, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,249,0,0,0,0,0,0,0,0, 105,109,118,120,125,141,142,144,148,150,154,157,159,160,164,167,169,304,310,313,315,321,325,330,332,474,480,482,483,487,496,498,502,503,507,510,516,520,526,528,533,543,549,558,561,674,676,681,688,696,698,703,707,711,712,717,724,824,830,836,839,841,844,846,852,856,860,865,866,868,870,872,875,877,879,881,885,891,893,895,898,904,908,912,914,1039,1042,1046,1048,1050,1052,1055,1057,1063,1065,1067,1071,1074,1075,1078,1080,1084,1086,1090,1091,1093,1097,1101,1106,1108,1112,1125,1131,1224,1227,1228,1235,1237,1241,1244,1247,1250,1253,1258,1259,1262,1267,1270,1274,1278,1281,1284,1287,1289,1297,1298,1300,1305,1308,1311,1313,1317,1320,1323,1327,1336,1339,1340,1439,1444,1448,1450,1452,1454,1455,1459,1468,1471,1474,1482,1484,1487,1493,1495,1613,1623,1625,1632,1637,1640,1764,1782,1785,1787,1788,1791,1795,1799,1806,1811,1814,1819,1982,1999,2003,2005,2008,2015,2022,2026,2028,2146,2153,2160,2162,2164,2167,2169,2182,2185,2186,2189,2191,2197,2200,2203,2217,2219,2227,2365,2367,2368,2371,2373,2380,2385,2387,2390,2397,2398,2400,2542,2546,2555,2557,2570,2583,2587,2697,2698,2703,2717,2721,2722,2725,2729,2730,2731,2732,2736,2737,2741,2850,2854,2856,2858,2860,2883,2884,2885,2888,2890,2892,2893,2894,2898,2900,2905,2909,2912,2914,2916,2917,2920,2922,2925,2932,2939,3066,3207,3227,3229,3231,3236,3237,3241,3243,3246,3248,3255,3384,3388,3392,3408,3411,3414,3415,3420,3421,3423,3424,3426,3429,3430,3434,3436,3437,3446,3449,3452,3455,3459,3590,3598,3620,3621,3626,3629,3632,3781,3782,3793,3797,3799,3801,3805,3806,3812,3822,3824,3829,3840,3961,3963,3966,3973,3978,3980,3985,3987,3990,3994,3996,3997,4002,4011,4029,4130,4146,4148,4152,4154,4158,4167,4235,4302,4305,4307,4310,4312,4314,4316,4317,4318,4321,4322,4325,4331,4339,4349,4353,4355,4459,4473,4476,4479,4482,4483,4488,4489,4490,4495,4497,4500,4504,4506,4508,4511,4521,4523,4627,4630,4639,4642,4651,4652,4654,4657,4658,4663,4666,4667,4669,4673,4674,4678,4680,4682,4685,4688,4693,4695,4699,4702,4705,4707,4712,4713,4715,4717,4721,4724,4727,4730,4731,4733,4735,4742,4743,4747,4749,4753,4758,4760,4761,4762,4766,4768,4769,4771,4774,4775,4779,4783,4784,4786,4788,4791,4794,4795,4799,4804,4806,4809,4811,4813,4815,4819,4820,4825,4826,4834,4924,4926,4930,4933,4934,4937,4939,4940,4943,4945,4952,4956,4960,4961,4963,4966,4968,4975,4979,4983,4990,5077,5088,5091,5096,5098,5104,5111,5114,5118,5122,5124,5126,5127,5130,5135,5137,5142,5146,5150,5151,5154,5158,5163,5165,5277,5281,5284,5286,5288,5293,5297,5301,5304,5306,5310,5312,5314,5320,5327,5424,5429,5431,5434,5436,5440,5445,5450,5452,5455,5459,5461,5465,5467,5473,5478,5479,5480,5482,5483,5485,5487,5488,5490,5491,5493,5495,5497,5504,5505,5507,5508,5509,5511,5513,5520,5526,5543,5546,5567,5636,5638,5642,5648,5651,5656,5662,5668,5679,5767,5776,5778,5781,5783,5786,5790,5793,5795,5800,5802,5805,5811,5812,5815,5818,5819,5822,5825,5827,5832,5835,5836,5838,5842,5844,5846,5847,5851,5937,5942,5951,5973,5977,5983,5985,5987,5994,5996,6108,6126,6130,6136,6139,6142,6146,6149,6150,6155,6256,6263,6267,6268,6278,6283,6286,6290,6293,6294,6297,6299,6301,6303,6306,6307,6309,6314,6319,6323,6329,6330,6331,6335,6338,6340,6342,6346,6348,6352,6356,6366,6379,6382,6385,6392,6488,6495,6498,6499,6500,6503,6505,6508,6509,6511,6519,6520,6522,6524,6526,6529,6531,6534,6539,6540,6541,6546,6547,6549,6550,6552,6553,6555,6556,6559,6566,6570,6576,6579,6583,6586,6588,6589,6590,6592,6593,6600,6605,6606,6608,6613,6616,6619,6621,6622,6625,6626,6629,6631,6633,6634,6636,6639,6641,6642,6646,6648,6651,6652,6655,6657,6659,6660,6661,6664,6668,6670,6674,6678,6685,6689,6691,6693,6694,6699,6769,6790,6793, -chr19 47506222 47514314 m84008_230107_003043_s1/177932302/ccs 80,246,416,577,767,977,1182,1410,1581,1759,1976,2169,2333,2533,2735,2884,3063,3257,3478,3669,3898,4081,4254,4430,4646,4866,5044,5214,5449,5644,5811,5974,6180,6374,6719,6876,7056,7244,7426,7573,7741, 105,118,120,124,117,138,150,118,147,153,123,115,132,97,106,135,193,151,144,125,143,133,147,190,151,150,169,164,139,131,117,159,146,274,107,131,146,148,141,146,145, 185,364,536,701,884,1115,1332,1528,1728,1912,2099,2284,2465,2630,2841,3019,3256,3408,3622,3794,4041,4214,4401,4620,4797,5016,5213,5378,5588,5775,5928,6133,6326,6648,6826,7007,7202,7392,7567,7719,7886, 61,52,41,66,93,67,78,53,31,64,70,49,68,105,43,44,1,70,47,104,40,40,29,26,69,28,1,71,56,36,46,47,48,71,50,49,42,34,6,22,40, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 10,12,15,20,25,39,42,56,79,185,187,189,193,196,199,201,205,206,208,211,217,221,245,364,369,373,375,381,383,398,401,404,406,408,415,536,538,542,551,554,563,567,576,701,708,710,713,716,722,725,730,734,736,737,740,753,758,766,884,886,888,891,898,901,905,907,915,918,922,927,932,934,936,940,948,953,958,960,964,965,976,1115,1117,1122,1124,1125,1129,1132,1138,1144,1147,1150,1155,1157,1170,1174,1177,1178,1181,1220,1332,1337,1343,1345,1351,1367,1387,1394,1401,1409,1528,1532,1542,1546,1551,1556,1559,1564,1566,1577,1580,1728,1743,1750,1754,1757,1758,1912,1927,1935,1939,1943,1947,1959,1965,1975,2021,2099,2103,2109,2112,2118,2131,2133,2136,2139,2142,2153,2157,2160,2162,2168,2284,2295,2307,2309,2312,2332,2465,2467,2468,2473,2475,2489,2493,2496,2498,2504,2507,2512,2520,2523,2526,2530,2532,2630,2634,2648,2654,2656,2660,2662,2665,2669,2675,2677,2679,2681,2683,2685,2690,2691,2693,2696,2698,2710,2714,2715,2718,2722,2729,2734,2841,2843,2847,2849,2878,2883,3019,3023,3027,3031,3034,3035,3046,3048,3050,3059,3062,3256,3408,3417,3422,3427,3429,3442,3445,3461,3465,3468,3477,3575,3622,3631,3636,3664,3665,3668,3794,3805,3815,3827,3828,3831,3836,3838,3842,3844,3851,3852,3854,3856,3877,3878,3880,3881,3885,3888,3892,3897,4041,4051,4080,4214,4231,4250,4253,4295,4369,4401,4421,4422,4428,4429,4504,4593,4620,4623,4632,4635,4644,4645,4797,4804,4806,4812,4813,4827,4830,4837,4839,4843,4845,4851,4855,4857,4863,4865,5016,5019,5020,5021,5025,5027,5032,5034,5037,5043,5213,5378,5398,5404,5407,5411,5413,5416,5422,5424,5427,5429,5438,5443,5445,5448,5588,5609,5610,5612,5615,5616,5643,5775,5778,5794,5797,5803,5810,5928,5940,5942,5948,5951,5952,5956,5973,6133,6137,6140,6141,6144,6146,6148,6151,6155,6157,6159,6161,6163,6167,6168,6170,6173,6175,6176,6179,6326,6331,6333,6337,6339,6343,6347,6350,6373,6648,6659,6661,6680,6682,6684,6689,6690,6695,6700,6703,6715,6718,6826,6851,6868,6873,6875,7007,7009,7016,7020,7029,7039,7041,7046,7055,7202,7203,7207,7211,7218,7219,7225,7226,7237,7243,7392,7394,7398,7410,7422,7425,7567,7569,7572,7719,7727,7730,7736,7740,7886,7888,7890,7893,7896,7898,7900,7902,7903,7905,7907,7910,7913,7914,7922,7925,8050,8060,8062,8069, -chr19 47506398 47523529 m54329U_210326_192251/95750173/ccs 139,321,518,732,919,1096,1311,1485,1662,1829,2011,2158,2357,2518,2676,2829,3169,3329,3536,3722,3925,4102,4300,4484,4652,4831,5048,5267,5420,5619,5798,5929,6156,6300,6646,6802,6993,7136,7288,7575,7726,7897,8090,8299,8448,9255,9615,9759,9901,10077,10261,10479,10832,10995,11201,11340,11520,11693,11994,12214,12367,12637,12801,13035,13201,13368,13539,13749,13910,14242,14415,14613,14797,14995,15136,15334,15507,16027,16199,16334,16668, 136,140,123,104,122,129,116,138,139,134,119,126,97,119,100,237,117,127,134,140,104,121,144,146,146,139,139,126,139,133,130,123,102,271,126,133,142,124,254,114,128,113,112,121,116,234,118,130,107,124,151,145,134,113,110,152,117,103,109,128,253,135,147,106,139,141,140,139,270,117,124,122,124,120,143,116,430,130,132,291,347, 82,275,461,641,836,1041,1225,1427,1623,1801,1963,2130,2284,2454,2637,2776,3066,3286,3456,3670,3862,4029,4223,4444,4630,4798,4970,5187,5393,5559,5752,5928,6052,6258,6571,6772,6935,7135,7260,7542,7689,7854,8010,8202,8420,8564,9489,9733,9889,10008,10201,10412,10624,10966,11108,11311,11492,11637,11796,12103,12342,12620,12772,12948,13141,13340,13509,13679,13888,14180,14359,14539,14735,14921,15115,15279,15450,15937,16157,16331,16625,17015, 57,46,57,91,83,55,86,58,39,28,48,28,73,64,39,53,103,43,80,52,63,73,77,40,22,33,78,80,27,60,46,1,104,42,75,30,58,1,28,33,37,43,80,97,28,691,126,26,12,69,60,67,208,29,93,29,28,56,198,111,25,17,29,87,60,28,30,70,22,62,56,74,62,74,21,55,57,90,42,3,43,1, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,250,0,0,0,0,0,0,0,0,0,0,0,0,251,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 81,83,86,92,97,117,121,132,138,275,278,291,293,295,297,299,300,304,310,313,315,319,320,428,461,465,469,470,473,475,476,478,480,487,491,493,517,598,641,647,653,656,658,661,669,673,677,682,683,685,687,689,692,696,698,702,708,710,712,731,809,836,838,840,846,859,860,863,865,867,869,872,874,880,882,884,888,892,901,903,918,1041,1044,1045,1050,1052,1054,1058,1064,1067,1070,1079,1082,1084,1087,1091,1095,1225,1231,1242,1244,1247,1248,1256,1258,1260,1261,1265,1267,1269,1272,1276,1278,1279,1280,1285,1288,1291,1310,1427,1430,1438,1440,1442,1449,1454,1457,1461,1470,1474,1477,1478,1484,1623,1628,1631,1637,1643,1648,1652,1656,1658,1661,1801,1820,1825,1828,1963,1966,1970,1977,1981,1984,1986,1992,2003,2010,2130,2132,2135,2155,2157,2284,2289,2291,2299,2303,2313,2315,2317,2320,2322,2326,2328,2331,2336,2339,2347,2354,2356,2454,2455,2458,2461,2473,2475,2480,2484,2486,2489,2493,2505,2507,2509,2517,2637,2647,2667,2673,2675,2776,2785,2794,2797,2808,2822,2826,2828,3066,3073,3094,3095,3097,3101,3105,3108,3113,3119,3124,3127,3129,3131,3134,3139,3141,3144,3151,3168,3286,3290,3293,3298,3302,3303,3309,3316,3318,3325,3328,3456,3474,3476,3482,3488,3489,3490,3493,3510,3513,3515,3516,3518,3524,3528,3529,3533,3535,3670,3688,3695,3696,3698,3701,3702,3712,3716,3721,3862,3865,3871,3875,3896,3905,3924,4029,4031,4038,4055,4060,4062,4066,4074,4077,4081,4084,4096,4099,4101,4223,4225,4233,4245,4252,4253,4255,4267,4271,4272,4274,4276,4284,4293,4296,4299,4444,4459,4469,4483,4630,4632,4636,4637,4642,4643,4647,4651,4798,4799,4802,4809,4822,4828,4830,4970,4974,4979,4981,4988,4991,4993,4995,4998,5001,5005,5007,5010,5013,5016,5018,5021,5024,5026,5030,5033,5036,5040,5041,5043,5045,5047,5187,5190,5192,5193,5194,5201,5204,5208,5210,5213,5223,5227,5230,5234,5236,5252,5266,5393,5398,5402,5406,5408,5410,5412,5416,5419,5559,5565,5571,5574,5577,5583,5588,5589,5592,5594,5618,5752,5764,5766,5775,5781,5785,5788,5794,5797,5928,6052,6055,6064,6068,6072,6075,6076,6077,6078,6082,6083,6089,6091,6093,6098,6101,6105,6108,6109,6112,6118,6122,6124,6129,6131,6150,6153,6155,6258,6260,6262,6264,6268,6272,6274,6277,6281,6285,6299,6571,6583,6587,6589,6592,6593,6595,6597,6599,6604,6607,6609,6611,6613,6615,6616,6618,6620,6622,6631,6633,6636,6639,6641,6645,6772,6776,6779,6784,6788,6789,6791,6795,6797,6798,6801,6935,6939,6952,6953,6957,6959,6962,6963,6966,6968,6971,6972,6973,6975,6977,6979,6981,6983,6985,6986,6988,6992,7135,7260,7271,7287,7542,7546,7550,7553,7559,7563,7568,7570,7571,7574,7689,7709,7711,7725,7854,7856,7862,7864,7868,7871,7873,7875,7883,7896,8010,8017,8023,8027,8028,8030,8034,8036,8042,8046,8047,8049,8051,8059,8063,8067,8081,8086,8089,8202,8210,8214,8215,8221,8222,8224,8226,8228,8232,8234,8236,8239,8241,8242,8243,8247,8249,8250,8261,8265,8267,8268,8274,8276,8280,8284,8289,8291,8298,8420,8422,8429,8432,8438,8439,8440,8442,8447,8564,8566,8570,8572,8576,8580,8581,8583,8585,8587,8606,8607,8609,8611,8613,8614,8618,8622,8624,8633,8637,8638,8640,8643,8647,8658,8662,8663,8690,8695,8696,8699,8706,8709,8711,8742,8745,8764,8766,8768,8771,8773,8781,8782,8783,8789,8792,8802,8806,8812,8823,8824,8831,8834,8836,8838,8840,8845,8850,8852,8854,8855,8858,8860,8863,8867,8870,8872,8876,8878,8881,8882,8886,8887,8888,8892,8895,8906,8924,8925,8928,8931,8934,8935,8938,8941,8944,8947,8948,8951,8954,8957,8962,8967,8973,8993,8999,9008,9009,9011,9013,9017,9019,9021,9023,9026,9028,9033,9035,9037,9039,9041,9044,9046,9048,9051,9060,9069,9073,9075,9077,9080,9085,9087,9088,9090,9091,9094,9109,9112,9114,9121,9122,9123,9125,9126,9128,9134,9135,9136,9141,9143,9145,9152,9155,9156,9157,9161,9162,9164,9167,9168,9169,9171,9174,9199,9200,9212,9214,9221,9222,9224,9226,9228,9230,9243,9254,9489,9496,9499,9502,9505,9509,9518,9520,9521,9524,9528,9530,9533,9535,9538,9542,9548,9550,9552,9554,9560,9561,9564,9566,9592,9594,9596,9600,9614,9733,9734,9736,9738,9740,9742,9744,9758,9889,9891,9892,9895,9896,9900,10008,10031,10034,10037,10046,10049,10051,10062,10076,10201,10202,10205,10207,10210,10216,10225,10226,10227,10230,10232,10234,10237,10238,10239,10241,10243,10245,10249,10255,10257,10258,10260,10412,10415,10421,10423,10426,10428,10431,10435,10437,10438,10441,10444,10445,10446,10448,10449,10452,10457,10460,10468,10470,10475,10478,10624,10627,10630,10631,10635,10637,10642,10644,10647,10650,10655,10661,10668,10684,10752,10754,10756,10773,10775,10780,10795,10800,10802,10804,10805,10806,10809,10810,10812,10819,10822,10824,10827,10829,10831,10966,10971,10974,10979,10985,10987,10990,10994,11108,11111,11114,11120,11121,11123,11126,11136,11139,11145,11147,11150,11151,11153,11157,11161,11163,11167,11169,11171,11173,11175,11178,11179,11181,11200,11311,11316,11318,11320,11339,11492,11496,11500,11502,11505,11511,11514,11515,11519,11637,11640,11641,11645,11649,11651,11654,11661,11662,11663,11665,11666,11667,11674,11677,11687,11692,11796,11799,11811,11817,11818,11821,11823,11824,11830,11831,11835,11837,11842,11845,11846,11850,11852,11853,11855,11856,11860,11861,11867,11868,11870,11872,11874,11875,11877,11878,11879,11881,11882,11884,11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-chr19 47506417 47532580 m64076_221119_202646/93981333/ccs 212,417,570,740,926,1139,1290,1487,1655,1845,2021,2198,2395,2548,2711,2860,3069,3274,3422,3613,3812,4008,4160,4394,4605,4789,4974,5154,5341,5522,5661,5985,6166,6509,6647,6836,7018,7190,7364,7540,7732,7934,8112,8228,8397,9219,9464,9564,9706,9931,10225,10403,10561,10760,10950,11178,11370,11519,12032,12340,12520,12665,12879,13092,13258,13493,13662,13764,13917,14107,14253,14439,14673,14820,15002,15204,15382,15564,15888,16091,16279,16394,16871,17091,17241,17393,17565,17789,17955,18133,18307,18468,18649,18807,18991,19199,19350,19964,20152,20239,20328,20491,20826,21048,21219,21374,21549,21750,21945,22089,22260,22423,22568,22743,22920,23117,23294,23469,23628,23839,23992,24122,24345,24518,24698,24858,25027,25259,25486,25684,25858, 129,129,131,146,149,118,147,132,153,115,94,146,117,130,134,160,131,135,144,153,144,151,157,137,98,130,120,141,152,138,323,162,117,90,93,126,133,124,120,117,147,113,115,168,110,82,91,129,127,217,148,113,137,162,125,121,127,143,301,127,136,134,83,165,77,96,101,81,131,101,135,152,87,103,150,127,131,280,162,106,114,476,151,144,151,132,123,140,109,135,127,131,153,160,179,150,613,166,86,79,131,316,173,138,116,165,139,128,143,131,110,97,120,123,142,133,138,130,120,123,106,160,129,142,144,137,161,126,126,115,146, 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-chr19 47506533 47518567 m54329U_210326_192251/68487112/ccs 211,400,578,784,953,1127,1308,1497,1691,1865,2033,2199,2545,2728,2857,3060,3222,3413,3619,3819,3992,4152,4327,4522,4699,4917,5105,5323,5487,5667,5855,6033,6244,6585,6752,6897,7166,7342,7513,7683,8099,8267,9139,9284,9438,9614,9769,9920,10133,10332,10517,10735,10912,11096,11586, 123,118,133,122,141,168,156,131,129,131,122,122,130,128,171,160,154,147,123,122,151,120,128,141,135,110,156,128,157,159,152,170,118,136,144,259,165,167,129,394,140,144,144,115,135,125,150,133,157,129,154,128,132,471,128, 169,334,518,711,906,1094,1295,1464,1628,1820,1996,2155,2321,2675,2856,3028,3220,3376,3560,3742,3941,4143,4272,4455,4663,4834,5027,5261,5451,5644,5826,6007,6203,6362,6721,6896,7156,7331,7509,7642,8077,8239,8411,9283,9399,9573,9739,9919,10053,10290,10461,10671,10863,11044,11567,11714, 42,66,60,73,47,33,13,33,63,45,37,44,224,53,1,32,2,37,59,77,51,9,55,67,36,83,78,62,36,23,29,26,41,223,31,1,10,11,4,41,22,28,728,1,39,41,30,1,80,42,56,64,49,52,19,180, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,249,0,0,0,0,0,0,0,0,0,0,0,0,251, 10,14,22,25,27,29,33,37,169,175,178,180,184,185,189,192,201,208,210,334,338,358,363,370,385,393,394,399,518,521,523,526,534,538,542,547,548,550,552,554,559,561,563,567,573,577,711,715,721,724,725,728,730,732,734,737,739,747,749,753,757,766,768,783,906,909,917,919,923,926,929,932,935,940,944,952,1094,1112,1121,1123,1125,1126,1295,1305,1307,1464,1467,1469,1473,1477,1481,1488,1493,1496,1628,1664,1677,1687,1690,1820,1825,1828,1831,1835,1842,1844,1849,1864,1996,1998,2001,2012,2014,2015,2019,2021,2023,2029,2032,2155,2157,2179,2181,2187,2189,2198,2321,2322,2325,2328,2339,2345,2351,2353,2356,2360,2372,2384,2453,2469,2472,2478,2480,2486,2489,2494,2497,2506,2511,2514,2518,2538,2540,2542,2544,2675,2685,2688,2689,2691,2701,2710,2714,2722,2727,2856,3028,3030,3033,3038,3040,3042,3043,3054,3056,3059,3220,3221,3376,3381,3382,3384,3386,3387,3388,3390,3394,3395,3399,3401,3405,3412,3560,3568,3576,3579,3583,3588,3590,3592,3595,3596,3601,3605,3618,3742,3746,3763,3765,3771,3774,3775,3776,3778,3781,3782,3784,3797,3802,3818,3941,3944,3948,3951,3958,3960,3962,3963,3966,3968,3970,3971,3972,3975,3978,3989,3991,4143,4151,4272,4287,4288,4290,4292,4326,4455,4463,4472,4475,4478,4479,4483,4488,4490,4493,4495,4497,4499,4503,4504,4518,4521,4663,4666,4667,4670,4673,4676,4684,4688,4689,4691,4698,4834,4842,4847,4849,4854,4859,4861,4863,4866,4867,4869,4873,4875,4878,4881,4884,4886,4889,4892,4894,4898,4901,4911,4916,5027,5030,5035,5037,5039,5045,5055,5058,5060,5061,5062,5069,5072,5076,5078,5081,5082,5083,5089,5090,5093,5095,5097,5098,5102,5104,5261,5266,5270,5272,5276,5278,5280,5284,5287,5301,5302,5304,5322,5451,5460,5462,5465,5467,5470,5471,5486,5644,5645,5656,5666,5826,5834,5837,5844,5848,5854,6007,6019,6022,6024,6030,6032,6203,6208,6210,6215,6218,6230,6233,6242,6243,6362,6382,6388,6394,6397,6403,6409,6410,6412,6415,6419,6420,6422,6425,6427,6430,6431,6435,6437,6441,6444,6448,6453,6457,6462,6469,6474,6548,6566,6572,6577,6581,6584,6611,6721,6733,6735,6738,6740,6751,6869,6896,7156,7159,7160,7165,7331,7333,7341,7509,7512,7642,7654,7661,7664,7672,7682,8077,8098,8239,8242,8246,8250,8252,8254,8257,8258,8261,8264,8266,8411,8414,8419,8421,8423,8426,8428,8434,8436,8440,8442,8446,8450,8451,8453,8457,8463,8476,8477,8479,8481,8483,8484,8488,8492,8494,8503,8507,8508,8510,8513,8517,8528,8532,8533,8594,8602,8604,8612,8615,8624,8634,8636,8638,8641,8643,8650,8651,8652,8658,8660,8661,8663,8681,8692,8693,8700,8703,8705,8707,8709,8714,8719,8721,8723,8724,8728,8730,8740,8742,8746,8748,8751,8752,8756,8757,8758,8762,8764,8765,8776,8788,8793,8795,8796,8799,8802,8805,8806,8809,8812,8815,8818,8819,8820,8822,8825,8828,8833,8838,8844,8857,8863,8865,8880,8881,8883,8885,8889,8891,8893,8895,8898,8900,8905,8907,8909,8911,8913,8916,8918,8920,8932,8941,8947,8949,8952,8957,8959,8960,8962,8981,8984,8986,8993,8994,8995,8997,8998,9000,9002,9003,9006,9007,9008,9013,9014,9015,9017,9021,9022,9024,9027,9029,9033,9034,9036,9039,9040,9070,9076,9077,9078,9083,9085,9092,9093,9095,9097,9099,9101,9106,9112,9119,9122,9125,9127,9131,9133,9136,9137,9138,9283,9399,9404,9409,9413,9419,9423,9427,9429,9431,9433,9435,9437,9573,9578,9579,9581,9588,9595,9597,9598,9599,9602,9603,9605,9607,9611,9613,9739,9746,9748,9751,9754,9757,9759,9760,9768,9890,9919,10053,10056,10083,10084,10095,10098,10100,10102,10105,10106,10109,10111,10113,10125,10132,10290,10292,10297,10300,10304,10307,10310,10317,10320,10321,10331,10461,10493,10496,10499,10500,10511,10513,10516,10671,10673,10674,10675,10678,10679,10681,10683,10688,10691,10693,10696,10698,10700,10712,10714,10716,10717,10722,10731,10734,10863,10867,10872,10875,10877,10878,10881,10885,10887,10889,10890,10911,11044,11069,11077,11095,11567,11570,11574,11578,11580,11585,11714,11724,11729,11730,11736,11737,11739,11741,11743,11744,11746,11747,11748,11750,11751,11753,11754,11755,11756,11758,11760,11761,11765,11768,11771,11774,11775,11777,11778,11780,11783,11784,11788,11790,11792,11794,11797,11799,11802,11804,11806,11809,11812,11818,11820,11824,11827,11828,11830,11833,11835,11836,11841,11842,11843,11844,11847,11848,11852,11854,11856,11858,11862,11866,11868,11870,11871,11872,11874,11881,11882,11884,11886,11887,11888,11893, -chr19 47506600 47515470 m84008_230107_003043_s1/59839140/ccs 77,354,530,709,1111,1277,1460,1627,1785,1957,2154,2340,2535,2684,2930,3073,3286,3473,3662,3835,4042,4255,4433,4574,4767,4972,5120,5347,5480,5662,5839,6040,6259,6412,6601,6921,7094,7365,7569,7689,7903,8073,8263,8444,8551, 241,142,124,108,110,120,154,137,144,129,104,162,120,170,117,130,139,136,121,131,118,115,139,149,146,147,130,107,142,107,129,116,102,123,278,121,270,120,119,141,114,121,139,76,80, 318,496,654,817,1221,1397,1614,1764,1929,2086,2258,2502,2655,2854,3047,3203,3425,3609,3783,3966,4160,4370,4572,4723,4913,5119,5250,5454,5622,5769,5968,6156,6361,6535,6879,7042,7364,7485,7688,7830,8017,8194,8402,8520, 36,34,55,294,56,63,13,21,28,68,82,33,29,76,26,83,48,53,52,76,95,63,2,44,59,1,97,26,40,70,72,103,51,66,42,52,1,84,1,73,56,69,42,31, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 20,23,26,28,30,59,61,65,69,73,76,318,330,332,338,339,353,496,500,506,510,529,654,657,661,663,665,667,670,672,680,682,686,689,701,708,817,839,842,843,848,850,852,856,859,862,865,868,873,874,877,882,889,893,896,902,912,920,923,930,938,940,942,1000,1002,1016,1018,1020,1023,1029,1031,1040,1042,1046,1054,1058,1059,1063,1065,1067,1069,1070,1074,1102,1108,1110,1221,1225,1228,1234,1252,1255,1268,1272,1276,1397,1400,1403,1406,1410,1421,1426,1431,1432,1442,1446,1450,1457,1459,1614,1618,1623,1626,1764,1775,1777,1779,1782,1784,1929,1931,1934,1945,1948,1954,1956,2035,2086,2089,2094,2096,2100,2102,2114,2117,2119,2125,2128,2133,2136,2140,2141,2144,2147,2151,2153,2258,2269,2275,2281,2283,2286,2296,2298,2300,2302,2304,2306,2311,2312,2331,2336,2339,2502,2504,2512,2514,2523,2526,2534,2655,2667,2669,2671,2675,2677,2680,2683,2854,2856,2859,2861,2873,2876,2890,2900,2903,2908,2914,2929,3047,3049,3065,3068,3072,3203,3234,3239,3242,3250,3251,3256,3271,3277,3285,3384,3425,3427,3429,3435,3437,3442,3444,3447,3451,3456,3460,3462,3464,3466,3472,3609,3610,3615,3617,3620,3624,3637,3648,3650,3655,3658,3661,3783,3786,3789,3795,3798,3804,3805,3808,3811,3812,3813,3816,3819,3821,3827,3828,3830,3834,3966,3969,3979,3983,3984,3986,3989,3990,3994,4009,4019,4021,4033,4041,4160,4162,4166,4169,4171,4173,4177,4178,4183,4184,4186,4192,4196,4200,4202,4205,4207,4210,4215,4218,4220,4237,4239,4242,4245,4254,4370,4387,4395,4396,4400,4407,4411,4416,4421,4423,4425,4431,4432,4526,4572,4573,4723,4730,4734,4736,4739,4742,4747,4754,4762,4763,4766,4913,4922,4924,4926,4930,4932,4942,4946,4949,4958,4968,4971,5119,5250,5254,5256,5260,5263,5266,5268,5270,5280,5282,5285,5288,5291,5296,5299,5301,5303,5321,5346,5454,5456,5458,5459,5462,5463,5465,5471,5476,5479,5622,5640,5642,5644,5646,5647,5650,5653,5654,5658,5661,5769,5776,5782,5784,5788,5791,5793,5794,5797,5800,5806,5809,5811,5813,5816,5826,5828,5838,5968,5980,5985,5986,5990,5993,5996,6003,6009,6013,6018,6020,6026,6029,6039,6156,6159,6180,6185,6193,6216,6218,6231,6235,6236,6258,6361,6367,6370,6374,6383,6385,6388,6391,6409,6411,6535,6537,6549,6550,6553,6555,6562,6566,6568,6569,6572,6575,6577,6579,6580,6584,6585,6587,6589,6591,6593,6594,6597,6600,6879,6881,6885,6901,6904,6907,6920,7042,7045,7054,7056,7057,7063,7067,7070,7073,7076,7078,7080,7087,7093,7364,7485,7507,7509,7515,7517,7519,7521,7524,7529,7533,7541,7544,7549,7551,7559,7565,7568,7688,7830,7832,7835,7838,7842,7843,7845,7847,7855,7870,7886,7896,7899,7902,8017,8022,8024,8035,8043,8045,8046,8061,8063,8072,8194,8211,8218,8230,8234,8235,8238,8243,8245,8250,8256,8262,8402,8403,8405,8407,8409,8410,8418,8433,8443,8520,8528,8538,8541,8550,8631,8633,8640,8645,8647,8653,8655,8658,8662,8665,8667,8671,8673,8682,8683,8713,8717,8723,8726,8730,8762,8768,8780,8786,8788,8794,8806,8808,8812,8814,8816,8821, -chr19 47506953 47527720 m84008_230107_003043_s1/212800855/ccs 177,375,576,1159,1343,1603,1690,2033,2327,2976,3468,3995,4209,4737,5001,5144,5313,5532,5726,5912,6383,6859,7025,7166,7366,7544,7928,8768,8886,9260,9742,10110,10307,10439,10626,10921,11085,11519,11721,11837,11973,12164,12395,12579,12890,13125,13322,13479,13683,13867,14197,14369,14725,14984,15360,15532,15756,15926,16147,16450,16614,16766,16970,17197,17550,17904,18477,18658,18819,19005,19206,19476,19605,19997,20185,20359, 131,168,149,130,137,86,156,75,243,141,142,140,128,112,132,161,107,110,143,128,147,146,140,178,139,123,127,113,183,440,153,136,116,133,294,160,137,201,98,135,167,152,153,298,80,116,117,142,154,152,171,181,142,144,138,82,146,154,145,148,76,169,115,141,153,161,180,148,185,200,188,128,184,173,160,151, 308,543,725,1289,1480,1689,1846,2108,2570,3117,3610,4135,4337,4849,5133,5305,5420,5642,5869,6040,6530,7005,7165,7344,7505,7667,8055,8881,9069,9700,9895,10246,10423,10572,10920,11081,11222,11720,11819,11972,12140,12316,12548,12877,12970,13241,13439,13621,13837,14019,14368,14550,14867,15128,15498,15614,15902,16080,16292,16598,16690,16935,17085,17338,17703,18065,18657,18806,19004,19205,19394,19604,19789,20170,20345, 67,33,434,54,123,1,187,219,406,351,385,74,400,152,11,8,112,84,43,343,329,20,1,22,39,261,713,5,191,42,215,61,16,54,1,4,297,1,18,1,24,79,31,13,155,81,40,62,30,178,1,175,117,232,34,142,24,67,158,16,76,35,112,212,201,412,1,13,1,1,82,1,208,15,14, 0,0,245,0,0,0,247,243,247,247,246,0,247,0,0,0,0,0,0,245,244,0,0,0,0,246,243,0,246,0,0,0,0,0,0,0,244,0,0,0,0,0,0,0,0,0,0,0,0,244,0,242,0,247,0,0,0,0,0,0,0,0,0,242,0,0,0,0,0,0,0,0,0,0,0, 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-chr19 47506979 47526118 m64076_221119_202646/23463766/ccs 141,747,890,1081,1297,1466,1645,1837,2002,2157,2303,2500,2737,2880,3017,3268,3496,3675,3848,4031,4203,4382,4524,4713,4958,5117,5286,5534,5701,5985,6359,6559,6701,6841,7033,7216,7560,7686,7854,8597,8854,9162,9397,9533,9664,9900,10180,10318,10622,10792,11138,11312,11523,11730,11903,12127,12329,12528,12703,12959,13104,13301,13478,13675,13844,14041,14217,14396,14596,14789,15007,15206,15361,15477,16096,16259,16408,16589,16810,17006,17192,17494,17833,18024,18194,18363,18535,18725,18889, 128,95,110,121,99,133,133,128,122,145,128,90,89,113,147,96,97,111,144,132,116,134,126,108,96,109,83,76,104,120,84,98,86,136,104,106,78,100,103,149,96,81,89,113,169,171,112,256,108,116,126,107,153,114,115,118,89,96,217,140,132,109,122,85,92,87,130,127,107,97,108,119,115,118,126,118,114,125,80,123,130,103,112,122,119,153,123,107,138, 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-chr19 47507279 47524132 m64076_210328_012155/147784005/ccs 77,163,295,710,827,1193,1376,1591,2283,2486,2676,2846,3054,3241,3432,3794,4011,4229,4405,4605,4842,5087,5427,5532,5752,5924,6074,6233,6420,6788,6868,7111,7286,7592,8520,8738,9061,9247,9434,9650,9846,10008,10185,10384,10666,11016,11153,11355,11521,11835,12197,12382,12538,12766,12903,13093,13282,13650,13849,14070,14278,14455,14631,14846,15052,15193,15386,15562,16074,16282,16482, 85,123,330,105,301,143,156,652,137,135,169,154,149,161,337,161,179,169,162,145,244,284,104,184,156,142,129,150,367,79,188,129,305,79,217,282,171,181,136,129,128,121,117,164,268,136,135,137,289,317,166,143,153,136,152,132,349,159,132,127,119,131,126,114,134,132,137,507,166,167,150, 162,286,625,815,1128,1336,1532,2243,2420,2621,2845,3000,3203,3402,3769,3955,4190,4398,4567,4750,5086,5371,5531,5716,5908,6066,6203,6383,6787,6867,7056,7240,7591,7671,8737,9020,9232,9428,9570,9779,9974,10129,10302,10548,10934,11152,11288,11492,11810,12152,12363,12525,12691,12902,13055,13225,13631,13809,13981,14197,14397,14586,14757,14960,15186,15325,15523,16069,16240,16449,16632, 1,9,85,12,65,40,59,40,66,55,1,54,38,30,25,56,39,7,38,92,1,56,1,36,16,8,30,37,1,1,55,46,1,849,1,41,15,6,80,67,34,56,82,118,82,1,67,29,25,45,19,13,75,1,38,57,19,40,89,81,58,45,89,92,7,61,39,5,42,33,49, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,252,0,0,0,0,0,0,0,0,0,243,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 76,162,286,288,292,294,625,628,680,706,709,815,817,824,826,1128,1131,1145,1149,1170,1173,1178,1185,1192,1336,1354,1358,1375,1532,1542,1546,1550,1562,1566,1583,1584,1587,1590,2243,2254,2257,2261,2282,2420,2423,2432,2439,2448,2451,2455,2458,2477,2484,2485,2621,2644,2653,2675,2845,3000,3053,3203,3210,3213,3220,3222,3228,3237,3240,3293,3372,3402,3407,3424,3427,3430,3431,3769,3779,3783,3793,3892,3955,3980,3982,3987,3989,3992,3995,3998,4002,4006,4010,4190,4228,4398,4404,4567,4573,4604,4750,4781,4829,4832,4841,5086,5371,5395,5397,5399,5401,5403,5405,5411,5415,5418,5422,5426,5531,5716,5725,5729,5739,5746,5749,5751,5792,5908,5914,5921,5923,5956,6018,6056,6066,6073,6203,6229,6232,6383,6387,6390,6391,6393,6397,6399,6401,6402,6415,6418,6419,6787,6867,7056,7061,7071,7092,7107,7110,7240,7243,7246,7257,7263,7278,7285,7591,7671,7675,7707,7709,7715,7719,7724,7726,7728,7730,7736,7749,7750,7752,7754,7756,7757,7765,7776,7780,7786,7790,7801,7805,7806,7825,7839,7849,7852,7867,7875,7877,7886,7889,7898,7909,7911,7913,7916,7918,7926,7944,7968,7969,7976,7979,7981,7983,7985,7991,7996,7998,8000,8001,8004,8006,8009,8013,8018,8022,8024,8027,8028,8032,8033,8034,8038,8040,8041,8066,8070,8072,8073,8076,8079,8082,8083,8086,8089,8092,8095,8096,8099,8102,8105,8110,8115,8121,8139,8166,8168,8170,8172,8175,8177,8182,8184,8186,8188,8190,8193,8195,8197,8200,8209,8222,8224,8226,8229,8234,8237,8258,8261,8263,8274,8277,8283,8284,8285,8290,8294,8298,8299,8300,8301,8304,8306,8310,8311,8313,8316,8351,8355,8356,8361,8371,8372,8374,8376,8380,8385,8390,8391,8393,8396,8406,8408,8410,8412,8415,8416,8417,8419,8427,8428,8431,8433,8434,8436,8446,8450,8456,8463,8465,8466,8470,8473,8477,8498,8502,8508,8510,8511,8513,8515,8516,8517,8519,8737,9020,9039,9046,9050,9055,9057,9060,9232,9240,9246,9428,9433,9570,9574,9591,9594,9605,9610,9612,9621,9623,9627,9628,9631,9635,9640,9642,9649,9779,9782,9785,9786,9790,9792,9799,9802,9805,9806,9810,9820,9823,9826,9839,9845,9974,9977,9979,10000,10007,10129,10140,10142,10145,10149,10161,10167,10171,10173,10184,10302,10326,10328,10355,10365,10375,10376,10381,10383,10548,10552,10553,10554,10558,10565,10569,10572,10573,10576,10581,10587,10589,10591,10593,10596,10600,10602,10604,10607,10608,10609,10611,10615,10625,10627,10630,10654,10659,10662,10665,10934,10938,10940,10944,10950,10953,10955,10957,10961,10977,10978,10984,10985,10989,11015,11152,11288,11292,11296,11297,11304,11311,11316,11320,11323,11326,11332,11334,11335,11339,11340,11345,11346,11349,11351,11354,11446,11492,11514,11517,11520,11810,11822,11824,11827,11831,11834,12152,12155,12158,12162,12164,12169,12171,12181,12186,12190,12196,12363,12370,12372,12381,12525,12530,12537,12691,12708,12715,12718,12722,12727,12730,12732,12734,12738,12740,12746,12751,12765,12902,13055,13063,13067,13068,13069,13071,13074,13092,13225,13229,13231,13232,13261,13262,13268,13271,13274,13281,13631,13632,13646,13649,13809,13812,13815,13818,13822,13824,13826,13828,13836,13841,13845,13847,13848,13981,13998,14002,14007,14011,14019,14023,14029,14033,14038,14041,14043,14048,14051,14052,14054,14060,14063,14064,14069,14197,14201,14206,14219,14222,14224,14229,14233,14245,14247,14249,14253,14266,14272,14277,14397,14405,14413,14422,14426,14441,14444,14446,14454,14586,14599,14602,14606,14618,14630,14663,14757,14777,14787,14797,14801,14803,14805,14807,14810,14811,14816,14817,14830,14845,14960,14981,14988,14993,14996,14998,15001,15002,15019,15020,15025,15032,15036,15039,15043,15051,15157,15186,15188,15192,15325,15328,15350,15352,15355,15359,15369,15375,15380,15381,15383,15385,15492,15523,15525,15527,15529,15531,15533,15537,15539,15541,15547,15551,15556,15561,16069,16073,16240,16243,16264,16266,16270,16274,16276,16281,16390,16449,16450,16453,16465,16474,16476,16477,16479,16481,16632,16634,16640,16655,16657,16660,16677,16680, -chr19 47507325 47527172 m84039_230401_034725_s4/174002742/ccs 168,383,729,897,1092,1269,1426,1589,1756,1893,2084,2243,2429,2600,2752,2951,3127,3309,3497,3638,3784,3969,4288,4406,4643,4987,5156,5250,5528,5725,5856,5947,6064,6183,6326,6487,6635,6832,7054,7191,7362,7531,8406,8588,8773,8973,9123,9314,9455,9642,9826,9925,10164,10325,10582,10744,11140,11257,11461,11617,11900,12074,12225,12424,12599,12771,12943,13166,13316,13505,13852,14076,14472,14612,14828,14988,15177,15368,15530,15950,16148,16294,16497,16696,16898,17181,17310,17501,17680,17844,18016,18103,18179,18375,18555,18704,18885,19063,19254,19472, 129,105,126,134,126,146,117,139,136,156,113,109,134,131,109,122,137,97,122,120,184,318,117,218,107,131,93,194,108,116,90,105,94,122,119,115,125,114,102,128,128,111,98,134,128,144,129,109,140,142,98,184,160,237,129,102,116,164,140,259,136,79,166,125,116,138,138,97,94,137,103,93,111,124,95,133,146,111,419,176,119,156,124,116,135,87,124,127,98,147,86,75,143,105,128,164,122,146,151,131, 136,297,488,855,1031,1218,1415,1543,1728,1892,2049,2197,2352,2563,2731,2861,3073,3264,3406,3619,3758,3968,4287,4405,4624,4750,5118,5249,5444,5636,5841,5946,6052,6158,6305,6445,6602,6760,6946,7156,7319,7490,7642,8504,8722,8901,9117,9252,9423,9595,9784,9924,10109,10324,10562,10711,10846,11256,11421,11601,11876,12036,12153,12391,12549,12715,12909,13081,13263,13410,13642,13955,14169,14583,14736,14923,15121,15323,15479,15949,16126,16267,16450,16621,16812,17033,17268,17434,17628,17778,17991,18102,18178,18322,18480,18683,18868,19007,19209,19405,19603, 32,86,241,42,61,51,11,46,28,1,35,46,77,37,21,90,54,45,91,19,26,1,1,1,19,237,38,1,84,89,15,1,12,25,21,42,33,72,108,35,43,41,764,84,51,72,6,62,32,47,42,1,55,1,20,33,294,1,40,16,24,38,72,33,50,56,34,85,53,95,210,121,303,29,92,65,56,45,51,1,22,27,47,75,86,148,42,67,52,66,25,1,1,53,75,21,17,56,45,67,31, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,251,0,0,0,0,0,0,0,0,0,0,0,0,0,244,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,243,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 2,5,6,29,136,139,147,148,151,154,167,297,305,310,314,320,328,332,333,337,341,344,348,360,363,366,373,376,382,488,495,502,512,514,521,529,546,556,608,616,621,667,671,674,676,677,680,684,688,695,700,703,708,720,724,728,855,857,861,863,871,873,887,891,893,896,972,1031,1034,1037,1041,1048,1050,1052,1055,1057,1063,1064,1070,1073,1074,1077,1091,1218,1220,1221,1227,1229,1236,1238,1246,1253,1256,1257,1262,1263,1268,1415,1418,1421,1425,1543,1549,1555,1557,1560,1570,1578,1580,1585,1588,1728,1736,1742,1744,1746,1748,1755,1892,2049,2051,2056,2058,2060,2083,2197,2199,2204,2209,2211,2214,2222,2232,2234,2237,2238,2242,2352,2353,2360,2372,2379,2388,2395,2398,2408,2411,2417,2425,2428,2563,2565,2566,2580,2585,2598,2599,2731,2741,2751,2809,2861,2890,2897,2917,2925,2930,2933,2950,3073,3080,3083,3091,3102,3111,3126,3264,3296,3304,3308,3406,3430,3445,3447,3449,3453,3454,3459,3468,3472,3483,3486,3494,3496,3619,3635,3637,3758,3760,3770,3778,3783,3968,4287,4347,4351,4405,4624,4642,4699,4750,4780,4783,4787,4793,4795,4798,4803,4811,4814,4817,4836,4838,4844,4897,4907,4928,4933,4936,4941,4943,4961,4963,4968,4974,4977,4983,4986,5037,5118,5137,5138,5144,5149,5155,5249,5444,5461,5464,5468,5475,5491,5493,5498,5504,5511,5514,5527,5636,5642,5654,5658,5660,5663,5668,5670,5675,5678,5680,5682,5686,5689,5691,5693,5707,5710,5711,5712,5724,5841,5844,5847,5850,5855,5946,6002,6052,6063,6158,6161,6170,6182,6305,6320,6325,6445,6446,6447,6453,6460,6462,6464,6467,6478,6483,6486,6602,6617,6621,6624,6634,6760,6769,6777,6780,6784,6787,6792,6794,6799,6801,6804,6805,6808,6815,6816,6819,6824,6831,6899,6927,6946,6954,6956,6976,6983,6987,6989,6995,6998,7001,7006,7012,7015,7017,7019,7023,7034,7037,7039,7053,7156,7167,7170,7174,7176,7180,7184,7190,7319,7331,7337,7344,7346,7354,7359,7361,7454,7490,7492,7499,7502,7525,7530,7603,7619,7642,7646,7650,7651,7653,7657,7676,7677,7679,7681,7683,7684,7688,7692,7710,7713,7717,7728,7732,7766,7769,7776,7779,7781,7794,7802,7804,7815,7834,7838,7841,7843,7850,7851,7852,7858,7861,7865,7868,7892,7893,7900,7905,7907,7909,7919,7921,7923,7927,7929,7932,7936,7939,7945,7947,7950,7951,7955,7956,7957,7961,7963,7964,7975,7987,7991,7993,7994,7997,8000,8003,8004,8007,8010,8023,8026,8031,8036,8042,8054,8060,8062,8068,8077,8078,8080,8082,8086,8088,8092,8097,8102,8108,8113,8115,8117,8120,8129,8138,8142,8144,8146,8149,8154,8156,8157,8178,8181,8183,8190,8191,8192,8194,8195,8197,8199,8200,8203,8204,8205,8210,8212,8214,8218,8221,8224,8225,8226,8230,8231,8233,8236,8242,8246,8250,8252,8254,8260,8262,8265,8268,8269,8271,8274,8276,8281,8283,8288,8291,8293,8295,8297,8299,8302,8303,8309,8314,8316,8319,8320,8322,8330,8349,8352,8364,8368,8372,8374,8379,8384,8388,8399,8405,8504,8506,8520,8523,8524,8526,8528,8535,8537,8539,8541,8544,8546,8556,8566,8569,8577,8585,8587,8722,8725,8728,8733,8738,8740,8743,8744,8749,8756,8759,8765,8767,8772,8901,8914,8916,8918,8928,8930,8932,8938,8942,8945,8947,8950,8953,8956,8964,8972,9117,9122,9252,9255,9257,9259,9262,9263,9266,9282,9290,9292,9293,9297,9299,9301,9304,9305,9308,9312,9313,9423,9434,9447,9453,9454,9527,9595,9598,9601,9604,9609,9614,9623,9625,9628,9634,9640,9641,9784,9786,9791,9793,9796,9806,9808,9809,9811,9825,9924,9983,10109,10118,10163,10324,10562,10566,10581,10621,10711,10717,10724,10743,10846,10849,10851,10865,10867,10877,10882,10883,10887,10889,10896,10897,10903,10908,10911,10927,10936,10938,10941,10944,10965,10968,10972,10996,10999,11006,11017,11021,11024,11025,11030,11032,11033,11038,11044,11049,11051,11053,11055,11063,11065,11067,11078,11079,11081,11083,11090,11096,11097,11098,11099,11101,11112,11115,11122,11124,11139,11256,11421,11425,11429,11432,11436,11441,11445,11446,11448,11460,11601,11616,11876,11880,11890,11899,12036,12039,12047,12048,12050,12052,12055,12056,12057,12060,12061,12063,12066,12069,12073,12153,12160,12200,12211,12213,12217,12224,12290,12353,12360,12391,12392,12397,12399,12409,12423,12549,12551,12553,12563,12566,12567,12575,12578,12598,12715,12721,12726,12736,12741,12745,12752,12760,12770,12882,12909,12912,12915,12942,13081,13082,13085,13088,13094,13097,13099,13103,13107,13109,13112,13115,13123,13135,13140,13165,13263,13265,13270,13272,13274,13277,13280,13287,13293,13296,13301,13302,13307,13315,13410,13418,13452,13462,13474,13478,13480,13484,13486,13491,13492,13504,13642,13644,13646,13650,13658,13668,13672,13675,13678,13694,13704,13774,13779,13781,13785,13802,13807,13821,13824,13826,13832,13833,13837,13840,13846,13851,13955,13975,13981,14010,14011,14013,14018,14023,14024,14026,14033,14035,14039,14041,14046,14051,14059,14064,14068,14071,14075,14169,14175,14180,14209,14213,14216,14217,14224,14227,14230,14232,14235,14236,14241,14245,14249,14252,14257,14262,14268,14273,14275,14276,14280,14283,14293,14295,14316,14349,14366,14368,14376,14379,14386,14393,14395,14398,14401,14404,14411,14412,14416,14418,14421,14424,14434,14436,14438,14443,14450,14451,14456,14462,14465,14471,14583,14593,14597,14609,14611,14736,14748,14760,14762,14778,14780,14783,14785,14787,14790,14794,14798,14803,14806,14811,14812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-chr19 47507405 47523090 m54329U_210326_192251/77267415/ccs 100,298,424,650,922,1079,1220,1416,1551,1740,2063,2249,2441,2618,2792,2990,3136,3294,3465,3624,3808,3965,4144,4321,4461,4635,4782,4939,5060,5232,5479,5610,5796,5930,6114,6248,6408,6565,6778,6938,7061,7244,7454,8314,8491,8635,8776,8894,9038,9198,9365,9510,9679,9811,10043,10212,10362,10527,10791,11071,11359,11724,11947,12104,12263,12376,12534,12729,12969,13108,13280,13451,13602,13784,14014,14346,14501,14649,14829,15062,15202,15386, 106,121,136,221,127,130,141,134,148,302,132,140,112,145,119,115,147,158,124,138,120,121,150,130,150,146,134,120,140,122,80,137,129,154,113,126,107,110,83,112,117,111,80,83,114,104,117,143,129,114,129,123,130,144,105,120,105,118,164,119,244,113,88,76,112,148,110,137,92,140,133,134,99,92,90,116,99,96,115,112,124,101, 73,206,419,560,871,1049,1209,1361,1550,1699,2042,2195,2389,2553,2763,2911,3105,3283,3452,3589,3762,3928,4086,4294,4451,4611,4781,4916,5059,5200,5354,5559,5747,5925,6084,6227,6374,6515,6675,6861,7050,7178,7355,7534,8397,8605,8739,8893,9037,9167,9312,9494,9633,9809,9955,10148,10332,10467,10645,10955,11190,11603,11837,12035,12180,12375,12524,12644,12866,13061,13248,13413,13585,13701,13876,14104,14462,14600,14745,14944,15174,15326,15487, 27,92,5,90,51,30,11,55,1,41,21,54,52,65,29,79,31,11,13,35,46,37,58,27,10,24,1,23,1,32,125,51,49,5,30,21,34,50,103,77,11,66,99,780,94,30,37,1,1,31,53,16,46,2,88,64,30,60,146,116,169,121,110,69,83,1,10,85,103,47,32,38,17,83,138,242,39,49,84,118,28,60,37, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,250,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,243,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 72,77,80,88,97,99,206,213,215,218,222,224,231,232,235,237,240,241,249,251,253,254,258,260,262,264,265,269,272,273,278,281,284,297,419,420,423,560,561,566,567,571,574,575,592,595,597,598,601,605,609,621,624,649,871,875,880,882,888,892,895,899,901,905,907,910,911,916,921,1049,1054,1060,1066,1078,1209,1219,1361,1364,1373,1374,1377,1390,1394,1398,1400,1402,1407,1409,1411,1415,1550,1699,1701,1703,1704,1709,1711,1716,1720,1723,1725,1729,1731,1733,1736,1739,2042,2048,2054,2062,2195,2199,2203,2208,2222,2225,2226,2231,2232,2235,2237,2240,2241,2247,2248,2389,2391,2401,2409,2426,2432,2437,2440,2553,2559,2577,2587,2589,2592,2593,2598,2604,2607,2608,2612,2617,2737,2763,2767,2769,2772,2774,2778,2784,2786,2789,2791,2911,2914,2915,2918,2923,2928,2929,2933,2937,2941,2943,2949,2954,2957,2959,2963,2965,2969,2973,2978,2981,2989,3105,3113,3116,3118,3121,3122,3123,3125,3129,3132,3135,3283,3293,3452,3461,3464,3589,3601,3605,3614,3621,3623,3762,3766,3770,3771,3773,3776,3778,3785,3792,3807,3928,3932,3934,3937,3940,3945,3952,3956,3960,3961,3964,4086,4090,4093,4110,4113,4115,4118,4119,4121,4123,4126,4129,4131,4138,4139,4142,4143,4294,4299,4300,4302,4304,4314,4320,4405,4451,4457,4460,4611,4624,4634,4781,4916,4919,4921,4923,4932,4934,4938,5059,5200,5207,5208,5210,5215,5217,5218,5221,5223,5224,5226,5231,5354,5357,5366,5367,5378,5381,5383,5391,5394,5396,5398,5401,5408,5413,5414,5416,5421,5422,5424,5427,5429,5433,5434,5437,5439,5446,5447,5449,5450,5454,5456,5460,5476,5478,5559,5565,5568,5572,5577,5581,5583,5586,5589,5593,5598,5607,5609,5747,5758,5760,5764,5766,5767,5770,5773,5775,5778,5783,5785,5789,5791,5795,5925,5929,6084,6093,6097,6099,6113,6227,6228,6232,6234,6235,6237,6243,6245,6247,6317,6374,6378,6383,6385,6388,6407,6515,6518,6521,6527,6531,6534,6535,6537,6539,6540,6541,6543,6546,6552,6556,6561,6564,6675,6677,6682,6699,6702,6704,6709,6712,6714,6716,6718,6719,6721,6723,6726,6727,6729,6730,6737,6738,6741,6746,6748,6751,6753,6756,6765,6769,6777,6861,6866,6868,6875,6876,6878,6882,6885,6889,6898,6905,6909,6910,6911,6912,6915,6917,6920,6923,6937,7050,7056,7060,7178,7182,7186,7188,7190,7193,7195,7200,7201,7202,7203,7207,7208,7214,7215,7217,7219,7221,7225,7227,7229,7232,7236,7242,7243,7355,7369,7373,7375,7377,7380,7381,7384,7387,7389,7391,7395,7396,7399,7415,7422,7423,7425,7427,7435,7453,7534,7546,7549,7551,7557,7563,7565,7569,7573,7574,7576,7580,7586,7599,7600,7602,7604,7606,7607,7611,7617,7626,7630,7633,7640,7651,7655,7656,7666,7667,7670,7675,7677,7683,7688,7689,7692,7699,7702,7704,7717,7725,7727,7735,7738,7747,7757,7761,7764,7766,7773,7775,7781,7783,7784,7786,7788,7793,7794,7798,7799,7804,7806,7807,7808,7815,7816,7823,7826,7828,7830,7832,7837,7842,7844,7846,7847,7850,7852,7855,7859,7862,7864,7868,7870,7873,7874,7878,7879,7880,7884,7886,7887,7910,7914,7916,7917,7920,7923,7926,7927,7930,7933,7940,7943,7946,7949,7954,7959,7965,7978,7986,7992,8001,8002,8004,8006,8010,8012,8014,8016,8019,8021,8026,8028,8030,8034,8037,8039,8041,8044,8053,8062,8066,8068,8070,8071,8073,8078,8080,8081,8083,8102,8105,8107,8114,8115,8116,8118,8119,8121,8127,8128,8129,8134,8136,8138,8145,8148,8149,8150,8154,8155,8157,8160,8161,8162,8163,8164,8166,8167,8170,8174,8176,8178,8184,8186,8187,8189,8192,8195,8198,8199,8200,8205,8207,8212,8214,8215,8217,8219,8221,8226,8227,8228,8234,8244,8245,8247,8249,8251,8253,8255,8258,8260,8263,8274,8277,8279,8289,8293,8298,8313,8397,8403,8405,8421,8423,8426,8430,8432,8434,8437,8439,8442,8446,8449,8450,8452,8454,8457,8461,8463,8465,8467,8471,8473,8474,8475,8479,8490,8605,8610,8614,8627,8629,8631,8634,8739,8759,8762,8764,8767,8770,8773,8775,8893,9037,9167,9169,9175,9178,9180,9192,9195,9197,9312,9317,9321,9327,9332,9333,9335,9336,9337,9339,9340,9344,9347,9349,9351,9357,9358,9364,9494,9497,9503,9509,9633,9638,9639,9641,9642,9646,9650,9652,9656,9659,9662,9663,9675,9678,9809,9810,9955,9957,9960,9962,9965,9967,9970,9972,9976,9978,9981,9985,9991,9993,9994,9997,9999,10000,10001,10003,10005,10007,10009,10011,10012,10018,10021,10025,10028,10029,10033,10039,10042,10099,10148,10160,10162,10164,10166,10169,10170,10172,10174,10191,10193,10199,10211,10332,10337,10361,10467,10483,10487,10491,10493,10496,10499,10502,10503,10505,10506,10510,10515,10520,10522,10526,10645,10649,10652,10660,10665,10668,10670,10672,10674,10678,10681,10683,10685,10688,10690,10694,10696,10700,10702,10705,10707,10728,10787,10790,10955,10957,10958,10973,10974,10984,10988,11037,11039,11040,11043,11046,11047,11049,11051,11054,11055,11070,11190,11193,11197,11201,11204,11222,11223,11224,11228,11235,11240,11246,11248,11252,11254,11256,11257,11260,11262,11264,11265,11270,11274,11277,11279,11282,11284,11288,11291,11292,11294,11296,11299,11301,11303,11307,11310,11312,11316,11318,11321,11322,11323,11325,11326,11329,11331,11332,11334,11335,11337,11358,11603,11607,11609,11612,11614,11616,11620,11624,11626,11630,11632,11634,11636,11637,11638,11644,11647,11659,11661,11663,11666,11670,11673,11674,11678,11679,11680,11682,11685,11686,11688,11689,11691,11695,11698,11700,11705,11707,11714,11716,11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-chr19 47507421 47529309 m64076_210328_012155/50858372/ccs 207,342,509,720,1055,1188,1337,1486,1742,1887,2158,2319,2463,2652,2817,3020,3235,3432,3619,3834,4010,4218,4352,4518,4690,4890,5027,5222,5415,5605,5876,6105,6289,6402,6628,6859,7009,7307,7453,8397,8737,8927,9146,9421,9580,9773,9888,10149,10340,10673,11082,11275,11477,11792,11944,12149,12349,12514,12725,12895,13069,13233,13455,13660,13851,14037,14191,14376,14629,14813,15020,15178,15330,15503,15677,15838,16035,16495,16696,16869,17053,17236,17416,17617,17815,17956,18187,18408,18573,18756,18940,19117,19311,19516,19709,19885,20093,20255,20464,20651,20817,21045,21216,21406,21631, 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-chr19 47507794 47513324 m84039_230404_003541_s3/99686134/ccs 107,326,522,708,927,1114,1488,1663,1770,1904,2063,2283,2478,2856,3071,3254,3455,3630,3893,4104,4331,4528,4776,4946,5245, 182,127,185,216,138,349,174,106,83,141,196,176,377,214,168,188,149,174,162,174,169,167,148,277,185, 85,289,453,707,924,1065,1463,1662,1769,1853,2045,2259,2459,2855,3070,3239,3442,3604,3804,4055,4278,4500,4695,4924,5223, 22,37,69,1,3,49,25,1,1,51,18,24,19,1,1,15,13,26,89,49,53,28,81,22,22, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,1,5,85,88,93,106,289,294,325,453,467,492,509,521,707,924,926,1065,1109,1113,1463,1476,1478,1487,1662,1688,1696,1769,1853,1871,1874,1883,1884,1891,1894,1899,1903,2045,2048,2057,2062,2259,2264,2282,2459,2467,2477,2855,3070,3239,3253,3442,3454,3604,3624,3629,3804,3811,3824,3837,3850,3853,3855,3871,3872,3874,3886,3892,4055,4067,4070,4081,4095,4098,4103,4278,4282,4283,4286,4289,4290,4296,4307,4309,4312,4315,4325,4330,4451,4500,4506,4509,4527,4695,4702,4705,4709,4713,4716,4718,4722,4775,4924,4928,4945,5223,5225,5241,5244,5430,5433,5443,5445,5519,5520,5522, -chr19 47507921 47523781 m84039_230404_003541_s3/109972366/ccs 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-chr19 47508600 47519371 m84008_230107_003043_s1/156697421/ccs 119,470,644,817,993,1180,1425,1979,2189,2359,2571,2765,2979,3137,3345,3535,3763,4071,4298,4431,4596,4855,5043,5189,5398,5614,5751,5896,6249,6454,7044,7194,7508,7808,7978,8162,8376,8564,8760,8964,9134,9302,9514,9715,9900,10094,10274,10472, 307,147,141,166,148,142,507,150,153,165,130,155,144,155,158,197,238,162,83,122,134,149,145,171,166,136,121,324,90,100,132,303,136,138,128,150,116,126,136,132,153,159,139,146,142,141,143,139, 80,426,617,785,983,1141,1322,1932,2129,2342,2524,2701,2920,3123,3292,3503,3732,4001,4233,4381,4553,4730,5004,5188,5360,5564,5750,5872,6220,6339,6554,7176,7497,7644,7946,8106,8312,8492,8690,8896,9096,9287,9461,9653,9861,10042,10235,10417, 39,44,27,32,10,39,103,47,60,17,47,64,59,14,53,32,31,70,65,50,43,125,39,1,38,50,1,24,29,115,490,18,11,164,32,56,64,72,70,68,38,15,53,62,39,52,39,55, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,250,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 80,85,87,113,118,426,435,440,443,447,461,463,469,617,618,639,643,785,792,797,799,805,808,811,816,983,985,988,992,1141,1149,1155,1160,1162,1164,1168,1171,1172,1174,1176,1179,1322,1327,1340,1341,1354,1378,1383,1385,1390,1394,1418,1424,1932,1935,1942,1958,1964,1978,2129,2132,2134,2140,2147,2150,2159,2161,2165,2176,2182,2188,2285,2342,2358,2524,2529,2534,2536,2540,2544,2547,2553,2555,2570,2701,2706,2708,2712,2717,2721,2732,2734,2737,2745,2752,2756,2760,2761,2764,2815,2920,2922,2924,2928,2937,2939,2943,2944,2947,2961,2963,2965,2969,2972,2978,3123,3130,3136,3292,3319,3324,3344,3503,3506,3510,3514,3516,3518,3526,3528,3529,3534,3732,3733,3735,3758,3762,4001,4011,4016,4018,4022,4024,4027,4050,4056,4058,4062,4064,4067,4070,4233,4237,4239,4241,4242,4250,4256,4260,4263,4265,4267,4268,4269,4272,4297,4381,4383,4393,4398,4401,4407,4412,4414,4427,4430,4553,4558,4560,4564,4566,4567,4570,4573,4575,4578,4583,4585,4589,4595,4730,4739,4740,4745,4746,4748,4752,4756,4758,4759,4761,4766,4768,4774,4776,4779,4783,4785,4788,4793,4797,4799,4800,4805,4806,4812,4814,4819,4824,4828,4835,4842,4843,4845,4851,4854,5004,5007,5009,5011,5028,5032,5034,5035,5037,5042,5188,5360,5386,5389,5395,5397,5564,5593,5613,5750,5872,5895,6220,6230,6242,6245,6248,6339,6343,6346,6347,6348,6354,6356,6360,6362,6366,6370,6371,6373,6375,6377,6383,6396,6397,6399,6401,6403,6404,6412,6414,6423,6427,6428,6433,6437,6448,6452,6453,6522,6544,6554,6556,6558,6561,6572,6578,6613,6620,6623,6625,6627,6629,6641,6644,6647,6652,6659,6665,6667,6670,6671,6675,6676,6677,6681,6711,6713,6717,6720,6723,6724,6756,6762,6774,6780,6788,6797,6800,6802,6810,6812,6815,6817,6822,6824,6828,6833,6840,6858,6866,6870,6898,6901,6903,6910,6912,6914,6917,6919,6920,6923,6924,6925,6930,6932,6934,6938,6941,6950,6953,6956,6966,6970,6983,6985,6989,6991,6996,7008,7011,7013,7015,7017,7019,7022,7032,7043,7176,7181,7183,7190,7192,7193,7497,7499,7506,7507,7552,7644,7648,7717,7721,7722,7765,7780,7796,7807,7946,7972,7975,7977,8106,8112,8124,8132,8141,8143,8144,8146,8148,8159,8161,8312,8316,8319,8353,8355,8375,8492,8497,8499,8505,8507,8509,8512,8514,8517,8521,8530,8532,8536,8538,8544,8546,8559,8561,8563,8690,8720,8724,8727,8735,8739,8748,8752,8754,8759,8896,8916,8921,8924,8925,8927,8933,8938,8941,8945,8949,8951,8963,9096,9126,9129,9133,9287,9289,9295,9301,9461,9464,9470,9479,9484,9490,9492,9498,9501,9503,9507,9513,9653,9672,9677,9678,9705,9714,9835,9861,9892,9899,10042,10064,10068,10076,10093,10235,10242,10244,10247,10250,10255,10258,10261,10263,10273,10417,10419,10423,10437,10449,10456,10463,10466,10467,10470,10471,10611,10631,10634,10637,10649,10651,10657,10660,10663,10665,10668,10669,10671,10673,10677,10679,10680,10684,10685,10689,10692,10694,10699,10709,10710, -chr19 47508710 47528217 m54329U_210810_004956/105973473/ccs 77,264,457,784,979,1158,1360,1531,1828,2173,2341,2514,2715,2912,3125,3283,3465,3623,3831,3967,4127,4335,4495,4637,4856,5061,5269,5406,5568,5781,5984,6117,7024,7263,7484,7652,7797,7956,8138,8271,8480,8691,8917,9371,9772,9953,10088,10266,10450,10752,10940,11118,11284,11674,11808,12016,12231,12421,12625,12809,12986,13185,13350,13518,13730,13894,14209,14355,14581,14767,14885,15129,15328,15484,15711,15891,16113,16323,16524,16879,17099,17264,17442,17636,17806,18002,18196,18408,18583,18809,18983,19153, 146,140,318,136,148,130,148,296,305,152,140,142,137,146,132,127,127,134,129,140,131,130,141,159,128,118,109,144,160,134,132,128,125,158,126,117,137,152,116,144,138,119,391,104,126,134,176,151,272,144,142,143,314,115,171,148,172,146,138,122,138,145,138,158,108,262,145,148,185,98,169,136,134,173,157,136,128,162,354,186,164,177,193,169,191,193,145,147,147,145,160,170, 223,404,775,920,1127,1288,1508,1827,2133,2325,2481,2656,2852,3058,3257,3410,3592,3757,3960,4107,4258,4465,4636,4796,4984,5179,5378,5550,5728,5915,6116,6245,7149,7421,7610,7769,7934,8108,8254,8415,8618,8810,9308,9475,9898,10087,10264,10417,10722,10896,11082,11261,11598,11789,11979,12164,12403,12567,12763,12931,13124,13330,13488,13676,13838,14156,14354,14503,14766,14865,15054,15265,15462,15657,15868,16027,16241,16485,16878,17065,17263,17441,17635,17805,17997,18195,18341,18555,18730,18954,19143,19323, 41,53,9,59,31,72,23,1,40,16,33,59,60,67,26,55,31,74,7,20,77,30,1,60,77,90,28,18,53,69,1,779,114,63,42,28,22,30,17,65,73,107,63,297,55,1,2,33,30,44,36,23,76,19,37,67,18,58,46,55,61,20,30,54,56,53,1,78,1,20,75,63,22,54,23,86,82,39,1,34,1,1,1,1,5,1,67,28,79,29,10,1, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,251,0,0,0,0,0,0,0,0,0,0,0,251,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 28,33,36,39,43,45,48,52,56,59,61,63,68,69,76,137,223,227,231,236,238,242,243,245,247,251,254,262,263,404,406,415,418,420,426,428,431,436,438,446,449,456,775,778,783,920,921,930,935,936,940,955,958,978,1127,1132,1138,1143,1144,1149,1157,1183,1288,1299,1303,1311,1318,1320,1322,1328,1330,1337,1340,1346,1349,1351,1353,1359,1508,1530,1827,2133,2136,2148,2157,2158,2160,2169,2172,2325,2326,2331,2336,2340,2481,2488,2492,2506,2510,2513,2656,2669,2671,2681,2683,2685,2691,2695,2697,2700,2714,2852,2857,2861,2862,2865,2867,2874,2877,2880,2891,2894,2895,2898,2900,2911,3058,3061,3064,3067,3070,3073,3077,3083,3088,3092,3096,3098,3102,3106,3109,3124,3257,3267,3273,3282,3410,3412,3414,3417,3422,3425,3430,3432,3436,3443,3447,3455,3457,3464,3592,3615,3618,3622,3757,3758,3770,3775,3783,3785,3790,3793,3797,3800,3801,3804,3806,3808,3810,3821,3830,3960,3962,3964,3966,4107,4112,4113,4115,4126,4258,4264,4267,4271,4276,4280,4282,4285,4292,4297,4300,4302,4306,4308,4311,4313,4315,4319,4324,4326,4329,4332,4333,4334,4465,4494,4636,4796,4798,4804,4810,4812,4813,4817,4823,4824,4828,4831,4843,4846,4847,4850,4853,4855,4984,5008,5010,5012,5018,5020,5022,5024,5028,5030,5033,5041,5057,5060,5179,5197,5200,5210,5216,5228,5238,5262,5268,5378,5383,5386,5400,5405,5515,5550,5558,5562,5567,5728,5730,5733,5736,5740,5743,5745,5753,5757,5761,5775,5780,5915,5922,5928,5930,5933,5937,5943,5944,5955,5959,5961,5968,5970,5974,5978,5983,6116,6245,6258,6260,6264,6266,6270,6274,6275,6277,6279,6281,6300,6301,6303,6305,6307,6308,6312,6316,6318,6327,6331,6334,6337,6341,6352,6356,6357,6393,6400,6405,6426,6428,6439,6448,6458,6460,6462,6465,6467,6475,6476,6477,6483,6485,6486,6488,6493,6517,6518,6525,6528,6530,6532,6534,6539,6544,6546,6548,6549,6552,6554,6557,6561,6564,6566,6573,6576,6577,6581,6582,6583,6587,6589,6590,6613,6617,6619,6623,6626,6629,6630,6633,6636,6639,6643,6644,6646,6649,6652,6657,6662,6668,6681,6687,6689,6695,6704,6705,6707,6709,6713,6715,6717,6719,6722,6724,6731,6737,6765,6769,6771,6773,6774,6776,6781,6783,6784,6787,6788,6790,6805,6808,6810,6817,6819,6821,6824,6826,6830,6831,6832,6837,6838,6839,6841,6845,6848,6851,6852,6853,6857,6860,6863,6890,6895,6908,6910,6915,6917,6918,6920,6922,6924,6930,6931,6933,6937,6944,6947,6950,6952,6956,6958,6961,6963,6965,6977,6979,6980,6992,6996,7000,7001,7007,7012,7016,7019,7023,7149,7152,7153,7155,7157,7160,7166,7168,7170,7173,7175,7176,7177,7181,7195,7198,7206,7214,7216,7217,7220,7224,7226,7229,7231,7234,7238,7244,7246,7250,7252,7254,7256,7260,7262,7295,7388,7421,7424,7425,7429,7431,7433,7435,7437,7439,7453,7454,7455,7460,7474,7477,7479,7483,7610,7617,7621,7629,7635,7651,7696,7769,7776,7779,7784,7790,7792,7794,7796,7934,7938,7952,7955,8108,8111,8113,8119,8124,8131,8134,8137,8254,8257,8263,8270,8415,8420,8422,8425,8429,8435,8438,8440,8444,8446,8448,8450,8452,8454,8467,8469,8471,8476,8479,8618,8628,8632,8635,8641,8643,8647,8649,8656,8659,8660,8662,8665,8667,8670,8683,8690,8810,8819,8822,8824,8829,8831,8835,8839,8841,8843,8847,8849,8853,8857,8859,8861,8865,8867,8869,8871,8874,8875,8877,8916,9308,9328,9331,9333,9336,9337,9341,9345,9347,9350,9354,9357,9358,9361,9370,9475,9481,9485,9492,9495,9499,9503,9505,9507,9514,9517,9519,9526,9527,9531,9533,9538,9541,9542,9546,9548,9549,9551,9552,9556,9557,9563,9564,9566,9568,9570,9571,9573,9574,9575,9577,9578,9580,9581,9582,9583,9585,9587,9588,9592,9595,9598,9601,9602,9604,9607,9610,9615,9617,9619,9629,9631,9633,9636,9639,9645,9647,9651,9654,9663,9674,9681,9683,9685,9689,9692,9693,9695,9697,9698,9699,9701,9704,9705,9708,9709,9711,9713,9714,9715,9717,9720,9722,9726,9727,9729,9731,9737,9742,9744,9745,9748,9752,9762,9769,9771,9898,9952,10059,10087,10264,10265,10417,10422,10424,10426,10431,10433,10449,10722,10731,10737,10744,10751,10896,10905,10909,10914,10920,10923,10925,10928,10932,10935,10936,10939,11082,11085,11089,11096,11100,11111,11113,11117,11261,11265,11270,11273,11275,11283,11598,11604,11610,11612,11615,11616,11627,11630,11631,11633,11637,11639,11641,11644,11646,11663,11668,11673,11789,11792,11794,11802,11804,11807,11979,11996,12015,12164,12166,12168,12172,12173,12178,12183,12186,12188,12190,12195,12196,12198,12205,12213,12215,12230,12403,12405,12410,12412,12416,12420,12567,12576,12583,12586,12592,12594,12597,12598,12603,12606,12612,12624,12763,12775,12777,12781,12783,12786,12787,12800,12806,12808,12931,12956,12966,12975,12978,12980,12985,13124,13126,13163,13169,13184,13330,13334,13336,13338,13340,13343,13349,13488,13491,13514,13517,13676,13679,13680,13682,13684,13688,13690,13692,13698,13699,13704,13712,13714,13717,13723,13729,13838,13859,13865,13873,13878,13886,13893,14156,14159,14184,14187,14191,14196,14208,14354,14503,14505,14515,14527,14531,14534,14536,14542,14547,14580,14766,14865,14881,14884,15054,15060,15068,15071,15073,15076,15079,15082,15084,15086,15090,15095,15097,15100,15107,15110,15115,15117,15120,15124,15128,15161,15265,15267,15272,15280,15283,15286,15292,15298,15301,15302,15304,15306,15312,15327,15462,15464,15466,15478,15483,15657,15665,15680,15681,15685,15687,15688,15692,15705,15707,15710,15868,15872,15880,15887,15890,16027,16029,16032,16033,16045,16047,16049,16057,16061,16064,16067,16073,16077,16080,16081,16083,16085,16088,16107,16112,16241,16267,16269,16271,16287,16289,16292,16293,16297,16301,16306,16310,16312,16322,16485,16489,16493,16507,16510,16519,16523,16878,17065,17066,17072,17077,17098,17263,17375,17441,17635,17805,17997,18001,18195,18341,18352,18359,18362,18369,18371,18373,18376,18377,18382,18384,18386,18389,18391,18394,18407,18555,18561,18573,18582,18730,18737,18751,18754,18759,18762,18770,18776,18779,18781,18784,18787,18795,18808,18954,18958,18968,18970,18974,18976,18982,19143,19146,19152,19323,19468,19492,19495,19498, -chr19 47509060 47513962 m84039_230401_031619_s3/221582713/ccs 176,329,461,661,798,956,1089,1486,1628,1818,2001,2169,2340,2519,2747,3295,3412,3714,3893,4095,4280,4408, 133,131,129,109,118,119,123,76,110,83,109,115,118,100,116,83,212,108,111,100,109,106, 137,309,460,590,770,916,1075,1212,1562,1738,1901,2110,2284,2458,2619,2863,3378,3624,3822,4004,4195,4389,4514, 39,20,1,71,28,40,14,274,66,80,100,59,56,61,128,432,34,90,71,91,85,19,244, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,2,3,5,137,146,155,158,159,161,175,309,315,317,320,326,328,460,590,593,602,622,624,634,638,645,657,659,660,770,774,786,792,797,916,925,935,947,953,955,1075,1080,1088,1127,1212,1216,1267,1306,1308,1324,1336,1339,1346,1347,1349,1353,1357,1368,1375,1433,1461,1465,1466,1468,1485,1562,1578,1579,1580,1582,1585,1589,1590,1592,1595,1604,1608,1609,1611,1613,1621,1627,1677,1738,1740,1749,1752,1757,1758,1760,1762,1766,1768,1770,1771,1772,1775,1776,1779,1781,1784,1786,1787,1789,1793,1796,1805,1808,1811,1817,1901,1912,1914,1922,1923,1925,1928,1933,1937,1938,1974,1979,1980,1984,1991,1998,2000,2110,2114,2115,2117,2132,2143,2144,2154,2168,2284,2289,2300,2305,2308,2312,2317,2319,2324,2329,2333,2336,2339,2458,2460,2471,2474,2475,2476,2481,2484,2487,2488,2491,2495,2497,2500,2518,2619,2621,2627,2639,2644,2645,2647,2649,2671,2682,2683,2684,2686,2718,2719,2725,2740,2742,2746,2798,2841,2863,2872,2878,2882,2888,2891,2909,2912,2945,2947,2976,2979,2992,2996,2998,3000,3001,3005,3007,3008,3011,3017,3018,3021,3024,3028,3031,3034,3035,3039,3054,3075,3103,3105,3148,3150,3152,3157,3161,3163,3164,3167,3172,3174,3178,3179,3181,3182,3184,3186,3188,3189,3192,3195,3196,3200,3203,3207,3208,3210,3213,3217,3228,3230,3235,3238,3239,3241,3244,3249,3250,3253,3254,3262,3265,3269,3272,3290,3293,3294,3378,3380,3382,3385,3387,3388,3391,3394,3398,3399,3404,3405,3407,3411,3624,3657,3659,3662,3663,3665,3673,3674,3676,3677,3678,3680,3683,3685,3688,3692,3694,3695,3700,3701,3703,3704,3706,3707,3710,3712,3713,3733,3791,3822,3824,3828,3832,3835,3836,3839,3841,3843,3845,3847,3848,3852,3853,3858,3864,3867,3871,3872,3873,3879,3880,3882,3885,3889,3890,3892,4004,4006,4007,4010,4015,4016,4018,4022,4023,4024,4029,4032,4036,4037,4039,4042,4044,4046,4047,4051,4054,4057,4061,4063,4066,4075,4081,4083,4087,4088,4090,4093,4094,4195,4197,4199,4203,4205,4208,4210,4215,4219,4221,4224,4226,4231,4238,4241,4244,4247,4248,4254,4255,4257,4260,4262,4264,4271,4279,4340,4389,4405,4407,4514,4518,4519,4522,4524,4530,4531,4535,4538,4540,4541,4543,4545,4547,4551,4552,4554,4556,4558,4562,4567,4568,4569,4570,4574,4575,4579,4581,4582,4584,4586,4589,4590,4592,4594,4596,4598,4601,4614,4617,4620,4622,4667,4675,4677,4699,4700,4704,4707,4714,4722,4726,4729,4731,4733,4736,4740,4742,4743,4747,4752,4755,4757,4881,4884,4886,4889,4890,4892,4895, -chr19 47509233 47523608 m54329U_210326_192251/88801936/ccs 146,311,615,818,989,1192,1394,1569,1760,1918,2116,2292,2432,2629,2841,3020,3183,3356,3541,3760,3954,4095,4316,4450,4632,4758,4915,5106,5318,5398,5615,6433,6597,6764,6946,7069,7215,7367,7532,7709,7871,8027,8417,8738,9061,9235,9458,9608,9936,10114,10309,10454,10691,10860,11028,11208,11434,11595,11775,11995,12177,12360,12552,12757,12952,13138,13367,13516,13671,13811, 100,286,140,146,140,134,138,164,138,129,136,116,157,146,115,136,129,143,129,128,98,157,111,163,115,133,134,106,79,216,103,158,155,127,122,134,127,141,157,123,121,389,293,275,147,222,77,309,146,125,139,185,120,152,148,138,139,129,153,145,127,138,152,145,151,144,90,147,139,138, 246,597,755,964,1129,1326,1532,1733,1898,2047,2252,2408,2589,2775,2956,3156,3312,3499,3670,3888,4052,4252,4427,4613,4747,4891,5049,5212,5397,5614,5718,6591,6752,6891,7068,7203,7342,7508,7689,7832,7992,8416,8710,9013,9208,9457,9535,9917,10082,10239,10448,10639,10811,11012,11176,11346,11573,11724,11928,12140,12304,12498,12704,12902,13103,13282,13457,13663,13810,13949, 65,18,63,25,63,68,37,27,20,69,40,24,40,66,64,27,44,42,90,66,43,64,23,19,11,24,57,106,1,1,715,6,12,55,1,12,25,24,20,39,35,1,28,48,27,1,73,19,32,70,6,52,49,16,32,88,22,51,67,37,56,54,53,50,35,85,59,8,1,34, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,243,0,0,251,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,243,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 145,246,271,276,282,285,287,289,292,297,299,302,310,597,609,614,755,759,770,774,782,789,792,793,797,799,801,806,817,964,971,974,988,1129,1131,1135,1139,1142,1144,1147,1150,1152,1159,1162,1164,1170,1176,1191,1326,1330,1332,1333,1335,1338,1350,1353,1354,1358,1383,1385,1393,1532,1540,1541,1546,1547,1549,1559,1561,1563,1565,1568,1733,1759,1898,1904,1907,1908,1911,1917,2047,2050,2053,2060,2064,2069,2071,2075,2077,2080,2084,2087,2091,2115,2252,2255,2257,2264,2268,2275,2291,2408,2422,2431,2589,2608,2614,2616,2620,2623,2628,2775,2795,2798,2809,2811,2815,2817,2819,2824,2840,2956,2958,2960,2962,2963,2967,2969,2976,2980,2983,3001,3003,3011,3014,3015,3019,3156,3159,3182,3312,3316,3318,3322,3326,3329,3330,3332,3336,3349,3352,3355,3499,3516,3517,3519,3520,3522,3525,3528,3529,3537,3540,3670,3676,3679,3691,3697,3701,3704,3707,3709,3712,3717,3719,3723,3726,3735,3739,3741,3744,3751,3756,3759,3888,3896,3900,3901,3903,3906,3907,3909,3911,3916,3918,3922,3924,3925,3928,3931,3933,3947,3949,3953,4052,4065,4073,4075,4082,4086,4092,4094,4252,4256,4258,4262,4264,4270,4272,4273,4277,4299,4310,4315,4427,4430,4437,4440,4443,4444,4449,4613,4615,4623,4627,4629,4631,4747,4757,4891,4902,4907,4909,4914,5049,5058,5065,5069,5070,5071,5072,5075,5077,5080,5083,5101,5105,5212,5216,5220,5227,5234,5239,5242,5243,5247,5248,5250,5256,5257,5259,5263,5267,5270,5273,5274,5276,5288,5293,5295,5297,5304,5314,5317,5397,5614,5718,5720,5727,5731,5735,5736,5738,5740,5742,5748,5761,5762,5764,5766,5768,5769,5773,5779,5788,5792,5795,5798,5802,5813,5817,5818,5825,5828,5829,5832,5835,5837,5839,5845,5850,5851,5854,5861,5864,5865,5866,5880,5888,5890,5898,5901,5920,5922,5924,5927,5929,5937,5938,5945,5948,5950,5954,5961,5962,5967,5969,5978,5979,5986,5989,5991,5993,5995,6002,6007,6009,6011,6012,6015,6017,6020,6027,6029,6033,6035,6038,6039,6043,6044,6045,6049,6051,6052,6076,6080,6082,6083,6086,6089,6092,6093,6096,6099,6102,6105,6106,6107,6109,6112,6115,6120,6125,6131,6143,6149,6151,6157,6167,6168,6170,6172,6176,6178,6180,6182,6185,6187,6192,6194,6196,6198,6200,6203,6205,6210,6231,6233,6235,6236,6238,6243,6245,6246,6267,6270,6272,6283,6285,6287,6288,6290,6296,6298,6303,6305,6307,6311,6313,6314,6317,6318,6319,6323,6324,6326,6329,6361,6362,6375,6377,6384,6385,6387,6389,6391,6393,6398,6406,6414,6417,6432,6557,6591,6593,6596,6752,6753,6755,6757,6761,6763,6891,6897,6919,6926,6928,6929,6932,6934,6937,6940,6943,6945,7068,7167,7203,7210,7214,7342,7344,7347,7351,7352,7354,7355,7360,7361,7364,7366,7508,7516,7518,7520,7526,7527,7531,7689,7692,7695,7698,7708,7832,7835,7845,7848,7851,7854,7857,7858,7861,7863,7865,7870,7992,7998,8006,8014,8018,8022,8023,8026,8416,8710,8713,8737,9013,9018,9019,9025,9026,9028,9030,9032,9033,9037,9042,9044,9047,9049,9054,9057,9060,9208,9211,9214,9215,9217,9219,9234,9457,9535,9549,9552,9556,9558,9583,9585,9598,9607,9917,9923,9925,9929,9935,10082,10104,10107,10113,10239,10246,10253,10257,10261,10264,10268,10270,10274,10277,10279,10283,10285,10289,10291,10292,10299,10300,10305,10308,10448,10453,10639,10645,10649,10652,10661,10663,10664,10681,10690,10811,10831,10835,10838,10843,10853,10854,10856,10859,11012,11018,11027,11176,11179,11183,11191,11193,11199,11205,11207,11346,11348,11355,11360,11363,11370,11373,11376,11379,11384,11385,11399,11402,11403,11406,11407,11412,11416,11417,11419,11421,11423,11425,11427,11430,11433,11573,11574,11586,11594,11724,11738,11741,11743,11745,11748,11755,11758,11761,11774,11928,11930,11933,11940,11941,11942,11946,11952,11956,11961,11963,11965,11968,11970,11973,11983,11985,11990,11994,12140,12145,12149,12156,12160,12161,12165,12176,12304,12312,12315,12319,12321,12336,12340,12353,12359,12498,12501,12504,12518,12523,12527,12533,12542,12545,12551,12704,12708,12712,12720,12731,12737,12749,12756,12902,12905,12921,12925,12931,12932,12936,12951,13103,13105,13109,13116,13137,13282,13285,13299,13303,13306,13309,13312,13317,13326,13332,13334,13337,13341,13347,13349,13354,13356,13361,13362,13364,13366,13457,13466,13473,13477,13503,13507,13509,13515,13634,13663,13666,13668,13670,13810,13847,13879,13885,13949,13951,13961,13967,13968,13977,13980,13982,14301,14305,14307,14309,14310,14313,14323,14325,14328,14331,14334, -chr19 47509612 47524347 m84039_230401_034725_s4/123339260/ccs 74,581,769,1706,2204,2754,3393,3528,3724,4169,4523,4852,5213,5517,5650,6473,7304,7648,8226,9139,9558,10021,10888,11185,11596,12077,12246,12603,12822,13218,13384,13562,13744,14181,14305, 506,187,936,497,490,638,134,155,444,339,328,312,285,132,822,776,343,577,912,418,454,866,200,410,480,168,356,218,395,165,108,181,436,123,231, 580,768,1705,2203,2694,3392,3527,3683,4168,4508,4851,5164,5498,5649,6472,7249,7647,8225,9138,9557,10012,10887,11088,11595,12076,12245,12602,12821,13217,13383,13492,13743,14180,14304,14536, 1,1,1,1,60,1,1,41,1,15,1,49,19,1,1,55,1,1,1,1,9,1,97,1,1,1,1,1,1,1,70,1,1,1,1, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,1,5,6,73,580,768,1705,2203,2694,2722,2725,2753,3392,3527,3683,3723,4168,4508,4522,4851,5164,5212,5498,5516,5606,5649,6472,7249,7302,7303,7647,8225,9138,9557,10012,10020,10887,11088,11129,11184,11595,12076,12173,12245,12602,12821,13217,13383,13492,13498,13561,13675,13743,14180,14224,14304,14536,14723,14725,14727, -chr19 47509937 47521574 m54329U_210323_190418/72353082/ccs 121,302,506,698,895,1120,1292,1382,1538,1736,1907,2107,2281,2463,2753,3219,3399,3588,3764,3900,4179,4580,4743,4912,5799,6021,6325,6507,6689,6862,7042,7329,7515,7683,8084,8292,8500,8699,9194,9395,9586,9906,10088,10275,10452,10588,10784,10961,11166,11365, 158,149,185,174,200,151,89,86,155,152,186,122,161,285,465,179,188,130,135,278,269,134,127,129,136,260,133,179,165,140,282,182,167,362,201,151,198,481,192,109,297,161,174,147,135,195,174,147,141,140, 82,279,451,691,872,1095,1271,1381,1468,1693,1888,2093,2229,2442,2748,3218,3398,3587,3718,3899,4178,4448,4714,4870,5041,5935,6281,6458,6686,6854,7002,7324,7511,7682,8045,8285,8443,8698,9180,9386,9504,9883,10067,10262,10422,10587,10783,10958,11108,11307,11505, 39,23,55,7,23,25,21,1,70,43,19,14,52,21,5,1,1,1,46,1,1,132,29,42,758,86,44,49,3,8,40,5,4,1,39,7,57,1,14,9,82,23,21,13,30,1,1,3,58,58,46, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,250,0,0,251,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 81,85,89,96,112,120,279,280,285,292,294,301,451,454,463,469,475,476,479,482,499,505,691,693,697,769,872,889,890,892,894,1095,1097,1099,1101,1105,1119,1230,1271,1285,1289,1291,1381,1468,1471,1477,1480,1483,1486,1491,1496,1500,1506,1507,1511,1515,1517,1518,1531,1536,1537,1693,1697,1700,1703,1707,1709,1713,1720,1735,1775,1888,1892,1895,1906,2093,2106,2229,2234,2242,2244,2250,2253,2254,2275,2280,2323,2442,2449,2454,2456,2460,2462,2748,2750,2752,3218,3338,3398,3587,3718,3733,3736,3740,3742,3745,3763,3899,4178,4448,4453,4456,4458,4464,4472,4475,4486,4488,4495,4496,4497,4499,4501,4509,4511,4518,4519,4521,4526,4528,4531,4539,4541,4544,4552,4556,4567,4574,4579,4607,4714,4717,4721,4725,4727,4729,4732,4742,4870,4876,4911,5010,5041,5047,5060,5062,5066,5068,5072,5077,5079,5083,5089,5102,5103,5105,5107,5109,5110,5115,5118,5119,5130,5134,5135,5137,5138,5141,5145,5156,5160,5161,5188,5197,5205,5231,5233,5242,5245,5254,5264,5266,5271,5273,5280,5281,5282,5288,5298,5322,5323,5330,5335,5338,5340,5345,5350,5352,5355,5360,5366,5371,5375,5377,5380,5381,5385,5386,5387,5392,5395,5407,5423,5425,5429,5432,5436,5439,5442,5449,5450,5452,5455,5458,5463,5468,5474,5486,5501,5511,5512,5514,5516,5522,5524,5526,5529,5554,5563,5574,5576,5578,5588,5590,5591,5593,5614,5616,5623,5625,5627,5628,5632,5636,5638,5643,5644,5645,5647,5654,5659,5663,5666,5714,5723,5724,5726,5728,5730,5745,5747,5750,5762,5764,5767,5771,5783,5788,5798,5935,5939,5941,5958,5970,6020,6281,6296,6324,6458,6481,6506,6686,6688,6814,6854,6861,7002,7008,7010,7013,7025,7030,7031,7035,7041,7324,7328,7511,7514,7682,8045,8049,8051,8064,8067,8072,8080,8083,8285,8291,8443,8445,8461,8468,8469,8471,8474,8476,8477,8482,8493,8499,8698,9180,9182,9185,9193,9386,9394,9504,9527,9561,9566,9585,9883,9886,9888,9892,9893,9895,9898,9901,9905,10067,10075,10082,10087,10262,10266,10274,10422,10427,10428,10433,10451,10587,10783,10958,10960,11108,11110,11115,11122,11125,11133,11139,11141,11151,11165,11307,11335,11340,11352,11357,11364,11505,11517,11524,11525,11529,11540,11550, -chr19 47510024 47533653 m54329U_210326_192251/104792639/ccs 158,402,565,754,942,1140,1346,1511,1716,1875,2018,2165,2381,2544,2750,2924,3108,3258,3444,3627,3798,3962,4168,4320,4459,4646,4818,5654,5736,5919,6166,6388,6651,6906,7084,7245,7409,7567,7707,7902,8467,8576,8782,8923,9091,9271,9389,9585,9852,10007,10188,10340,10544,10712,10901,11057,11293,11445,11693,11876,12035,12252,12429,12734,12897,13378,13578,13760,13951,14163,14383,14582,14791,14962,15192,15346,15515,15686,15903,16038,16259,16445,16629,16817,16972,17196,17389,17552,17719,17879,18098,18296,18430,18634,18873,19090,19269,19414,19605,19760,19954,20201,20361,20559,20739,20902,21127,21333,21552,21754,21938,22157,22354,22536,22720,22920,23117,23281,23449, 131,100,138,109,131,128,112,100,96,81,127,105,111,146,135,146,112,128,136,141,131,123,121,121,140,111,100,81,173,134,113,181,134,123,122,116,86,128,132,269,108,166,140,138,130,114,144,223,125,174,121,145,129,158,139,115,115,132,118,117,151,130,257,145,475,122,136,148,161,167,128,141,123,156,104,162,148,139,134,182,139,150,175,150,169,150,157,162,127,135,139,97,122,140,133,118,124,131,126,116,115,156,157,134,156,162,145,147,146,119,141,130,134,138,136,129,150,159,140, 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78,113,63,51,79,67,78,53,105,63,62,20,111,52,60,39,38,38,58,47,30,33,83,31,18,47,61,736,1,10,113,109,82,121,55,39,48,72,12,63,296,1,40,1,30,50,4,52,44,30,7,31,59,39,31,17,121,37,116,65,42,66,47,48,18,6,78,46,43,51,53,71,68,48,74,50,7,23,78,1,39,47,34,13,5,55,43,6,5,33,84,59,37,82,99,84,61,21,60,29,78,132,4,41,46,7,63,61,72,56,65,78,67,48,46,64,68,14,9, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,247,0,0,0,0,0,0,0,0,0,0,0,0,252,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,243,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 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-chr19 47510045 47522679 m84039_230404_003541_s3/205851410/ccs 80,263,443,655,827,1034,1452,1660,1810,1992,2168,2382,2871,3034,3163,3448,3600,3773,3962,4171,4548,4673,4789,5588,5791,5982,6178,6365,6687,6860,7331,7538,7865,8031,8383,8518,8656,8785,9153,9360,9578,9736,9929,10328,10532,10746,10969,11156,11358,11603,11769,12008,12240, 119,157,140,91,159,161,140,149,181,118,133,171,99,107,165,125,132,110,133,229,84,105,118,124,159,149,123,288,136,407,153,266,136,142,134,137,128,327,113,111,112,132,291,128,159,152,109,130,144,111,144,83,111, 199,420,583,746,986,1195,1592,1809,1991,2110,2301,2553,2970,3141,3328,3573,3732,3883,4095,4400,4632,4778,4907,5712,5950,6131,6301,6653,6823,7267,7484,7804,8001,8173,8517,8655,8784,9112,9266,9471,9690,9868,10220,10456,10691,10898,11078,11286,11502,11714,11913,12091,12351, 64,23,72,81,48,257,68,1,1,58,81,318,64,22,120,27,41,79,76,148,41,11,681,79,32,47,64,34,37,64,54,61,30,210,1,1,1,41,94,107,46,61,108,76,55,71,78,72,101,55,95,149,83, 0,0,0,0,0,0,0,0,0,0,0,246,0,0,0,0,0,0,0,245,0,0,250,0,0,0,0,0,0,0,0,0,0,244,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 4,6,13,26,28,36,38,39,53,67,79,199,204,262,420,424,428,429,432,435,439,442,583,591,603,610,611,613,625,629,630,632,634,654,746,763,800,802,805,817,826,986,994,995,1000,1001,1005,1009,1012,1021,1023,1033,1195,1202,1207,1209,1210,1214,1216,1219,1222,1225,1229,1231,1233,1236,1249,1255,1279,1282,1297,1305,1310,1380,1385,1388,1403,1406,1411,1413,1416,1419,1451,1592,1594,1607,1610,1614,1626,1629,1639,1641,1647,1659,1778,1809,1991,2110,2122,2143,2160,2165,2167,2212,2301,2313,2317,2320,2321,2324,2326,2328,2331,2339,2341,2356,2359,2370,2378,2381,2553,2556,2580,2586,2587,2589,2594,2597,2616,2624,2626,2628,2630,2633,2637,2641,2661,2664,2666,2671,2676,2680,2697,2702,2705,2709,2711,2712,2717,2718,2720,2721,2723,2724,2726,2727,2737,2741,2744,2754,2763,2764,2771,2777,2779,2784,2790,2792,2796,2797,2800,2802,2804,2810,2812,2817,2819,2822,2823,2826,2828,2835,2839,2841,2845,2849,2860,2862,2869,2870,2970,2973,2975,2977,2990,2993,2996,2997,2998,3002,3007,3010,3012,3033,3083,3129,3141,3148,3152,3154,3155,3158,3161,3162,3328,3332,3338,3340,3342,3347,3349,3352,3357,3361,3363,3365,3370,3372,3384,3391,3392,3395,3404,3406,3407,3409,3418,3422,3424,3447,3573,3575,3579,3592,3596,3599,3732,3733,3739,3743,3746,3748,3750,3753,3757,3769,3772,3883,3892,3926,3929,3936,3944,3952,3955,3961,4095,4102,4106,4113,4116,4118,4127,4134,4142,4149,4152,4170,4400,4415,4444,4452,4453,4455,4458,4461,4462,4464,4468,4472,4475,4478,4481,4493,4498,4500,4502,4503,4509,4513,4518,4519,4522,4527,4530,4536,4538,4543,4547,4632,4649,4663,4666,4671,4672,4778,4780,4788,4907,4909,4924,4928,4934,4939,4945,4964,4965,4967,4969,4971,4972,4980,4982,4991,4995,4998,5001,5005,5016,5020,5021,5028,5031,5035,5038,5042,5048,5054,5057,5064,5067,5069,5082,5090,5092,5100,5103,5112,5122,5124,5126,5129,5131,5138,5146,5149,5151,5153,5163,5164,5169,5171,5180,5188,5193,5195,5197,5207,5209,5211,5212,5215,5220,5227,5229,5233,5235,5238,5239,5243,5244,5245,5249,5251,5252,5275,5279,5281,5285,5288,5291,5292,5295,5298,5306,5308,5311,5314,5324,5330,5342,5348,5350,5356,5365,5366,5368,5370,5374,5376,5378,5380,5383,5385,5390,5392,5394,5398,5401,5403,5405,5408,5430,5432,5434,5435,5437,5442,5445,5449,5451,5466,5469,5471,5482,5485,5487,5493,5498,5500,5502,5509,5512,5513,5514,5518,5521,5569,5571,5576,5579,5581,5583,5585,5587,5712,5717,5718,5728,5731,5741,5744,5749,5751,5758,5761,5779,5787,5790,5950,5952,5956,5974,5981,6131,6134,6137,6175,6177,6301,6308,6311,6358,6364,6653,6656,6659,6660,6668,6674,6676,6680,6682,6686,6823,6824,6826,6830,6834,6838,6841,6852,6859,7267,7327,7330,7484,7501,7507,7509,7517,7519,7521,7523,7525,7527,7529,7531,7534,7535,7537,7804,7831,7836,7849,7852,7864,8001,8007,8010,8014,8017,8030,8136,8173,8177,8179,8180,8186,8193,8198,8206,8208,8209,8211,8212,8217,8223,8224,8226,8228,8230,8231,8234,8235,8237,8238,8242,8247,8248,8252,8255,8258,8261,8262,8264,8267,8270,8277,8279,8299,8305,8307,8320,8322,8334,8338,8380,8382,8517,8546,8655,8784,9112,9117,9123,9125,9129,9152,9266,9279,9283,9286,9293,9294,9297,9300,9302,9305,9308,9310,9314,9326,9329,9337,9338,9347,9353,9359,9471,9475,9478,9486,9493,9509,9513,9517,9533,9541,9544,9546,9550,9556,9559,9560,9562,9568,9572,9575,9577,9690,9693,9718,9726,9730,9731,9733,9735,9767,9868,9870,9877,9891,9894,9913,9924,9928,10220,10253,10260,10274,10276,10279,10280,10297,10300,10301,10303,10305,10308,10316,10325,10327,10388,10456,10466,10468,10471,10474,10482,10484,10492,10500,10502,10514,10520,10525,10530,10531,10691,10695,10703,10707,10711,10725,10731,10733,10745,10898,10902,10906,10909,10915,10930,10935,10937,10939,10954,10956,10958,10965,10968,11078,11093,11095,11100,11106,11107,11108,11117,11119,11125,11130,11133,11139,11142,11144,11147,11154,11155,11286,11309,11316,11317,11322,11332,11334,11339,11344,11346,11349,11352,11357,11429,11502,11509,11517,11520,11523,11525,11528,11529,11532,11534,11538,11542,11547,11549,11550,11553,11559,11566,11572,11573,11576,11580,11584,11586,11588,11593,11602,11714,11731,11736,11743,11744,11762,11768,11913,11927,11931,11935,11941,11964,11971,12006,12007,12091,12101,12117,12120,12131,12133,12136,12140,12142,12146,12147,12151,12154,12157,12162,12166,12169,12171,12173,12175,12177,12180,12184,12185,12186,12189,12192,12194,12198,12202,12203,12204,12208,12209,12212,12216,12221,12228,12239,12351,12355,12358,12361,12362,12367,12375,12380,12382,12384,12386,12389,12392,12393,12398,12405,12410,12417,12428,12433,12627,12630, -chr19 47510306 47526564 m54329U_210323_190418/99550444/ccs 69,254,388,578,751,921,1124,1288,1511,1702,2051,2238,2424,2643,2808,3015,3191,3355,3518,3840,4033,4170,4300,4416,4535,5384,5669,5846,6004,6152,6353,6545,6691,6879,7205,7424,7584,7716,8178,8336,8499,8668,8836,8999,9161,9349,9506,9666,9836,10032,10226,10451,10643,10805,11046,11220,11455,11626,11762,11925,12143,12331,12515,12742,12865,13038,13151,13409,13588,13793,13964,14174,14372,14614,14781,14914,15141,15352,15541,15708,15924, 124,133,151,93,137,142,116,131,104,97,108,119,106,102,127,116,131,105,303,118,92,104,78,84,84,246,104,102,141,145,152,132,160,295,118,125,118,124,84,123,121,165,121,128,94,113,108,94,132,118,140,96,103,114,79,95,80,135,123,143,122,102,117,76,130,109,141,86,78,117,102,109,105,114,124,147,127,130,154,193,122, 193,387,539,671,888,1063,1240,1419,1615,1799,2159,2357,2530,2745,2935,3131,3322,3460,3821,3958,4125,4274,4378,4500,4619,5630,5773,5948,6145,6297,6505,6677,6851,7174,7323,7549,7702,7840,8262,8459,8620,8833,8957,9127,9255,9462,9614,9760,9968,10150,10366,10547,10746,10919,11125,11315,11535,11761,11885,12068,12265,12433,12632,12818,12995,13147,13292,13495,13666,13910,14066,14283,14477,14728,14905,15061,15268,15482,15695,15901,16046, 61,1,39,80,33,61,48,92,87,252,79,67,113,63,80,60,33,58,19,75,45,26,38,35,765,39,73,56,7,56,40,14,28,31,101,35,14,338,74,40,48,3,42,34,94,44,52,76,64,76,85,96,59,127,95,140,91,1,40,75,66,82,110,47,43,4,117,93,127,54,108,89,137,53,9,80,84,59,13,23,61, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,247,0,0,0,0,0,0,0,0,0,0,0,0,250,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 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77,82,84,88,93,96,103,113,115,118,123,130,258,267,274,292,297,459,480,489,492,657,658,668,827,844,858,873,877,888,1043,1046,1048,1052,1055,1058,1065,1069,1070,1077,1212,1218,1230,1235,1237,1243,1249,1256,1258,1263,1267,1269,1272,1278,1284,1290,1587,1596,1605,1628,1633,1650,1762,1768,1775,1779,1789,2082,2088,2219,2222,2239,2244,2252,2255,2278,2282,2286,2290,2292,2294,2296,2299,2307,2453,2456,2462,2468,2470,2471,2740,2758,2760,2766,2767,2769,2772,2773,2776,2778,2789,2792,2795,2800,2810,2814,2953,2978,3117,3121,3123,3126,3129,3156,3171,3175,3178,3314,3327,3330,3344,3346,3357,3370,3488,3646,3652,3656,3659,3668,3672,3675,3677,3680,3819,3822,3958,3975,3985,3998,3999,4001,4003,4010,4014,4023,4025,4027,4029,4034,4035,4040,4051,4053,4197,4322,4324,4329,4340,4343,4345,4362,4367,4400,4403,4404,4407,4410,4412,4414,4418,4448,4476,4580,4582,4588,4592,4596,4597,4599,4601,4603,4622,4623,4627,4629,4640,4649,4656,4659,4663,4674,4678,4679,4722,4750,4758,4761,4770,4780,4784,4787,4796,4797,4798,4804,4809,4811,4816,4817,4821,4822,4830,4838,4839,4846,4851,4853,4863,4865,4871,4876,4883,4889,4895,4900,4901,4905,4908,4937,4941,4944,4947,4948,4951,4954,4960,4962,4964,4967,4970,4975,4980,4987,4999,5005,5007,5022,5023,5027,5031,5035,5037,5040,5042,5047,5049,5058,5062,5065,5083,5085,5091,5092,5094,5123,5126,5128,5137,5142,5155,5157,5159,5163,5164,5165,5166,5169,5171,5181,5345,5351,5361,5364,5366,5369,5372,5374,5375,5377,5383,5385,5388,5398,5400,5424,5426,5431,5436,5442,5444,5447,5451,5453,5463,5470,5495,5549,5578,5601,5612,5639,5648,5792,5795,5797,5801,5812,5946,5947,5950,5959,5973,6094,6240,6247,6254,6256,6259,6276,6284,6295,6299,6310,6742,6746,6752,6755,6763,6765,6767,6769,6771,6775,6778,6779,6782,6784,6788,6791,6793,6795,6796,6801,6807,6808,6809,6817,6821,6826,6857,7001,7005,7119,7261,7264,7265,7268,7284,7289,7294,7321,7421,7425,7429,7437,7443,7445,7447,7449,7453,7457,7566,7574,7582,7587,7594,7597,7612,7613,7618,7620,7693,7700,7715,7721,7726,7739,7741,7743,7745,7747,7749,7757,7762,7784,7789,7790,7793,7795,7799,7811,7817,7820,7821,7827,7828,7831,7833,7834,7840,7841,7845,7860,7862,7863,7865,7866,7871,7884,7885,7887,7888,7889,7891,7892,7895,7896,7901,7902,7906,7915,7918,7921,7933,7935,7940,7943,7953,7959,7961,7965,7974,7982,7988,7993,7995,7997,7999,8003,8007,8011,8013,8019,8022,8025,8027,8031,8034,8040,8041,8043,8045,8059,8066,8068,8070,8075,8190,8194,8195,8200,8216,8220,8223,8236,8241,8383,8387,8390,8392,8396,8399,8401,8536,8544,8706,8710,8715,8716,8722,8726,8731,8736,8738,8743,8745,8748,8749,8878,8881,8898,8900,8901,8905,8906,8910,8913,8915,8920,8930,8935,8941,8944,8945,9048,9055,9060,9069,9081,9088,9094,9204,9208,9210,9220,9223,9231,9234,9236,9239,9241,9242,9243,9244,9246,9247,9250,9253,9254,9271,9274,9403,9412,9414,9418,9422,9428,9435,9560,9571,9580,9583,9585,9587,9591,9593,9596,9599,9732,9735,9737,9739,9747,9919,9921,9923,9927,9930,9950,10027,10079,10081,10099,10104,10112,10114,10138,10279,10289,10301,10306,10325,10443,10447,10451,10472,10474,10485,10486,10491,10494,10496,10502,10513,10643,10652,10654,10657,10660,10669,10671,10673,10681,10686,10689,10690,10828,10830,10833,10842,10845,10850,10857,10974,10978,10980,10985,10987,10992,10995,10997,10998,11003,11007,11010,11014,11017,11023,11033,11035,11339,11342,11362,11547,11569,11573,11847,11849,11852,11885,11892,11901,11912,11921,12202,12211,12450,12460,12462,12466,12469,12473,12477,12481,12624,12626,12627,12649,12660,12662,12674,12676,12680,12684,12808,12810,12820,12836,12839,12841,13002,13003,13008,13036,13157,13168,13169,13175,13181,13183,13186,13189,13201,13370,13375,13378,13381,13386,13396,13398,13401,13408,13409,13411,13416,13418,13421,13423,13425,13428,13429,13435,13438,13564,13581,13584,13588,13594,13747,13752,13765,13767,13769,13773,13776,13794,13897,13933,13940,13954,13957,13968,13988,13995,14013,14129,14130,14132,14135,14171,14175,14178,14183,14329,14331,14338,14340,14354,14359,14506,14526,14527,14529,14530,14534,14555,14686,14692,14694,14706,14708,14710,14713,14722,14875,14895,14898,14900,14902,14909,14915,14920,15094,15099,15114,15120,15258,15283,15286,15288,15291,15296,15311,15314,15317,15326,15328,15330,15470,15475,15477,15480,15482,15484,15490,15492,15494,15498,15500,15502,15506,15508,15613,15643,15662,15664,15669,15672,15678,15683,15685,15695,15701,15702,15822,15826,15829,15851,15853,15854,15859,15871,15892,16162,16167,16169,16172,16176,16183,16185,16191,16200,16203,16205,16207,16210,16213,16216,16218,16224,16229,16236,16238,16240,16242,16245,16251,16255,16270,16389,16391,16393,16397,16403,16406,16411,16413,16416,16419,16424,16426,16429,16431,16449,16457,16458,16460,16466,16472,16478,16600,16602,16605,16606,16618,16621,16625,16626,16642,16643,16646,16648,16650,16771,16776,16792,16794,16798,16801,16817,16824,16827,16830,16833,16835,16838,16842,16847,16848,16863,17018,17021,17026,17028,17032,17036,17041,17046,17057,17198,17213,17216,17221,17229,17236,17253,17256,17398,17404,17414,17419,17422,17439,17445,17516,17621,17624,17808,17961,17968,17976,17987,17991,17994,17996,18000,18135,18140,18148,18151,18154,18161,18168,18203,18334,18337,18340,18344,18347,18349,18355,18357,18358,18378,18381,18383,18386,18387,18389,18412,18414,18416,18429,18432,18445,18447,18459,18574,18589,18590,18602,18604,18605,18611,18617,18620,18625,18627,18779,18780,18784,18793,18794,18796,18805,18810,18815,18822,18828,18851,18948,18957,18973,18989,18992,18993,19007,19009,19019,19023,19026,19031,19034,19039,19044,19061,19064,19083,19087,19093,19095,19098,19219,19233,19247,19357,19361,19375,19381,19391,19394,19407,19411,19418,19428,19537,19547,19571,19581,19593,19595,19596,19597,19600,19602,19603,19608,19610,19615,19622,19625,19627,19648,19661,19783,19787,19789,19791,19805,19809,19812,19814,19817,19819,19823,19824,19826,19829,19834,19836,19838,19851,19856,19858,19870,19873,19877,19883,19989,19997,20000,20002,20005,20008,20013,20015,20016,20042,20176,20185,20197,20201,20341,20349,20358,20367,20370,20373,20397,20536,20541,20553,20555,20559,20561,20569,20574,20715,20717,20720,20721,20726,20730,20732,20733,20736,20737,20740,20745,20752,20753,20755,20759,20761,20762,20765,20767,20773,20786,20940,20942,20945,20949,20960,20967,20970,20972,21111,21134,21135,21140,21145,21165,21170,21273,21280,21287,21290,21294,21295,21297,21301,21304,21307,21308,21312,21315,21319,21324,21328,21349,21458,21464,21470,21480,21482,21487,21494,21496,21499,21501,21502,21507,21520,21522,21524,21534,21562,21699,21718,21721,21723,21725,21727,21737,21741,21885,21887,21891,21897,21900,21902,21906,21907,22408,22546,22562,22565,22567,22569,22580,22712,22721,22731,22737,22745,22754,22771,22902,22907,22912,22916,22922,22932,22938,22998,23036,23039,23090,23093,23102,23109,23221,23222,23224,23227,23231,23253,23260,23266,23410,23412,23547,23557,23561,23573,23577,23578,23581,23600,23605,23613,23742,23947,23952,23954,23955,23960,23964,23966,23971,24018,24126,24133,24152,24154,24158,24327,24380,24395,24687,24694,24714,24717,24725,24748,24751,24872,24891,25089,25095,25259,25262,25280,25283,25286,25463,25466,25468,25471,25488,25620,25640,25642,25644,25648,25651,25654,25656,25659,25662,25809,25815,25820,25826,25832,25834,25836,25846,25851,26003,26017,26025,26032,26040,26045, -chr19 47510518 47527257 m84039_230401_034725_s4/117245222/ccs 109,309,434,575,838,917,1306,1716,1993,2199,2393,2776,2976,3087,3420,3614,3841,4003,4201,4303,4454,4711,4904,5482,5665,5793,5888,5987,6084,6197,6417,6743,6848,7097,7583,7825,8076,8260,8357,8495,8630,9029,9138,9285,9505,9657,9778,9902,10012,10206,10398,10640,10794,10875,11167,11303,11471,11684,11855,12064,12259,12450,12643,12738,12988,13130,13235,13386,13550,13765,13968,14239,14381,14548,14705,14920,15273,15384,15746,15901,15990,16173,16295,16451, 152,120,105,262,78,381,345,239,176,137,163,101,110,326,142,226,161,197,101,150,139,160,572,77,127,94,98,96,112,191,325,104,156,437,186,222,137,96,137,134,166,94,103,190,151,120,87,109,94,191,149,153,77,194,88,97,129,170,168,119,103,137,94,142,141,103,105,155,141,154,125,141,158,128,214,352,110,361,154,86,166,105,155,177, 108,261,429,539,837,916,1298,1651,1955,2169,2336,2556,2877,3086,3413,3562,3840,4002,4200,4302,4453,4593,4871,5476,5559,5792,5887,5986,6083,6196,6388,6742,6847,7004,7534,7769,8047,8213,8356,8494,8629,8796,9123,9241,9475,9656,9777,9865,10011,10106,10397,10547,10793,10871,11069,11255,11400,11600,11854,12023,12183,12362,12587,12737,12880,13129,13233,13340,13541,13691,13919,14093,14380,14539,14676,14919,15272,15383,15745,15900,15987,16156,16278,16450,16628, 1,48,5,36,1,1,8,65,38,30,57,220,99,1,7,52,1,1,1,1,1,118,33,6,106,1,1,1,1,1,29,1,1,93,49,56,29,47,1,1,1,233,15,44,30,1,1,37,1,100,1,93,1,4,98,48,71,84,1,41,76,88,56,1,108,1,2,46,9,74,49,146,1,9,29,1,1,1,1,1,3,17,17,1,1, 0,0,0,0,0,0,0,0,0,0,0,246,0,0,0,0,0,0,0,0,0,243,0,0,243,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,245,0,0,0,0,0,0,0,0,0,243,0,0,0,0,0,0,0,0,0,243,0,0,0,0,0,0,0,0,0,244,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,1,4,9,108,261,300,308,429,433,539,546,548,554,574,837,916,1298,1302,1305,1651,1687,1692,1705,1712,1715,1955,1992,2169,2197,2198,2264,2289,2336,2392,2556,2606,2610,2624,2659,2693,2710,2744,2764,2775,2780,2834,2877,2880,2909,2953,2955,2975,3023,3025,3086,3413,3419,3451,3531,3562,3580,3586,3604,3611,3613,3840,3900,3947,4002,4200,4259,4283,4302,4453,4511,4593,4596,4611,4621,4655,4660,4702,4709,4710,4744,4804,4821,4871,4903,5476,5477,5479,5481,5559,5562,5567,5589,5661,5664,5746,5792,5887,5986,6083,6196,6388,6391,6408,6416,6742,6770,6847,7004,7059,7096,7534,7582,7769,7773,7824,8047,8069,8074,8075,8213,8239,8259,8356,8452,8494,8573,8629,8796,8821,8873,8875,8884,8925,8934,8937,8999,9018,9028,9123,9134,9137,9241,9255,9273,9280,9284,9475,9504,9560,9606,9656,9728,9777,9865,9879,9892,9901,9966,9985,10011,10106,10113,10156,10173,10175,10176,10205,10267,10325,10397,10460,10512,10547,10620,10639,10793,10871,10874,10913,10997,11069,11133,11148,11152,11166,11255,11268,11278,11302,11400,11416,11436,11447,11470,11600,11611,11659,11663,11683,11751,11854,11951,12023,12029,12055,12060,12063,12143,12183,12188,12205,12240,12254,12256,12258,12304,12310,12362,12366,12382,12386,12387,12405,12444,12449,12476,12512,12554,12587,12608,12632,12642,12737,12880,12884,12891,12895,12952,12956,12964,12987,13129,13188,13233,13234,13274,13312,13340,13341,13342,13385,13541,13549,13691,13699,13726,13755,13757,13761,13764,13881,13919,13946,13964,13967,14034,14093,14106,14109,14153,14161,14163,14228,14238,14332,14380,14539,14547,14640,14676,14704,14919,15272,15346,15383,15745,15846,15900,15987,15989,16048,16156,16172,16278,16291,16294,16356,16410,16450,16527,16555,16628,16642,16671,16733,16735,16736, -chr19 47510580 47527139 m84039_230404_003541_s3/257819209/ccs 243,353,585,830,932,1232,1435,1885,2006,2279,2439,2684,2810,3061,3242,3408,3579,3818,4120,5057,5296,5606,5767,6149,6347,6686,6872,7005,7172,7333,7521,7893,8396,8590,8865,9047,9243,9416,9740,9946,10097,10278,10501,10695,10880,11083,11256,11457,11639,11849,12733,12845,13069,13286,13492,13680,13870,14057,14249,14429,14613,14785,14878,15009,15184,15343,15531,15710,15913,16116, 104,166,128,85,117,89,101,77,89,100,144,76,150,100,137,138,127,123,108,106,150,160,128,130,145,107,85,135,138,144,86,129,112,140,77,112,96,108,133,146,129,124,105,87,118,100,119,99,106,105,111,147,121,113,117,136,130,112,122,113,119,92,102,110,101,133,136,101,108,118, 107,347,519,713,915,1049,1321,1536,1962,2095,2379,2583,2760,2960,3161,3379,3546,3706,3941,4228,5163,5446,5766,5895,6279,6492,6793,6957,7140,7310,7477,7607,8022,8508,8730,8942,9159,9339,9524,9873,10092,10226,10402,10606,10782,10998,11183,11375,11556,11745,11954,12844,12992,13190,13399,13609,13816,14000,14169,14371,14542,14732,14877,14980,15119,15285,15476,15667,15811,16021,16234, 136,6,66,117,17,183,114,349,44,184,60,101,50,101,81,29,33,112,179,829,133,160,1,254,68,194,79,48,32,23,44,286,374,82,135,105,84,77,216,73,5,52,99,89,98,85,73,82,83,104,779,1,77,96,93,71,54,57,80,58,71,53,1,29,65,58,55,43,102,95,194, 0,0,0,0,0,0,0,243,0,0,0,0,0,0,0,0,0,243,0,246,0,0,0,0,0,0,0,0,0,0,0,247,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 1,2,3,5,6,56,107,108,113,116,119,122,123,128,130,135,137,140,144,148,152,153,158,163,165,169,172,176,179,182,183,185,186,188,190,194,197,199,201,204,205,210,211,213,216,219,223,225,227,229,232,234,242,347,352,398,492,519,523,525,529,530,535,538,539,542,547,548,554,558,559,563,565,569,572,573,579,582,584,628,713,716,719,722,727,730,735,737,741,743,746,760,768,780,789,792,796,808,829,915,931,958,1049,1074,1091,1092,1094,1146,1148,1187,1194,1195,1206,1210,1216,1221,1225,1227,1231,1321,1330,1348,1353,1356,1367,1368,1373,1376,1380,1382,1383,1390,1394,1397,1400,1406,1415,1417,1420,1422,1425,1432,1434,1494,1528,1536,1540,1544,1546,1548,1551,1556,1558,1561,1564,1566,1569,1570,1577,1591,1597,1600,1610,1613,1617,1619,1622,1629,1653,1678,1681,1694,1696,1699,1716,1721,1724,1735,1739,1740,1748,1751,1753,1755,1758,1760,1763,1764,1766,1770,1782,1789,1790,1793,1795,1797,1800,1804,1806,1808,1810,1812,1815,1816,1817,1819,1821,1822,1824,1825,1828,1836,1840,1842,1843,1846,1847,1848,1853,1855,1870,1879,1883,1884,1962,1974,1977,1979,1985,1987,1995,2005,2095,2097,2106,2134,2138,2141,2143,2146,2156,2157,2159,2161,2163,2166,2168,2171,2175,2178,2183,2184,2186,2187,2189,2190,2193,2215,2258,2278,2335,2379,2409,2411,2414,2438,2475,2531,2545,2583,2588,2590,2594,2596,2597,2600,2603,2605,2619,2621,2622,2625,2628,2675,2679,2681,2683,2760,2776,2777,2783,2787,2790,2792,2801,2803,2805,2807,2809,2858,2960,2971,2978,2982,2985,2987,2996,2999,3004,3007,3009,3011,3016,3020,3036,3060,3129,3145,3161,3170,3173,3174,3176,3179,3186,3193,3196,3200,3201,3202,3208,3212,3217,3219,3222,3226,3229,3233,3238,3241,3379,3392,3397,3399,3400,3403,3407,3504,3546,3558,3567,3578,3659,3706,3716,3721,3723,3727,3729,3736,3743,3747,3749,3750,3753,3755,3758,3761,3772,3775,3777,3779,3783,3789,3794,3797,3799,3805,3813,3817,3867,3941,3945,3951,3952,3985,4045,4051,4073,4079,4091,4097,4104,4119,4168,4202,4228,4232,4233,4236,4252,4264,4272,4279,4290,4317,4333,4338,4381,4402,4405,4409,4410,4412,4414,4435,4436,4438,4440,4442,4443,4453,4466,4469,4472,4476,4487,4492,4519,4561,4563,4571,4574,4583,4593,4597,4600,4602,4609,4610,4611,4617,4620,4622,4624,4627,4630,4634,4635,4640,4642,4651,4652,4659,4662,4664,4666,4668,4678,4680,4682,4686,4688,4691,4695,4698,4700,4704,4706,4709,4710,4714,4715,4716,4720,4723,4734,4750,4752,4753,4756,4759,4762,4763,4766,4769,4772,4775,4776,4779,4782,4785,4790,4795,4819,4821,4836,4837,4839,4841,4844,4846,4848,4850,4860,4862,4864,4868,4871,4873,4875,4887,4901,4903,4906,4911,4914,4916,4935,4938,4940,4947,4948,4949,4951,4954,4956,4960,4961,4962,4971,4981,4983,4987,4988,4990,4993,5011,5017,5020,5025,5026,5038,5040,5045,5047,5048,5050,5052,5054,5056,5122,5163,5173,5176,5181,5184,5186,5189,5195,5197,5200,5209,5213,5218,5220,5227,5229,5230,5236,5237,5239,5242,5244,5249,5255,5257,5260,5264,5266,5268,5271,5273,5275,5276,5283,5291,5295,5369,5446,5450,5453,5499,5505,5546,5547,5598,5600,5602,5605,5663,5709,5728,5766,5895,5901,5903,5905,5908,5909,5911,5915,5916,5917,5920,5923,5929,5936,5939,5958,5960,5965,5969,5973,5974,5975,5977,6026,6037,6048,6068,6072,6073,6076,6132,6135,6137,6139,6140,6146,6148,6279,6280,6285,6287,6290,6294,6295,6296,6298,6302,6303,6306,6310,6313,6315,6317,6319,6323,6324,6328,6331,6334,6346,6418,6492,6495,6498,6501,6507,6523,6540,6546,6607,6630,6634,6637,6638,6640,6646,6647,6650,6659,6671,6675,6685,6745,6761,6793,6795,6803,6814,6816,6819,6823,6841,6843,6845,6847,6871,6957,6962,6968,6972,6974,6976,6980,6982,6986,6990,6998,7000,7002,7004,7031,7104,7140,7171,7310,7317,7318,7322,7326,7330,7332,7477,7479,7482,7486,7489,7502,7505,7520,7607,7613,7614,7617,7627,7629,7631,7632,7635,7637,7638,7639,7649,7651,7652,7657,7658,7662,7664,7672,7678,7680,7682,7683,7687,7688,7694,7697,7699,7701,7702,7704,7705,7706,7708,7709,7711,7712,7713,7716,7718,7719,7723,7726,7729,7732,7734,7735,7737,7747,7749,7751,7754,7759,7761,7763,7766,7769,7777,7781,7790,7792,7793,7798,7804,7809,7811,7813,7823,7825,7827,7828,7829,7831,7835,7838,7839,7841,7847,7850,7852,7853,7857,7861,7867,7874,7878,7881,7882,7884,7886,7890,7892,7929,8022,8025,8099,8100,8119,8145,8176,8190,8197,8204,8207,8209,8210,8221,8270,8285,8296,8338,8350,8354,8357,8362,8377,8386,8390,8391,8395,8472,8508,8517,8520,8530,8533,8540,8542,8546,8549,8551,8554,8556,8558,8563,8565,8568,8569,8575,8581,8589,8629,8730,8733,8735,8740,8743,8744,8745,8750,8751,8753,8755,8758,8760,8761,8766,8769,8771,8772,8777,8780,8782,8790,8793,8798,8801,8806,8807,8809,8810,8812,8814,8817,8818,8819,8822,8825,8829,8832,8836,8843,8845,8864,8942,8957,8963,8966,8973,8976,8979,8982,8983,8987,9012,9027,9030,9039,9043,9046,9133,9159,9167,9169,9179,9181,9185,9187,9189,9193,9194,9195,9197,9201,9206,9210,9211,9213,9216,9223,9242,9339,9342,9354,9359,9364,9365,9367,9368,9378,9379,9384,9392,9395,9415,9460,9524,9525,9531,9532,9534,9537,9541,9544,9559,9563,9571,9579,9583,9651,9676,9677,9679,9724,9733,9739,9873,9885,9887,9896,9899,9904,9906,9907,9914,9920,9921,9924,9929,9939,9945,10035,10092,10096,10226,10230,10239,10251,10256,10257,10269,10277,10364,10402,10407,1040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-chr19 47510789 47515778 m84039_230404_003541_s3/81792247/ccs 74,395,586,767,906,1161,1313,1514,1632,1752,1917,2478,2772,2906,3307,3446,3599,3739,3884,4037,4633, 110,110,110,94,108,76,115,106,119,119,121,106,92,87,111,114,110,123,118,109,131, 184,505,696,861,1014,1237,1428,1620,1751,1871,2038,2584,2864,2993,3418,3560,3709,3862,4002,4146,4764, 211,81,71,45,147,76,86,12,1,46,440,188,42,314,28,39,30,22,35,487,79, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,244,0, 2,3,5,8,11,15,19,21,24,26,27,29,31,34,35,37,39,49,52,56,58,61,63,73,184,189,193,197,200,202,206,210,214,215,217,219,222,225,226,230,235,237,240,242,244,246,250,251,265,333,351,355,357,361,365,368,374,376,382,387,391,392,394,505,508,511,514,519,522,527,529,533,535,538,542,545,549,553,555,558,561,566,568,573,577,582,585,696,702,704,708,709,713,716,718,723,725,729,736,738,741,742,744,746,754,759,762,765,766,861,863,865,866,868,872,877,878,884,885,887,897,899,905,1014,1026,1028,1032,1035,1050,1052,1055,1060,1070,1080,1083,1086,1088,1090,1092,1094,1100,1102,1105,1108,1111,1114,1116,1119,1121,1126,1141,1160,1237,1247,1253,1254,1257,1259,1261,1264,1267,1270,1274,1276,1278,1279,1283,1285,1286,1289,1296,1299,1309,1312,1428,1445,1450,1456,1460,1462,1464,1474,1478,1481,1485,1495,1513,1620,1631,1751,1871,1873,1875,1881,1885,1887,1889,1891,1894,1898,1902,1916,2011,2038,2040,2045,2053,2057,2063,2065,2068,2071,2073,2074,2078,2080,2083,2084,2087,2089,2091,2093,2096,2100,2102,2106,2110,2113,2121,2123,2125,2126,2130,2136,2142,2145,2149,2151,2157,2158,2160,2163,2170,2201,2205,2207,2215,2217,2222,2225,2227,2229,2231,2233,2234,2236,2238,2241,2243,2244,2249,2252,2254,2257,2258,2259,2263,2266,2268,2271,2273,2275,2277,2279,2282,2284,2285,2293,2300,2302,2307,2310,2315,2325,2384,2394,2397,2407,2422,2427,2430,2432,2434,2439,2443,2446,2449,2451,2456,2458,2460,2463,2465,2466,2469,2471,2473,2475,2477,2584,2586,2595,2597,2599,2603,2608,2618,2622,2638,2645,2708,2721,2723,2729,2735,2737,2742,2745,2747,2753,2756,2771,2864,2867,2878,2879,2884,2892,2895,2896,2898,2900,2902,2905,2993,2994,3000,3004,3007,3009,3011,3025,3033,3081,3083,3089,3106,3108,3109,3111,3124,3126,3131,3142,3144,3148,3151,3155,3159,3161,3163,3164,3165,3167,3170,3176,3180,3185,3187,3188,3191,3220,3222,3225,3233,3256,3259,3260,3262,3268,3272,3280,3281,3293,3295,3306,3418,3429,3431,3445,3560,3574,3582,3584,3590,3598,3709,3715,3718,3721,3725,3729,3732,3738,3862,3864,3865,3876,3880,3882,3883,4002,4005,4016,4029,4036,4146,4155,4163,4165,4167,4170,4172,4178,4180,4184,4186,4190,4194,4195,4197,4201,4220,4221,4223,4225,4227,4228,4236,4238,4247,4251,4272,4284,4287,4288,4291,4294,4296,4298,4299,4304,4309,4310,4313,4323,4346,4348,4359,4378,4385,4387,4395,4419,4437,4444,4447,4449,4451,4453,4463,4465,4467,4468,4471,4476,4494,4505,4519,4531,4535,4537,4541,4544,4547,4548,4612,4626,4630,4632,4664,4764,4767,4769,4773,4774,4776,4779,4785,4789,4811,4824,4826,4842,4971,4980,4982,4984, -chr19 47510878 47527135 m84008_230107_003043_s1/179442349/ccs 201,384,567,756,960,1092,1279,1429,1579,1734,2020,2320,2475,2666,2854,3016,3182,3483,3686,3805,3953,4867,5011,5130,5288,5471,5661,5846,6034,6247,6387,6644,6841,6985,7171,7618,7885,7991,8151,8442,8624,8786,8941,9128,9263,9487,9649,9842,10080,10229,10442,10620,10813,11013,11182,11356,11538,11680,11865,12061,12208,12417,12591,12758,12974,13177,13361,13575,13774,13958,14089,14308,14480,14705,14902,15077,15271,15414,15601,15824,15977, 147,147,126,132,116,127,100,136,110,107,225,115,156,122,137,138,253,121,109,140,118,115,118,133,141,139,166,119,142,92,116,106,86,83,125,266,105,134,242,113,96,114,117,112,160,118,139,131,134,125,121,138,128,136,154,133,141,117,139,124,167,125,140,181,124,153,150,124,86,97,153,116,150,172,87,124,106,129,107,110,132, 146,348,531,693,888,1076,1219,1379,1565,1689,1841,2245,2435,2631,2788,2991,3154,3435,3604,3795,3945,4071,4982,5129,5263,5429,5610,5827,5965,6176,6339,6503,6750,6927,7068,7296,7884,7990,8125,8393,8555,8720,8900,9058,9240,9423,9605,9788,9973,10214,10354,10563,10758,10941,11149,11336,11489,11679,11797,12004,12185,12375,12542,12731,12939,13098,13330,13511,13699,13860,14055,14242,14424,14630,14877,14989,15201,15377,15543,15708,15934,16109, 55,36,36,63,72,16,60,50,14,45,179,75,40,35,66,25,28,48,82,10,8,796,29,1,25,42,51,19,69,71,48,141,91,58,103,322,1,1,26,49,69,66,41,70,23,64,44,54,107,15,88,57,55,72,33,20,49,1,68,57,23,42,49,27,35,79,31,64,75,98,34,66,56,75,25,88,70,37,58,116,43,20, 0,0,0,0,0,0,0,0,0,0,250,0,0,0,0,0,0,0,0,0,0,251,0,0,0,0,0,0,0,0,0,244,0,0,0,251,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 8,15,16,146,157,161,162,179,186,188,200,348,374,377,381,383,531,533,536,539,542,544,547,550,552,556,563,566,660,693,701,703,727,730,734,736,755,862,888,890,893,894,897,900,903,909,913,919,924,928,930,932,934,938,942,959,1076,1079,1083,1085,1091,1219,1235,1238,1242,1246,1248,1250,1253,1258,1260,1263,1265,1266,1269,1278,1379,1395,1400,1404,1415,1422,1425,1428,1565,1567,1578,1644,1689,1707,1720,1723,1726,1733,1841,1846,1850,1852,1867,1870,1872,1875,1880,1881,1882,1887,1888,1890,1891,1893,1894,1896,1900,1902,1906,1907,1911,1912,1914,1916,1917,1920,1924,1929,1934,1941,1946,1947,1949,1954,1955,1957,1960,1962,1963,1966,1967,1970,1972,1974,1977,1980,1982,1983,1989,1992,1993,1996,1998,2000,2002,2005,2015,2019,2245,2251,2254,2271,2275,2276,2278,2281,2282,2285,2287,2292,2294,2298,2300,2301,2304,2307,2309,2312,2317,2319,2435,2442,2448,2450,2452,2455,2459,2463,2469,2471,2474,2631,2633,2639,2640,2645,2647,2648,2652,2654,2659,2663,2665,2788,2802,2805,2808,2810,2812,2815,2819,2825,2832,2835,2838,2841,2843,2847,2853,2991,2993,2997,3001,3015,3154,3157,3159,3178,3181,3435,3442,3449,3452,3454,3460,3465,3474,3476,3482,3604,3611,3619,3624,3627,3630,3633,3634,3636,3644,3650,3653,3665,3670,3672,3675,3681,3685,3795,3804,3902,3945,3952,4071,4083,4094,4096,4100,4102,4106,4110,4111,4113,4117,4136,4137,4139,4141,4143,4144,4148,4152,4154,4170,4173,4177,4188,4192,4193,4200,4203,4204,4207,4210,4212,4214,4215,4220,4225,4226,4229,4236,4239,4254,4262,4264,4272,4275,4284,4294,4296,4298,4301,4303,4310,4311,4312,4318,4321,4323,4325,4331,4335,4336,4341,4343,4345,4352,4353,4360,4365,4367,4369,4374,4381,4399,4401,4405,4407,4410,4411,4415,4416,4417,4421,4424,4435,4447,4451,4453,4457,4460,4463,4467,4473,4476,4477,4478,4480,4483,4486,4491,4496,4502,4514,4520,4537,4538,4540,4546,4548,4550,4552,4555,4557,4562,4573,4577,4580,4589,4602,4604,4606,4609,4617,4638,4641,4643,4650,4652,4654,4657,4659,4663,4664,4665,4670,4674,4681,4684,4685,4686,4690,4693,4696,4741,4743,4750,4751,4753,4755,4757,4759,4764,4770,4772,4775,4777,4780,4781,4783,4787,4791,4798,4807,4810,4813,4815,4829,4833,4834,4849,4866,4916,4966,4982,4985,4990,4993,4997,4999,5010,5129,5263,5265,5267,5271,5273,5287,5328,5400,5425,5429,5431,5436,5439,5442,5459,5462,5463,5470,5610,5619,5630,5641,5660,5827,5833,5834,5839,5842,5845,5965,5982,5987,5989,5992,5995,5998,6000,6002,6004,6005,6008,6012,6015,6017,6026,6031,6033,6176,6179,6180,6197,6200,6201,6208,6213,6216,6219,6225,6233,6238,6240,6246,6339,6348,6351,6353,6356,6358,6360,6366,6372,6374,6376,6377,6381,6382,6386,6503,6508,6510,6511,6514,6516,6519,6523,6529,6531,6532,6535,6537,6539,6541,6543,6549,6550,6557,6563,6565,6566,6571,6592,6594,6600,6603,6604,6606,6608,6611,6612,6615,6618,6625,6629,6643,6750,6769,6770,6772,6776,6777,6780,6784,6787,6807,6808,6815,6820,6840,6927,6939,6940,6944,6946,6947,6948,6951,6962,6971,6984,7068,7092,7096,7097,7100,7102,7108,7112,7115,7116,7128,7130,7131,7134,7136,7138,7166,7169,7170,7296,7303,7309,7314,7325,7328,7330,7339,7340,7346,7352,7353,7359,7360,7364,7366,7371,7374,7375,7379,7380,7381,7382,7385,7389,7390,7396,7397,7399,7401,7403,7404,7407,7408,7410,7411,7413,7414,7415,7416,7418,7420,7425,7434,7435,7437,7440,7443,7448,7450,7452,7454,7457,7459,7462,7464,7466,7469,7472,7480,7484,7487,7488,7490,7493,7495,7496,7501,7502,7507,7511,7512,7514,7516,7518,7520,7521,7522,7526,7528,7530,7531,7534,7537,7538,7541,7542,7544,7546,7550,7553,7555,7556,7559,7560,7564,7570,7572,7575,7577,7578,7581,7584,7585,7587,7589,7591,7592,7597,7602,7604,7608,7617,7884,7990,8125,8130,8150,8393,8411,8413,8415,8419,8421,8422,8426,8431,8434,8436,8441,8555,8570,8574,8579,8592,8594,8595,8601,8603,8610,8623,8720,8726,8729,8738,8742,8745,8747,8753,8756,8761,8766,8769,8785,8900,8905,8909,8910,8912,8915,8922,8929,8933,8940,9058,9063,9066,9083,9089,9091,9094,9106,9108,9116,9127,9240,9258,9262,9423,9430,9436,9438,9443,9444,9446,9449,9450,9456,9478,9486,9605,9620,9623,9626,9628,9644,9647,9648,9788,9792,9796,9797,9803,9805,9807,9810,9813,9816,9818,9825,9830,9834,9835,9841,9973,9975,9981,10005,10009,10010,10015,10018,10020,10022,10026,10030,10037,10045,10047,10068,10076,10079,10214,10221,10225,10228,10354,10357,10374,10378,10381,10384,10386,10396,10399,10400,10408,10415,10417,10420,10424,10426,10430,10435,10441,10563,10567,10572,10578,10581,10585,10588,10591,10592,10595,10599,10611,10613,10615,10619,10758,10771,10772,10776,10779,10782,10784,10788,10794,10801,10807,10810,10812,10906,10941,10943,10945,10946,10948,10956,10958,10965,10968,10969,10972,10974,10975,10978,10979,10981,10984,10986,10988,10991,10992,10993,10998,11002,11008,11012,11149,11153,11163,11167,11169,11171,11173,11181,11336,11343,11355,11489,11491,11495,11504,11509,11512,11517,11521,11523,11525,11532,11537,11679,11797,11810,11816,11826,11828,11829,11831,11832,11836,11837,11839,11847,11849,11860,11864,12004,12007,12012,12017,12020,12021,12023,12024,12029,12054,12060,12185,12207,12375,12383,12384,12386,12388,12389,12395,12399,12405,12408,12413,12416,12542,12546,12547,12549,12552,12562,12565,12568,12572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-chr19 47510884 47527565 m54329U_210813_020940/103744027/ccs 182,338,503,691,930,1116,1280,1480,1641,1808,1995,2163,2300,2459,2642,2838,3121,3275,3595,3841,3960,4794,5036,5273,5595,5788,6357,6550,6750,6991,7224,7369,7620,7828,7993,8277,8695,9295,9463,9640,9851,10039,10230,10398,10574,10774,10946,11107,11281,11450,11650,12205,12352,12521,12680,12923,13132,13307,13478,13663,13871,14042,14218,14398,14565,14768,14993,15411,15599,15765,15937,16107,16277,16464, 116,117,131,207,116,109,103,124,137,171,110,126,137,126,131,247,116,90,93,84,100,118,148,102,118,121,108,105,120,117,103,102,121,83,283,136,124,130,133,131,150,117,83,119,139,115,127,147,122,138,127,100,136,123,128,112,114,120,135,139,122,127,151,128,202,132,417,160,135,118,131,156,146,118, 121,298,455,634,898,1046,1225,1383,1604,1778,1979,2105,2289,2437,2585,2773,3085,3237,3365,3688,3925,4060,4912,5184,5375,5713,5909,6465,6655,6870,7108,7327,7471,7741,7911,8276,8413,8819,9425,9596,9771,10001,10156,10313,10517,10713,10889,11073,11254,11403,11588,11777,12305,12488,12644,12808,13035,13246,13427,13613,13802,13993,14169,14369,14526,14767,14900,15410,15571,15734,15883,16068,16263,16423, 61,40,48,57,32,70,55,97,37,30,16,58,11,22,57,65,36,38,230,153,35,734,124,89,220,75,448,85,95,121,116,42,149,87,82,1,282,476,38,44,80,38,74,85,57,61,57,34,27,47,62,428,47,33,36,115,97,61,51,50,69,49,49,29,39,1,93,1,28,31,54,39,14,41, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,250,0,0,0,0,0,0,0,0,0,0,244,0,0,0,244,244,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 120,127,131,132,136,141,146,148,150,152,156,157,162,167,171,174,181,298,300,305,316,337,455,461,467,472,479,488,495,500,502,634,641,643,647,649,651,654,657,690,898,904,914,919,923,925,929,1046,1051,1054,1055,1061,1065,1071,1074,1078,1080,1083,1086,1088,1098,1104,1110,1113,1115,1225,1230,1233,1237,1241,1243,1245,1248,1253,1255,1256,1260,1264,1267,1278,1279,1383,1386,1391,1393,1396,1411,1413,1418,1421,1424,1427,1445,1448,1450,1452,1455,1457,1463,1467,1473,1479,1604,1605,1613,1620,1623,1627,1634,1638,1640,1778,1780,1782,1784,1786,1790,1792,1803,1807,1979,1994,2105,2109,2119,2126,2129,2131,2133,2136,2138,2141,2143,2148,2149,2154,2162,2289,2296,2299,2437,2445,2447,2454,2458,2585,2607,2611,2613,2614,2617,2623,2627,2629,2632,2635,2641,2773,2778,2784,2785,2795,2801,2802,2804,2806,2808,2811,2814,2816,2820,2821,2837,3085,3089,3094,3096,3097,3100,3104,3105,3106,3107,3120,3237,3239,3245,3247,3254,3256,3259,3262,3263,3270,3274,3365,3372,3382,3390,3394,3397,3411,3418,3422,3424,3445,3500,3508,3511,3522,3528,3533,3535,3537,3539,3544,3545,3550,3554,3555,3557,3563,3566,3569,3573,3574,3576,3578,3584,3586,3590,3594,3688,3707,3716,3720,3722,3724,3727,3734,3737,3741,3742,3748,3749,3751,3753,3755,3759,3761,3763,3766,3768,3770,3774,3776,3777,3788,3792,3794,3795,3801,3803,3807,3811,3816,3818,3820,3827,3835,3840,3925,3930,3942,3947,3949,3956,3959,4060,4068,4072,4076,4078,4091,4097,4099,4103,4107,4108,4110,4112,4114,4120,4133,4134,4136,4138,4140,4141,4145,4149,4151,4160,4170,4174,4189,4190,4200,4201,4204,4207,4209,4211,4217,4222,4223,4226,4233,4236,4251,4259,4261,4269,4281,4291,4293,4295,4298,4300,4307,4308,4315,4318,4320,4322,4325,4328,4332,4338,4340,4349,4350,4357,4360,4362,4364,4366,4371,4376,4378,4380,4381,4384,4386,4389,4393,4396,4402,4404,4407,4408,4412,4413,4414,4418,4420,4421,4432,4444,4448,4450,4451,4452,4455,4458,4460,4462,4463,4466,4469,4472,4475,4476,4477,4479,4482,4485,4495,4501,4514,4520,4522,4528,4540,4542,4546,4548,4550,4552,4555,4557,4562,4564,4566,4568,4570,4573,4575,4577,4589,4614,4617,4637,4640,4642,4649,4653,4658,4659,4662,4664,4669,4673,4677,4680,4683,4684,4685,4689,4692,4695,4696,4728,4740,4742,4749,4750,4752,4754,4756,4758,4761,4762,4763,4769,4774,4776,4779,4780,4782,4788,4790,4793,4912,4920,4922,4931,4932,4938,4939,4945,4956,4958,4961,4965,4967,4969,4972,4974,4977,4981,4984,4987,4992,4997,4999,5001,5002,5004,5007,5009,5011,5015,5018,5019,5026,5029,5035,5155,5184,5195,5200,5202,5205,5206,5210,5218,5221,5223,5227,5238,5240,5247,5248,5254,5256,5257,5264,5266,5268,5270,5272,5375,5377,5379,5385,5399,5403,5406,5408,5411,5414,5421,5428,5433,5470,5512,5520,5531,5537,5544,5547,5550,5559,5562,5563,5574,5575,5577,5579,5583,5590,5594,5630,5713,5718,5720,5721,5723,5724,5730,5733,5743,5744,5751,5754,5755,5758,5760,5762,5765,5767,5769,5771,5773,5774,5787,5909,5927,5929,5930,5940,5943,5945,5947,5949,5951,5954,5959,5966,5969,5972,5979,5980,5985,5987,5993,5998,6000,6002,6003,6006,6015,6070,6075,6078,6084,6086,6089,6093,6095,6110,6121,6148,6159,6171,6173,6176,6179,6184,6188,6190,6248,6255,6258,6262,6273,6277,6279,6281,6285,6287,6298,6300,6302,6304,6309,6312,6317,6320,6323,6329,6331,6338,6348,6351,6353,6356,6465,6468,6474,6476,6480,6482,6492,6493,6495,6498,6500,6503,6505,6508,6514,6516,6519,6523,6545,6549,6571,6646,6655,6657,6662,6664,6668,6676,6679,6680,6682,6686,6690,6694,6698,6700,6702,6704,6707,6708,6710,6727,6731,6737,6749,6870,6875,6895,6899,6902,6907,6908,6910,6911,6913,6918,6923,6925,6929,6932,6940,6944,6946,6947,6948,6951,6952,6956,6957,6958,6962,6964,6966,6968,6971,6977,6979,6984,6986,6990,7108,7115,7116,7130,7131,7134,7135,7136,7138,7141,7162,7166,7169,7170,7174,7178,7180,7183,7189,7192,7193,7196,7200,7205,7214,7221,7223,7327,7330,7332,7342,7355,7368,7392,7466,7471,7474,7480,7482,7486,7489,7492,7495,7498,7503,7504,7505,7509,7510,7513,7514,7516,7518,7520,7528,7530,7532,7534,7536,7540,7543,7546,7548,7552,7557,7558,7561,7562,7563,7564,7566,7572,7574,7577,7579,7580,7583,7587,7589,7591,7593,7594,7598,7599,7604,7606,7610,7619,7741,7742,7744,7751,7756,7757,7758,7762,7764,7768,7775,7782,7787,7788,7793,7795,7796,7799,7801,7803,7804,7809,7813,7816,7818,7821,7823,7827,7911,7913,7956,7958,7959,7964,7971,7980,7987,7989,7992,8276,8413,8423,8428,8436,8438,8441,8443,8448,8453,8454,8456,8458,8461,8463,8464,8468,8469,8472,8474,8475,8477,8480,8483,8485,8489,8491,8493,8501,8504,8509,8512,8513,8515,8517,8520,8521,8522,8525,8528,8531,8538,8540,8553,8557,8564,8566,8603,8615,8622,8629,8631,8633,8637,8640,8644,8646,8650,8655,8659,8661,8662,8666,8668,8669,8671,8674,8676,8677,8679,8682,8683,8685,8686,8690,8694,8819,8831,8851,8855,8857,8858,8861,8863,8866,8869,8872,8881,8889,8903,8974,8977,8979,8983,8986,8988,8992,8995,9014,9016,9018,9019,9024,9025,9026,9028,9031,9032,9034,9040,9042,9043,9047,9049,9050,9052,9053,9055,9057,9058,9060,9063,9065,9066,9068,9069,9079,9080,9085,9096,9105,9108,9110,9112,9116,9118,9121,9124,9129,9130,9133,9136,9139,9140,9145,9147,9150,9217,9220,9224,9225,9226,9232,9233,9235,9238,9242,9254,9255,9257,9260,9262,9264,9266,9276,9280,9284,9292,9294,9425,9432,9434,9437,9462,9596,9609,9624,9627,9629,9639,9771,9783,9793,9797,9798,9803,9804,9806,9811,9814,9819,9820,9826,9831,9842,9850,10001,10006,10016,10019,10021,10038,10156,10161,10168,10175,10179,10182,10185,10188,10203,10211,10222,10229,10313,10315,10318,10325,10331,10333,10337,10341,10353,10355,10358,10367,10370,10375,10379,10382,10385,10387,10388,10397,10517,10520,10522,10523,10528,10535,10539,10542,10543,10547,10548,10550,10552,10558,10564,10568,10573,10713,10716,10720,10721,10724,10732,10739,10744,10747,10751,10755,10764,10773,10889,10903,10908,10912,10916,10934,10945,11073,11075,11087,11094,11098,11102,11106,11218,11254,11262,11279,11280,11403,11410,11415,11416,11418,11420,11422,11424,11427,11449,11588,11592,11595,11596,11599,11600,11604,11616,11619,11621,11632,11637,11640,11645,11646,11649,11777,11781,11792,11796,11798,11801,11805,11808,11809,11816,11817,11820,11822,11827,11832,11833,11840,11845,11854,11861,11865,11921,11927,11935,11945,11960,11967,11971,11975,11976,11977,11979,11982,11986,11988,11997,11999,12000,12003,12007,12010,12011,12012,12015,12016,12020,12023,12024,12026,12027,12044,12046,12112,12123,12132,12134,12137,12141,12146,12151,12153,12154,12170,12173,12175,12177,12181,12182,12185,12188,12190,12199,12202,12204,12305,12308,12314,12339,12341,12347,12351,12488,12491,12498,12502,12504,12508,12519,12520,12644,12660,12671,12674,12679,12808,12812,12815,12819,12827,12832,12836,12838,12839,12841,12843,12845,12848,12853,12856,12860,12879,12881,12882,12886,12889,12892,12894,12896,12900,12905,12908,12911,12914,12916,12918,12922,13035,13042,13045,13047,13056,13057,13061,13079,13081,13085,13086,13096,13098,13105,13113,13116,13131,13246,13249,13254,13257,13261,13262,13276,13277,13279,13281,13282,13285,13295,13297,13299,13303,13306,13427,13432,13435,13440,13454,13456,13458,13459,13463,13466,13468,13470,13477,13613,13615,13620,13625,13631,13634,13638,13644,13646,13647,13660,13662,13802,13810,13812,13820,13822,13824,13826,13828,13866,13870,13993,14016,14020,14022,14036,14041,14169,14175,14179,14185,14188,14191,14193,14196,14210,14211,14217,14369,14371,14374,14380,14384,14390,14397,14526,14529,14533,14548,14559,14562,14564,14767,14900,14904,14921,14927,14938,14992,15410,15571,15580,15598,15734,15735,15738,15742,15764,15883,15888,15893,15900,15936,16068,16076,16077,16079,16088,16092,16095,16098,16099,16102,16106,16263,16271,16276,16423,16425,16431,16435,16437,16447,16457,16459,16463,16582,16589,16608,16614,16618,16619,16622,16624,16625,16630,16633,16640,16642,16646,16652,16654,16655,16658,16662, -chr19 47510892 47522730 m64076_210328_012155/128584028/ccs 169,319,550,702,895,1043,1205,1383,1561,1753,2019,2167,2917,3066,3430,3582,3753,3923,4109,4377,4839,5109,5286,5457,5606,5803,6072,6355,6517,6760,6888,7100,7209,7611,7825,8086,8275,8399,8576,8701,8873,9064,9315,9441,9663,9837,10045,10258,10468,10835,11025,11166,11327,11499,11669, 115,143,108,152,147,141,136,150,120,125,85,128,89,89,83,103,84,185,101,84,77,104,103,120,138,235,195,112,83,127,154,108,116,128,247,130,95,128,121,171,109,108,125,128,105,152,146,114,110,130,138,144,162,112,132, 113,284,462,658,854,1042,1184,1341,1533,1681,1878,2104,2295,3006,3155,3513,3685,3837,4108,4210,4461,4916,5213,5389,5577,5744,6038,6267,6467,6600,6887,7042,7208,7325,7739,8072,8216,8370,8527,8697,8872,8982,9172,9440,9569,9768,9989,10191,10372,10578,10965,11163,11310,11489,11611,11801, 56,35,88,44,41,1,21,42,28,72,141,63,622,60,275,69,68,86,1,167,378,193,73,68,29,59,34,88,50,160,1,58,1,286,86,14,59,29,49,4,1,82,143,1,94,69,56,67,96,257,60,3,17,10,58,28, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,245,246,0,0,0,0,0,0,0,0,0,0,0,0,249,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 113,117,120,123,128,133,138,139,143,149,150,151,156,161,168,284,288,307,314,315,318,462,474,478,482,483,486,490,495,497,509,514,517,521,523,526,529,532,537,540,542,546,549,658,659,661,678,683,685,692,695,701,854,877,881,882,886,890,894,1042,1145,1184,1193,1198,1201,1204,1341,1353,1358,1360,1361,1363,1371,1374,1375,1379,1382,1533,1535,1543,1548,1560,1681,1683,1687,1691,1694,1695,1697,1700,1701,1703,1706,1707,1708,1709,1710,1711,1715,1718,1721,1728,1735,1736,1737,1739,1746,1747,1752,1878,1885,1888,1891,1892,1894,1909,1915,1922,1929,1932,1939,1944,1945,1947,1952,1953,1962,1965,1969,1971,1981,1982,1986,1988,2004,2008,2010,2018,2104,2115,2130,2133,2135,2137,2139,2141,2144,2147,2153,2158,2163,2166,2295,2297,2301,2303,2304,2307,2310,2312,2322,2328,2375,2410,2412,2432,2439,2451,2453,2455,2462,2466,2467,2470,2472,2473,2474,2477,2480,2538,2544,2548,2551,2558,2633,2641,2647,2649,2655,2661,2662,2666,2668,2669,2673,2677,2679,2681,2686,2689,2692,2694,2699,2706,2711,2714,2716,2732,2743,2750,2755,2806,2809,2822,2823,2828,2847,2851,2857,2859,2861,2863,2867,2872,2875,2878,2879,2881,2884,2885,2895,2916,3006,3010,3016,3020,3022,3023,3025,3030,3034,3045,3056,3062,3065,3155,3158,3174,3176,3177,3179,3186,3191,3194,3195,3207,3209,3213,3215,3220,3234,3235,3240,3242,3244,3247,3248,3251,3253,3255,3257,3323,3333,3334,3337,3344,3346,3348,3349,3351,3360,3367,3370,3371,3374,3375,3377,3378,3380,3386,3388,3397,3406,3429,3513,3516,3528,3539,3541,3543,3545,3550,3551,3568,3570,3581,3685,3689,3695,3706,3711,3712,3715,3717,3722,3726,3730,3732,3752,3837,3842,3843,3847,3850,3860,3864,3871,3876,3884,3887,3914,3922,4108,4210,4211,4217,4221,4227,4232,4233,4236,4243,4246,4261,4269,4280,4283,4292,4302,4304,4306,4309,4311,4320,4329,4330,4332,4334,4344,4350,4369,4376,4461,4463,4464,4467,4470,4473,4474,4477,4480,4483,4486,4487,4488,4490,4493,4496,4506,4512,4531,4533,4547,4550,4552,4556,4558,4560,4562,4565,4567,4572,4574,4576,4578,4580,4583,4585,4587,4608,4610,4612,4614,4616,4617,4619,4624,4627,4653,4660,4663,4675,4677,4690,4691,4692,4693,4696,4697,4698,4702,4705,4708,4713,4723,4725,4731,4733,4734,4736,4739,4740,4742,4745,4746,4747,4752,4759,4761,4762,4764,4766,4768,4773,4774,4775,4776,4782,4787,4789,4792,4793,4795,4797,4808,4819,4823,4838,4916,4936,4943,4952,4954,4957,4972,4975,4979,4981,4983,4986,4988,4990,4991,4995,4998,4999,5001,5006,5012,5016,5019,5023,5098,5102,5108,5213,5215,5218,5234,5240,5244,5245,5247,5253,5267,5269,5270,5274,5275,5277,5279,5281,5283,5285,5389,5391,5412,5416,5419,5424,5427,5430,5432,5434,5436,5437,5441,5443,5448,5450,5453,5456,5577,5598,5605,5744,5747,5749,5757,5765,5768,5769,5774,5776,5779,5780,5783,5787,5788,5791,5792,5793,5799,5802,6038,6071,6267,6272,6285,6287,6291,6297,6299,6310,6316,6318,6321,6323,6324,6327,6344,6346,6354,6401,6467,6473,6476,6490,6492,6498,6511,6516,6600,6617,6623,6625,6628,6629,6634,6635,6638,6642,6646,6650,6654,6657,6660,6663,6666,6667,6669,6672,6674,6679,6681,6682,6685,6689,6691,6693,6696,6697,6699,6703,6707,6709,6711,6713,6715,6717,6719,6721,6724,6725,6727,6736,6746,6748,6754,6759,6887,6916,7042,7046,7048,7051,7054,7057,7061,7065,7067,7070,7075,7077,7081,7085,7087,7099,7208,7325,7329,7331,7335,7342,7345,7347,7353,7355,7357,7362,7363,7364,7367,7369,7377,7388,7391,7392,7396,7398,7399,7401,7402,7413,7416,7418,7420,7421,7424,7427,7428,7430,7431,7432,7435,7437,7438,7442,7445,7448,7451,7452,7454,7457,7460,7468,7470,7472,7475,7477,7480,7482,7484,7487,7490,7496,7498,7505,7508,7511,7513,7514,7519,7520,7522,7525,7530,7532,7536,7544,7546,7548,7549,7550,7556,7559,7560,7562,7564,7565,7568,7571,7574,7577,7578,7582,7588,7595,7596,7599,7602,7603,7605,7607,7610,7739,7740,7742,7745,7752,7759,7766,7772,7777,7800,7802,7806,7824,8072,8075,8080,8085,8216,8219,8231,8235,8246,8248,8254,8274,8370,8382,8390,8398,8527,8532,8536,8537,8543,8549,8553,8557,8560,8562,8568,8572,8575,8611,8697,8700,8872,8982,8992,8994,8998,9001,9024,9027,9029,9031,9032,9039,9041,9044,9045,9047,9048,9053,9057,9060,9062,9063,9172,9179,9182,9191,9196,9197,9199,9203,9206,9211,9213,9214,9218,9219,9223,9227,9230,9231,9233,9235,9237,9238,9245,9246,9248,9251,9255,9258,9260,9262,9265,9267,9270,9274,9279,9281,9287,9299,9312,9314,9440,9569,9584,9590,9593,9594,9595,9596,9602,9604,9606,9607,9610,9611,9617,9621,9623,9632,9641,9646,9650,9656,9659,9662,9688,9768,9771,9774,9777,9783,9793,9796,9797,9800,9801,9804,9805,9810,9814,9815,9817,9821,9823,9825,9828,9836,9989,9993,10014,10016,10026,10028,10033,10036,10038,10044,10130,10191,10198,10204,10207,10211,10213,10215,10217,10225,10230,10233,10234,10241,10245,10255,10257,10372,10377,10386,10387,10394,10398,10401,10404,10406,10407,10416,10419,10420,10425,10426,10435,10444,10447,10450,10455,10458,10461,10464,10467,10578,10584,10588,10593,10597,10599,10601,10606,10609,10616,10620,10621,10624,10625,10626,10628,10630,10632,10634,10636,10639,10653,10660,10678,10690,10739,10745,10758,10790,10793,10794,10798,10801,10810,10816,10823,10829,10834,10965,10973,10978,10987,10990,10994,11006,11010,11013,11024,11163,11165,11310,11313,11319,11326,11489,11491,11498,11611,11622,11639,11640,11642,11644,11663,11668,11801,11805,11822,11829, -chr19 47511145 47534069 m64076_221119_202646/33490605/ccs 118,314,490,706,861,1214,1769,2289,2489,2643,2812,2972,3128,3620,3883,3978,4140,4245,4474,4800,5147,5488,5729,5904,6118,6315,6533,6717,7092,7281,7627,7779,7908,8108,8249,8448,8654,8755,9754,9916,10133,10511,11157,11349,11521,11710,12135,12347,12505,12688,12842,13176,13316,13556,13805,13976,14143,14380,14584,14896,15089,15276,15444,15615,15750,15991,16279,16449,16620,16964,17159,17328,17546,17704,18183,18542,18835,19003,19337,19532,19694,19927,20123,20267,20628,20973,21138,21353,21610,21727,21916,22484, 158,140,215,104,308,518,480,165,150,168,156,155,362,232,94,161,78,128,287,311,307,180,139,143,161,136,150,288,122,256,151,128,181,140,193,205,80,957,154,83,290,628,163,139,149,424,211,93,162,145,333,130,161,156,152,166,168,192,311,143,162,151,170,129,196,162,148,167,307,162,161,152,157,429,326,292,153,322,194,161,172,154,138,360,327,164,193,256,116,169,561,168, 112,276,454,705,810,1169,1732,2249,2454,2639,2811,2968,3127,3490,3852,3977,4139,4218,4373,4761,5111,5454,5668,5868,6047,6279,6451,6683,7005,7214,7537,7778,7907,8089,8248,8442,8653,8734,9712,9908,9999,10423,11139,11320,11488,11670,12134,12346,12440,12667,12833,13175,13306,13477,13712,13957,14142,14311,14572,14895,15039,15251,15427,15614,15744,15946,16153,16427,16616,16927,17126,17320,17480,17703,18133,18509,18834,18988,19325,19531,19693,19866,20081,20261,20627,20955,21137,21331,21609,21726,21896,22477,22652, 6,38,36,1,51,45,37,40,35,4,1,4,1,130,31,1,1,27,101,39,36,34,61,36,71,36,82,34,87,67,90,1,1,19,1,6,1,21,42,8,134,88,18,29,33,40,1,1,65,21,9,1,10,79,93,19,1,69,12,1,50,25,17,1,6,45,126,22,4,37,33,8,66,1,50,33,1,15,12,1,1,61,42,6,1,18,1,22,1,1,20,7,22, 0,0,0,0,0,0,0,0,0,0,0,0,0,245,0,0,0,0,244,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,244,243,0,0,0,0,0,0,0,0,0,0,0,0,243,0,0,0,0,0,0,0,0,0,0,0,245,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 112,114,117,221,276,285,291,295,300,302,313,454,474,478,480,483,489,705,810,812,818,828,842,856,860,1169,1179,1189,1213,1732,1736,1738,1762,1763,1768,2249,2281,2288,2454,2456,2463,2465,2470,2488,2639,2642,2811,2968,2971,3031,3127,3490,3546,3551,3552,3554,3559,3569,3573,3575,3579,3619,3852,3859,3863,3869,3878,3882,3977,4139,4218,4230,4236,4238,4244,4325,4373,4379,4380,4390,4457,4459,4469,4471,4473,4761,4763,4773,4776,4778,4791,4795,4799,5111,5120,5146,5454,5468,5475,5479,5481,5483,5487,5668,5669,5675,5681,5689,5697,5699,5702,5705,5710,5723,5728,5868,5877,5880,5886,5888,5903,6047,6061,6066,6068,6080,6082,6094,6099,6102,6117,6279,6288,6314,6451,6474,6477,6481,6501,6505,6512,6513,6526,6528,6532,6590,6683,6685,6688,6689,6707,6710,6714,6716,7005,7011,7015,7017,7066,7068,7091,7131,7214,7228,7229,7231,7233,7241,7261,7262,7264,7266,7277,7279,7280,7537,7588,7591,7594,7598,7608,7610,7617,7622,7626,7778,7907,8089,8098,8107,8164,8248,8442,8445,8447,8653,8734,8754,9712,9716,9736,9738,9743,9753,9908,9915,9999,10012,10083,10086,10087,10107,10111,10113,10114,10116,10117,10122,10128,10132,10423,10429,10443,10445,10450,10455,10458,10459,10463,10469,10471,10475,10485,10488,10490,10494,10497,10499,10510,11139,11150,11156,11320,11338,11348,11488,11499,11510,11512,11516,11520,11670,11679,11682,11697,11702,11705,11706,11709,12134,12346,12440,12459,12462,12471,12478,12485,12487,12492,12493,12496,12497,12500,12504,12667,12673,12687,12833,12841,13175,13306,13308,13311,13315,13477,13494,13526,13532,13535,13537,13541,13555,13712,13719,13721,13733,13735,13736,13740,13741,13743,13745,13747,13755,13757,13760,13761,13763,13777,13779,13780,13782,13787,13793,13795,13797,13799,13800,13804,13957,13969,13972,13975,14142,14311,14343,14349,14358,14360,14361,14379,14572,14583,14895,15039,15044,15048,15052,15054,15057,15060,15070,15072,15076,15081,15085,15088,15251,15257,15269,15273,15275,15427,15431,15434,15436,15440,15443,15614,15744,15749,15946,15960,15971,15988,15990,16153,16156,16159,16161,16166,16167,16170,16172,16174,16176,16177,16179,16182,16185,16186,16187,16205,16207,16209,16211,16213,16216,16218,16221,16236,16241,16249,16251,16256,16260,16267,16273,16278,16427,16434,16448,16616,16619,16927,16928,16959,16960,16963,17126,17132,17144,17151,17153,17158,17320,17327,17480,17484,17493,17499,17521,17524,17525,17527,17531,17534,17539,17542,17544,17545,17703,18133,18177,18178,18182,18509,18541,18834,18988,18991,18996,18998,19002,19325,19329,19332,19333,19336,19531,19693,19866,19876,19878,19880,19883,19901,19906,19909,19911,19926,20081,20090,20104,20106,20109,20114,20122,20261,20266,20627,20955,20972,21137,21331,21347,21352,21609,21726,21896,21899,21915,22477,22483,22652,22668,22671,22674, -chr19 47511426 47524219 m54329U_210326_192251/44827220/ccs 215,472,660,844,1012,1209,1413,1603,1777,1961,2135,2312,2457,2621,2839,2980,3357,4240,4387,4611,4769,4923,5093,5301,5521,5688,5925,6064,6260,6493,6659,6852,7072,7329,7478,7662,7886,8068,8274,8437,8624,8811,9021,9191,9346,9526,9733,9916,10068,10271,10450,10630,10793,10968,11197,11471,11643,11806,12186,12403,12596, 157,106,148,145,138,130,132,135,118,123,160,136,103,136,106,376,168,119,116,146,117,139,168,143,119,140,113,144,135,136,109,122,137,123,131,170,135,141,157,128,148,145,130,147,171,132,129,143,122,128,138,123,142,126,191,142,150,319,149,137,148, 165,372,578,808,989,1150,1339,1545,1738,1895,2084,2295,2448,2560,2757,2945,3356,3525,4359,4503,4757,4886,5062,5261,5444,5640,5828,6038,6208,6395,6629,6768,6974,7209,7452,7609,7832,8021,8209,8431,8565,8772,8956,9151,9338,9517,9658,9862,10059,10190,10399,10588,10753,10935,11094,11388,11613,11793,12125,12335,12540, 50,100,82,36,23,59,74,58,39,66,51,17,9,61,82,35,1,715,28,108,12,37,31,40,77,48,97,26,52,98,30,84,98,120,26,53,54,47,65,6,59,39,65,40,8,9,75,54,9,81,51,42,40,33,103,83,30,13,61,68,56, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,251,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 8,11,15,21,165,168,170,179,182,186,188,191,192,193,203,212,214,372,377,381,383,385,387,391,395,398,409,412,413,415,421,431,433,436,437,439,443,446,451,457,463,471,578,597,606,610,613,617,620,627,637,641,646,659,808,819,821,822,824,826,832,835,836,840,843,989,992,996,1002,1011,1150,1156,1160,1162,1167,1168,1172,1175,1178,1202,1208,1248,1339,1342,1351,1352,1372,1379,1393,1399,1409,1412,1545,1551,1558,1569,1572,1573,1575,1577,1579,1584,1587,1593,1595,1596,1598,1600,1602,1702,1738,1740,1745,1747,1751,1753,1754,1757,1760,1762,1765,1769,1772,1776,1895,1898,1903,1908,1912,1916,1917,1936,1941,1947,1949,1958,1960,2084,2086,2089,2092,2093,2098,2100,2101,2105,2107,2111,2112,2116,2118,2129,2131,2134,2295,2297,2299,2301,2307,2309,2311,2448,2456,2560,2584,2597,2608,2610,2620,2757,2773,2777,2783,2786,2794,2796,2798,2801,2803,2810,2812,2817,2820,2828,2838,2945,2948,2956,2963,2964,2966,2975,2977,2979,3356,3406,3525,3533,3535,3537,3541,3548,3550,3554,3556,3560,3564,3565,3567,3571,3577,3590,3591,3593,3595,3597,3606,3608,3617,3621,3627,3631,3642,3646,3647,3679,3680,3683,3690,3693,3708,3716,3718,3729,3748,3752,3755,3757,3764,3765,3774,3775,3777,3779,3782,3785,3789,3795,3797,3806,3807,3814,3817,3819,3821,3828,3833,3837,3841,3846,3850,3855,3861,3864,3865,3869,3870,3871,3875,3877,3901,3905,3907,3908,3911,3914,3917,3918,3921,3924,3927,3930,3931,3932,3934,3937,3940,3945,3950,3975,3995,3997,4001,4003,4005,4007,4010,4012,4017,4019,4021,4023,4025,4028,4030,4032,4035,4055,4057,4059,4061,4062,4064,4069,4071,4072,4074,4076,4094,4097,4099,4106,4108,4110,4111,4113,4115,4116,4119,4120,4121,4126,4134,4135,4136,4137,4140,4141,4142,4146,4147,4149,4152,4153,4155,4156,4158,4162,4176,4178,4179,4181,4184,4185,4187,4190,4191,4192,4197,4199,4206,4207,4209,4211,4213,4215,4220,4236,4237,4239,4359,4369,4371,4372,4377,4386,4503,4505,4513,4515,4518,4520,4523,4533,4535,4537,4539,4541,4543,4545,4546,4547,4549,4551,4553,4572,4574,4575,4577,4579,4583,4601,4610,4757,4763,4768,4886,4891,4894,4903,4906,4918,4921,4922,5062,5068,5073,5074,5077,5079,5083,5085,5092,5261,5267,5280,5282,5285,5289,5292,5294,5297,5300,5444,5447,5450,5452,5453,5455,5457,5459,5460,5463,5467,5472,5474,5476,5478,5480,5481,5483,5485,5486,5488,5491,5494,5497,5499,5508,5509,5513,5516,5519,5520,5541,5606,5640,5646,5650,5653,5656,5659,5661,5664,5669,5675,5681,5687,5828,5830,5834,5837,5842,5846,5847,5850,5856,5858,5859,5864,5865,5868,5870,5871,5877,5880,5881,5887,5888,5896,5901,5905,5907,5908,5917,5921,5924,6038,6059,6063,6208,6224,6227,6231,6232,6249,6259,6395,6399,6403,6413,6417,6421,6423,6432,6434,6438,6439,6441,6460,6464,6471,6476,6477,6480,6484,6489,6492,6629,6635,6642,6645,6653,6658,6768,6779,6782,6784,6786,6790,6792,6794,6801,6804,6806,6813,6814,6818,6820,6825,6828,6829,6833,6834,6835,6836,6838,6839,6843,6844,6850,6851,6974,6980,6992,6998,7004,7007,7013,7018,7024,7029,7031,7032,7035,7038,7039,7041,7043,7045,7047,7051,7056,7058,7062,7071,7209,7214,7220,7251,7261,7268,7270,7273,7275,7282,7283,7285,7287,7290,7292,7294,7298,7301,7303,7307,7309,7317,7328,7452,7455,7458,7470,7477,7609,7613,7615,7618,7622,7626,7633,7638,7640,7641,7644,7648,7649,7651,7654,7658,7661,7758,7832,7834,7835,7837,7844,7849,7850,7852,7853,7856,7862,7866,7872,7882,7885,8021,8028,8030,8033,8035,8042,8043,8045,8046,8052,8058,8061,8067,8209,8216,8219,8223,8227,8230,8231,8233,8236,8243,8246,8250,8255,8258,8260,8262,8266,8273,8431,8434,8436,8467,8565,8606,8610,8613,8616,8622,8623,8772,8778,8791,8794,8803,8808,8810,8956,8968,8986,8989,8993,8994,8997,9000,9009,9011,9020,9151,9166,9176,9178,9183,9185,9190,9338,9341,9345,9517,9521,9525,9658,9661,9662,9664,9669,9673,9683,9685,9690,9692,9696,9707,9711,9713,9718,9724,9725,9726,9732,9862,9867,9871,9873,9876,9882,9888,9891,9894,9903,9909,9915,10059,10063,10067,10190,10191,10194,10198,10202,10204,10206,10216,10219,10220,10224,10227,10230,10232,10236,10244,10249,10255,10258,10263,10265,10267,10270,10358,10399,10404,10408,10413,10416,10420,10431,10435,10440,10449,10588,10590,10596,10600,10610,10614,10616,10618,10620,10623,10624,10629,10753,10759,10761,10764,10768,10771,10774,10792,10935,10937,10950,10961,10963,10967,11094,11100,11114,11117,11131,11138,11141,11144,11146,11152,11157,11163,11165,11168,11172,11194,11196,11388,11435,11458,11463,11467,11470,11613,11616,11620,11624,11642,11793,11805,12125,12130,12131,12134,12137,12138,12140,12142,12143,12146,12148,12157,12159,12162,12185,12335,12338,12346,12349,12351,12354,12357,12360,12362,12364,12368,12373,12375,12378,12385,12398,12402,12540,12543,12545,12550,12556,12558,12561,12564,12567,12568,12576,12584,12590,12595,12744,12748,12758,12777,12787, -chr19 47511448 47535018 m84039_230401_034725_s4/159777178/ccs 92,271,624,808,927,1094,1464,1702,1836,1946,2128,2288,2445,2676,2947,3269,4317,4614,4827,5306,5481,5653,5823,6044,6205,6419,6570,6923,7120,7334,7516,7669,7960,8079,8238,8405,8620,8707,8879,9077,9300,9502,9719,9854,10021,10214,10381,10540,10711,10896,11226,11670,11806,11977,12478,12638,12809,12959,13140,13326,13567,13737,13877,14078,14174,14296,14466,14687,15070,15215,15524,15800,16055,16201,16383,16518,16706,16868,16954,17240,17431,17585,17828,18025,18204,18378,18564,18810,18950,19112,19326,19485,19685,19829,19927,20035,20204,20583,20740,20955,21131,21280,21480,21638,21807,22011,22172,22349,22518,22627,22886,23108,23267, 140,138,98,118,132,137,79,79,109,149,149,132,111,182,113,145,128,153,426,91,96,114,79,137,156,83,171,194,170,149,132,141,105,120,118,121,86,167,172,171,144,120,106,147,158,125,140,131,108,147,101,135,154,86,93,159,118,141,138,145,134,139,200,95,90,131,129,289,102,136,206,105,134,96,94,131,127,75,234,134,126,146,117,114,93,133,128,106,157,161,152,145,127,97,83,135,81,122,141,135,129,161,137,144,136,98,145,126,108,220,168,130,170, 232,409,722,926,1059,1231,1543,1781,1945,2095,2277,2420,2556,2858,3060,3414,4445,4767,5253,5397,5577,5767,5902,6181,6361,6502,6741,7117,7290,7483,7648,7810,8065,8199,8356,8526,8706,8874,9051,9248,9444,9622,9825,10001,10179,10339,10521,10671,10819,11043,11327,11805,11960,12063,12571,12797,12927,13100,13278,13471,13701,13876,14077,14173,14264,14427,14595,14976,15172,15351,15730,15905,16189,16297,16477,16649,16833,16943,17188,17374,17557,17731,17945,18139,18297,18511,18692,18916,19107,19273,19478,19630,19812,19926,20010,20170,20285,20705,20881,21090,21260,21441,21617,21782,21943,22109,22317,22475,22626,22847,23054,23238, 39,215,86,1,35,233,159,55,1,33,11,25,120,89,209,903,169,60,53,84,76,56,142,24,58,68,182,3,44,33,21,150,14,39,49,94,1,5,26,52,58,97,29,20,35,42,19,40,77,183,343,1,17,415,67,12,32,40,48,96,36,1,1,1,32,39,92,94,43,173,70,150,12,86,41,57,35,11,52,57,28,97,80,65,81,53,118,34,5,53,7,55,17,1,25,34,298,35,74,41,20,39,21,25,68,63,32,43,1,39,54,29, 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-chr19 47511804 47527683 m54329U_210326_192251/134482617/ccs 154,528,707,972,1313,1860,2009,2211,2415,2570,2782,3715,3855,4034,4161,4344,4568,4786,5108,5292,5464,5641,5847,6056,6257,6474,6674,6867,7086,7200,7378,7634,7753,7928,8060,8244,8415,8662,8857,8999,9198,9406,9597,9790,10018,10186,10373,10544,10717,10937,11099,11278,11475,11637,11827,12067,12220,12421,12611,12787,13011,13230,13414,13629,13832,14103,14258,14483,14670,14899,15071,15242,15400,15617, 77,119,88,94,92,88,132,104,105,105,103,115,76,90,128,100,105,106,138,106,94,107,129,121,120,117,108,110,108,119,113,79,132,116,117,95,125,91,125,115,92,78,128,110,97,136,111,142,129,108,124,127,84,97,101,105,136,116,79,91,113,106,127,125,132,102,134,129,106,107,126,97,153,106, 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-chr19 47511839 47526360 m54329U_210323_190418/33229501/ccs 119,278,445,627,797,987,1199,1393,1563,1750,1918,2233,2398,2619,2809,3004,3894,4073,4256,4395,4582,4772,4948,5291,5453,5616,5800,6013,6235,6416,6653,6878,7023,7171,7352,7564,7718,8111,8287,8522,8696,8914,9091,9296,9491,9960,10098,10319,10497,10664,10848,11021,11196,11383,11747,11964,12164,12358,12576,12806,12991,13189,13372,13568,13951,14041, 132,123,137,136,159,125,115,127,139,167,293,137,145,111,83,100,116,125,128,154,167,131,284,119,120,114,143,139,134,121,174,144,147,160,157,138,339,140,156,141,157,144,133,125,264,123,168,115,145,132,97,119,147,299,139,135,165,149,107,117,115,122,154,348,89,265, 100,251,401,582,763,956,1112,1314,1520,1702,1917,2211,2370,2543,2730,2892,3104,4010,4198,4384,4549,4749,4903,5232,5410,5573,5730,5943,6152,6369,6537,6827,7022,7170,7331,7509,7702,8057,8251,8443,8663,8853,9058,9224,9421,9755,10083,10266,10434,10642,10796,10945,11140,11343,11682,11886,12099,12329,12507,12683,12923,13106,13311,13526,13916,14040,14306, 19,27,44,45,34,31,87,79,43,48,1,22,28,76,79,112,790,63,58,11,33,23,45,59,43,43,70,70,83,47,116,51,1,1,21,55,16,54,36,79,33,61,33,72,70,205,15,53,63,22,52,76,56,40,65,78,65,29,69,123,68,83,61,42,35,1,1, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,251,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,251,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 99,115,118,251,269,277,401,409,419,422,423,427,430,435,437,440,444,582,585,588,590,592,595,601,605,607,608,612,617,618,621,625,626,763,773,783,788,790,796,956,960,967,981,986,1112,1122,1124,1132,1138,1141,1150,1154,1156,1159,1160,1164,1166,1171,1174,1176,1178,1180,1182,1185,1187,1198,1217,1288,1314,1317,1331,1333,1337,1339,1340,1343,1346,1348,1351,1356,1358,1360,1362,1364,1365,1368,1371,1392,1520,1538,1544,1546,1548,1550,1552,1559,1562,1702,1724,1727,1729,1741,1749,1917,2211,2212,2214,2217,2220,2227,2229,2232,2370,2374,2381,2390,2397,2543,2551,2553,2555,2562,2564,2566,2570,2575,2577,2579,2581,2586,2587,2592,2603,2605,2608,2611,2618,2730,2733,2738,2740,2741,2743,2745,2747,2749,2754,2758,2762,2764,2766,2769,2771,2776,2777,2778,2779,2783,2784,2790,2793,2797,2801,2803,2805,2808,2892,2898,2902,2907,2915,2918,2920,2924,2938,2942,2946,2950,2952,2954,2957,2958,2961,2964,2967,2969,2973,2974,2977,2986,2993,3000,3003,3104,3122,3135,3147,3151,3152,3154,3158,3177,3178,3180,3182,3184,3185,3189,3193,3195,3204,3208,3211,3214,3218,3229,3233,3234,3241,3244,3245,3248,3251,3253,3255,3261,3266,3267,3270,3277,3280,3295,3303,3305,3313,3316,3325,3335,3337,3339,3342,3344,3351,3353,3362,3364,3394,3401,3404,3406,3408,3410,3415,3420,3422,3424,3425,3428,3430,3433,3437,3440,3442,3446,3448,3451,3452,3456,3457,3458,3462,3464,3465,3488,3492,3494,3495,3498,3501,3504,3505,3508,3511,3514,3517,3518,3519,3521,3524,3527,3532,3537,3543,3556,3562,3564,3579,3580,3582,3584,3588,3590,3592,3594,3597,3599,3604,3606,3608,3610,3612,3615,3617,3622,3631,3640,3644,3646,3648,3651,3656,3659,3661,3665,3680,3683,3685,3692,3693,3694,3696,3698,3701,3703,3707,3708,3709,3714,3715,3716,3718,3722,3723,3724,3725,3728,3729,3730,3734,3735,3737,3740,3772,3773,3785,3787,3792,3795,3797,3801,3803,3808,3814,3816,3819,3821,3824,3825,3827,3829,3831,3833,3835,3838,3839,3840,3842,3849,3850,3851,3854,3856,3857,3869,3873,3877,3879,3889,3893,4010,4012,4026,4029,4034,4037,4041,4043,4045,4047,4050,4054,4058,4072,4198,4208,4210,4212,4215,4224,4228,4231,4232,4234,4244,4246,4249,4250,4254,4255,4384,4386,4392,4394,4520,4549,4550,4554,4555,4556,4559,4563,4564,4566,4570,4575,4580,4581,4749,4751,4755,4757,4760,4762,4771,4903,4922,4924,4926,4928,4929,4931,4933,4934,4936,4939,4940,4944,4946,4947,5232,5234,5238,5241,5245,5247,5249,5252,5253,5257,5260,5263,5266,5269,5273,5275,5277,5282,5285,5290,5410,5416,5418,5420,5422,5425,5426,5430,5435,5438,5441,5442,5444,5446,5447,5452,5573,5576,5579,5581,5582,5585,5589,5591,5594,5610,5615,5730,5740,5744,5746,5748,5752,5754,5771,5773,5775,5781,5783,5787,5792,5793,5794,5796,5799,5943,5971,5973,5976,5977,5983,5984,5988,5990,5991,5992,5995,6000,6004,6006,6008,6010,6012,6152,6156,6172,6174,6175,6179,6180,6182,6185,6205,6208,6210,6213,6218,6227,6231,6234,6369,6372,6374,6380,6383,6384,6390,6391,6392,6394,6396,6403,6408,6410,6415,6537,6539,6540,6547,6552,6555,6556,6558,6562,6566,6569,6570,6572,6575,6576,6578,6582,6585,6586,6588,6590,6591,6592,6594,6597,6599,6600,6603,6604,6606,6608,6614,6619,6621,6622,6625,6628,6629,6631,6633,6637,6639,6646,6648,6652,6827,6829,6830,6833,6835,6837,6838,6841,6843,6845,6851,6855,6858,6860,6863,6865,6869,6875,6877,7022,7127,7170,7331,7333,7339,7341,7345,7351,7509,7513,7521,7524,7526,7534,7537,7542,7545,7558,7561,7562,7563,7650,7702,7708,7714,7717,8057,8059,8075,8081,8084,8085,8088,8090,8091,8094,8096,8098,8110,8251,8255,8258,8259,8261,8266,8273,8274,8276,8279,8286,8372,8443,8448,8452,8455,8457,8460,8464,8466,8473,8475,8479,8481,8485,8486,8487,8489,8492,8493,8496,8510,8514,8521,8663,8669,8671,8674,8675,8678,8679,8681,8684,8687,8690,8691,8695,8853,8877,8880,8884,8889,8892,8908,8913,9058,9061,9063,9065,9080,9084,9088,9090,9224,9247,9253,9256,9257,9259,9264,9268,9271,9278,9280,9285,9287,9291,9295,9421,9433,9434,9439,9442,9448,9451,9453,9458,9460,9461,9463,9467,9469,9470,9472,9473,9478,9484,9487,9490,9755,9779,9781,9785,9786,9789,9793,9797,9799,9801,9811,9814,9815,9819,9822,9825,9827,9831,9835,9836,9837,9839,9841,9843,9844,9845,9846,9850,9853,9855,9858,9860,9863,9866,9869,9870,9872,9874,9876,9878,9880,9882,9885,9892,9893,9897,9899,9901,9904,9907,9910,9913,9918,9921,9922,9924,9927,9930,9942,9944,9949,9959,10083,10089,10091,10097,10266,10272,10289,10296,10298,10318,10434,10448,10458,10460,10464,10467,10469,10486,10491,10493,10496,10642,10646,10661,10663,10796,10819,10821,10823,10824,10827,10830,10834,10838,10840,10843,10847,10945,10955,10962,10968,10969,10973,10986,10992,10995,11001,11014,11020,11140,11145,11148,11151,11153,11157,11173,11175,11178,11182,11185,11192,11195,11343,11346,11349,11355,11380,11382,11682,11684,11689,11707,11711,11713,11714,11716,11719,11720,11724,11727,11728,11730,11731,11734,11738,11740,11746,11886,11898,11901,11905,11909,11927,11931,11934,11937,11945,11950,11953,11963,12099,12100,12102,12104,12107,12125,12129,12130,12139,12140,12142,12144,12149,12150,12151,12153,12155,12157,12160,12163,12329,12335,12339,12341,12343,12347,12349,12350,12352,12357,12507,12510,12512,12514,12516,12518,12521,12523,12527,12528,12531,12534,12538,12539,12542,12544,12545,12547,12548,12549,12552,12557,12575,12683,12705,12737,12739,12742,12746,12750,12753,12758,12762,12765,12766,12768,12773,12777,12779,12783,12786,12788,12789,12802,12805,12923,12925,12927,12933,12935,12939,12942,12943,12945,12949,12951,12955,12958,12959,12971,12977,12985,12990,13106,13110,13117,13119,13125,13127,13131,13139,13140,13141,13145,13149,13152,13165,13167,13170,13171,13175,13179,13184,13188,13311,13327,13339,13342,13345,13350,13354,13356,13360,13367,13371,13526,13567,13916,13944,13950,14040,14306, -chr19 47511875 47531430 m84008_230107_003043_s1/79303852/ccs 89,258,419,552,768,1165,1379,1668,1818,2196,2334,2538,2646,2805,2964,3755,3934,4096,4240,4443,4632,4792,5033,5222,5393,5583,5710,5878,6280,6656,6911,7057,7250,7440,7628,7829,7987,8181,8349,8516,8710,8916,9137,9314,9732,9871,10111,10323,10487,10652,10858,11028,11199,11384,11560,11772,11989,12185,12390,12576,12745,12955,13089,13305,13541,13781,13933,14131,14366,14595,14796,14925,15151,15327,15508,15698,15884,16286,16470,16667,16861,17227,17410,17630,17839,18022,18196,18365,18532,19082,19316, 79,93,101,116,122,88,87,136,266,116,100,107,143,139,106,160,123,141,134,134,98,148,114,106,109,114,143,238,97,125,145,151,128,130,86,104,121,91,81,147,95,128,103,100,105,123,101,121,108,100,116,136,149,104,111,100,126,103,117,112,107,104,150,144,129,113,128,160,105,93,120,132,110,160,107,113,113,103,110,79,86,119,91,114,110,140,100,125,92,89,104, 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-chr19 47512947 47530027 m84039_230404_003541_s3/133760457/ccs 266,488,1454,1921,3169,3758,4515,4684,5475,5995,6551,6908,7095,7846,7978,8179,9200,9549,10320,10541,10726,11282,11437,11834,12210,12409,12638,12997,13781,13963,14338,14499,14674,14844,15022,15200,15368,15555,15737,15922,16104,16489,16698,16874, 108,107,110,111,102,101,102,142,117,105,95,120,113,131,156,117,115,87,101,134,103,116,101,81,142,110,104,129,122,89,150,139,124,99,98,104,115,135,100,103,149,116,111,144, 374,595,1564,2032,3271,3859,4617,4826,5592,6100,6646,7028,7208,7977,8134,8296,9315,9636,10421,10675,10829,11398,11538,11915,12352,12519,12742,13126,13903,14052,14488,14638,14798,14943,15120,15304,15483,15690,15837,16025,16253,16605,16809, 114,859,357,1137,487,656,67,649,403,451,262,67,638,1,45,904,234,684,120,51,453,39,296,295,57,119,255,655,60,286,11,36,46,79,80,64,72,47,85,79,236,93,65, 0,0,0,243,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 1,4,47,49,52,57,59,64,67,69,71,73,75,76,78,80,83,86,91,93,96,99,105,110,113,115,127,181,183,195,207,210,217,219,224,226,232,233,236,239,241,243,244,249,255,257,261,264,265,374,382,384,395,413,415,417,419,420,426,428,431,433,435,437,439,441,443,446,449,452,455,464,480,487,569,595,598,606,608,610,613,614,617,620,622,631,634,639,642,644,651,658,682,695,702,706,731,756,770,773,775,777,779,784,786,788,790,794,796,806,807,809,812,813,818,819,823,826,829,833,834,835,841,845,848,850,852,855,859,862,866,871,874,876,922,924,932,955,986,988,992,1011,1014,1020,1024,1039,1064,1090,1124,1137,1139,1145,1150,1153,1159,1163,1165,1170,1172,1174,1177,1180,1182,1184,1186,1187,1189,1191,1194,1195,1197,1198,1205,1209,1214,1219,1221,1224,1237,1262,1263,1291,1300,1303,1306,1307,1315,1317,1325,1329,1332,1334,1336,1346,1350,1353,1359,1366,1373,1377,1379,1380,1385,1388,1391,1395,1398,1401,1404,1406,1408,1412,1418,1423,1426,1428,1434,1442,1446,1453,1564,1566,1570,1574,1577,1580,1581,1583,1611,1621,1660,1684,1703,1709,1721,1725,1727,1728,1734,1736,1740,1744,1753,1765,1766,1768,1773,1832,1836,1844,1880,1889,1892,1894,1902,1909,1912,1915,1918,1920,1947,1962,2032,2036,2040,2041,2043,2047,2053,2066,2067,2069,2071,2073,2084,2093,2097,2100,2107,2118,2184,2192,2202,2205,2214,2224,2226,2228,2231,2233,2240,2241,2242,2248,2250,2251,2253,2255,2258,2261,2265,2266,2271,2273,2274,2282,2283,2290,2293,2295,2297,2299,2304,2309,2311,2313,2314,2317,2319,2326,2329,2331,2335,2337,2340,2341,2345,2346,2347,2351,2354,2365,2377,2381,2383,2384,2387,2390,2393,2394,2397,2400,2403,2407,2408,2410,2413,2416,2421,2426,2432,2444,2452,2467,2468,2470,2472,2476,2478,2480,2482,2485,2487,2492,2494,2496,2498,2500,2503,2505,2507,2510,2519,2532,2534,2536,2537,2539,2544,2546,2547,2553,2568,2571,2573,2580,2582,2584,2587,2589,2590,2593,2594,2595,2600,2601,2602,2604,2608,2611,2616,2620,2623,2626,2627,2632,2633,2636,2640,2642,2644,2650,2653,2658,2659,2661,2664,2666,2671,2673,2678,2680,2681,2683,2685,2687,2689,2692,2693,2694,2700,2705,2711,2713,2715,2719,2721,2724,2725,2726,2736,2740,2745,2755,2759,2775,2779,2782,2790,2806,2809,2871,2881,2887,2889,2892,2896,2898,2900,2903,2905,2907,2908,2912,2915,2916,2918,2920,2923,2927,2929,2931,2933,2936,2938,2939,2940,2944,2948,2955,2958,2977,2980,3011,3015,3058,3094,3096,3098,3101,3106,3110,3114,3117,3118,3120,3125,3130,3132,3135,3136,3140,3141,3148,3151,3168,3178,3241,3271,3273,3275,3279,3281,3283,3293,3296,3306,3308,3314,3316,3320,3330,3339,3348,3374,3407,3415,3453,3460,3462,3467,3468,3478,3481,3490,3493,3494,3505,3508,3510,3514,3543,3549,3555,3557,3605,3631,3644,3647,3649,3654,3658,3660,3661,3664,3674,3675,3676,3678,3682,3685,3686,3689,3691,3693,3696,3697,3698,3700,3704,3705,3719,3736,3757,3778,3816,3859,3872,3875,3877,3881,3886,3888,3891,3895,3897,3898,3901,3904,3912,3917,3919,3922,3925,3928,3930,3934,3935,3942,3956,3963,3966,3969,3988,3991,3995,4000,4007,4047,4079,4084,4087,4090,4091,4095,4100,4102,4104,4107,4108,4110,4115,4119,4121,4125,4128,4131,4132,4139,4144,4147,4150,4153,4162,4169,4202,4204,4235,4240,4251,4262,4266,4269,4270,4272,4278,4279,4282,4284,4289,4297,4317,4333,4363,4384,4413,4423,4424,4434,4436,4439,4442,4445,4447,4450,4454,4458,4462,4463,4466,4470,4472,4481,4490,4502,4508,4511,4514,4531,4560,4617,4621,4627,4631,4633,4635,4638,4639,4641,4660,4668,4670,4673,4680,4683,4725,4739,4806,4826,4830,4833,4842,4844,4858,4860,4863,4871,4875,4893,4895,4902,4914,4936,4953,4962,4974,4975,4984,4989,4993,4995,4999,5001,5004,5005,5012,5015,5020,5023,5028,5031,5036,5039,5043,5046,5047,5059,5061,5062,5065,5067,5069,5093,5097,5100,5111,5114,5118,5152,5171,5176,5205,5207,5210,5240,5243,5245,5249,5256,5259,5261,5267,5271,5276,5278,5283,5284,5289,5301,5345,5355,5387,5402,5417,5423,5425,5426,5431,5442,5444,5448,5452,5455,5456,5458,5462,5468,5474,5544,5547,5592,5597,5600,5601,5602,5617,5619,5620,5622,5624,5627,5633,5636,5639,5643,5644,5647,5649,5655,5658,5661,5670,5715,5721,5737,5793,5804,5810,5814,5819,5821,5822,5825,5829,5832,5834,5836,5839,5841,5845,5848,5850,5853,5884,5908,5928,5939,5946,5975,5982,5986,5994,6042,6082,6100,6139,6140,6143,6154,6157,6159,6161,6171,6180,6187,6199,6218,6232,6255,6260,6281,6292,6309,6313,6316,6321,6323,6327,6328,6329,6332,6335,6337,6340,6341,6343,6345,6349,6351,6352,6356,6357,6361,6364,6366,6369,6381,6408,6429,6445,6448,6449,6450,6481,6485,6500,6504,6507,6509,6512,6514,6522,6524,6525,6531,6540,6546,6550,6646,6652,6659,6668,6672,6675,6677,6683,6686,6688,6691,6695,6696,6698,6699,6702,6705,6706,6709,6710,6719,6720,6723,6726,6730,6738,6742,6746,6753,6796,6830,6842,6845,6852,6855,6858,6871,6874,6876,6885,6887,6889,6895,6902,6905,6907,6942,6968,7028,7038,7040,7044,7046,7052,7057,7058,7061,7067,7068,7070,7071,7075,7078,7089,7091,7094,7163,7185,7208,7212,7253,7259,7264,7275,7320,7360,7362,7366,7368,7374,7376,7380,7386,7391,7392,7395,7397,7403,7405,7406,7408,7410,7412,7414,7416,7421,7424,7426,7427,7430,7432,7433,7437,7446,7447,7449,7452,7453,7455,7456,7457,7460,7465,7467,7470,7474,7475,7478,7481,7484,7485,7488,7490,7492,7496,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6069,16074,16079,16082,16084,16087,16089,16092,16103,16135,16161,16194,16253,16255,16256,16258,16259,16284,16295,16313,16337,16390,16393,16396,16397,16398,16403,16404,16407,16410,16415,16417,16419,16423,16424,16425,16428,16430,16433,16435,16439,16441,16447,16448,16451,16454,16455,16461,16462,16465,16471,16485,16488,16527,16605,16608,16611,16613,16616,16620,16622,16628,16630,16633,16635,16637,16638,16642,16643,16646,16648,16652,16655,16658,16660,16662,16666,16673,16681,16685,16688,16690,16691,16693,16697,16809,16811,16813,16817,16819,16829,16835,16837,16843,16846,16847,16853,16856,16860,16862,16865,16869,16871,16873,17018,17021,17024,17028,17033,17034,17042,17062,17065,17067,17076,17077,17079,17080,17081,17082, -chr19 47513489 47534420 m64076_210328_012155/11535850/ccs 81,436,606,778,981,1185,1346,2160,2428,2591,2787,2939,3357,3586,3755,3970,4176,4364,4578,4800,4996,5356,5580,5695,5979,6114,6348,6549,6729,6924,7130,7340,7568,7755,7927,8115,8294,8518,8718,8910,9134,9322,9491,9673,9830,10022,10186,10385,10602,10796,11133,11329,11488,11658,11824,11991,12373,12562,12757,12969,13173,13347,13551,13745,13938,14137,14334,14499,14671,14859,15065,15272,15463,15660,15938,16093,16293,16492,16666,16861,17063,17256,17440,17635,17794,18010,18260,18473,18684,18890,19121,19282,19455,19618,20298,20530,20705, 301,124,129,138,114,129,143,153,118,105,129,400,144,140,159,128,131,143,128,119,317,139,114,154,83,145,140,179,159,157,140,124,123,126,122,120,145,134,154,128,120,140,118,135,127,156,134,129,154,281,142,141,127,149,151,325,139,179,168,161,173,162,145,172,141,151,102,140,133,148,163,150,159,155,77,150,143,155,178,174,151,144,162,155,172,131,113,151,136,98,127,126,126,626,98,126,102, 382,560,735,916,1095,1314,1489,2313,2546,2696,2916,3339,3501,3726,3914,4098,4307,4507,4706,4919,5313,5495,5694,5849,6062,6259,6488,6728,6888,7081,7270,7464,7691,7881,8049,8235,8439,8652,8872,9038,9254,9462,9609,9808,9957,10178,10320,10514,10756,11077,11275,11470,11615,11807,11975,12316,12512,12741,12925,13130,13346,13509,13696,13917,14079,14288,14436,14639,14804,15007,15228,15422,15622,15815,16015,16243,16436,16647,16844,17035,17214,17400,17602,17790,17966,18141,18373,18624,18820,18988,19248,19408,19581,20244,20396,20656, 54,46,43,65,90,32,671,115,45,91,23,18,85,29,56,78,57,71,94,77,43,85,1,130,52,89,61,1,36,49,70,104,64,46,66,59,79,66,38,96,68,29,64,22,65,8,65,88,40,56,54,18,43,17,16,57,50,16,44,43,1,42,49,21,58,46,63,32,55,58,44,41,38,123,78,50,56,19,17,28,42,40,33,4,44,119,100,60,70,133,34,47,37,54,134,49, 0,0,0,0,0,0,251,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,242,0,0,0,243,0,0,0,0,0,0, 80,382,384,386,388,390,392,396,398,400,406,410,412,415,418,420,424,427,430,435,560,563,569,572,576,579,581,587,595,600,603,605,735,751,761,766,769,777,916,933,935,940,957,959,962,980,1095,1101,1103,1108,1112,1116,1118,1120,1123,1125,1130,1131,1133,1137,1138,1145,1147,1151,1155,1157,1159,1162,1170,1172,1184,1314,1317,1319,1321,1326,1329,1338,1343,1345,1489,1493,1495,1499,1503,1517,1530,1531,1533,1535,1537,1538,1542,1546,1548,1557,1571,1582,1586,1587,1619,1620,1623,1635,1648,1656,1658,1666,1669,1688,1690,1692,1695,1697,1704,1705,1706,1712,1714,1715,1717,1719,1726,1730,1736,1738,1739,1740,1747,1755,1758,1760,1762,1764,1769,1774,1776,1778,1779,1782,1784,1788,1792,1795,1797,1801,1803,1806,1807,1811,1812,1813,1817,1819,1820,1847,1849,1853,1856,1859,1860,1863,1866,1869,1872,1873,1874,1876,1879,1882,1892,1898,1917,1919,1925,1934,1935,1937,1939,1943,1945,1947,1949,1952,1954,1959,1961,1963,1965,1967,1970,1972,1977,1986,1999,2001,2003,2006,2011,2014,2016,2017,2018,2020,2035,2038,2040,2051,2053,2054,2056,2058,2062,2063,2064,2069,2071,2073,2080,2083,2089,2090,2092,2140,2142,2147,2149,2159,2313,2381,2384,2385,2389,2392,2398,2400,2402,2405,2409,2427,2546,2551,2552,2554,2555,2564,2566,2571,2590,2696,2697,2699,2701,2704,2707,2710,2712,2716,2719,2720,2721,2725,2728,2729,2732,2736,2737,2741,2743,2745,2749,2751,2755,2757,2758,2776,2778,2780,2784,2786,2916,2920,2921,2938,3339,3341,3342,3344,3348,3350,3353,3355,3356,3501,3514,3527,3545,3550,3556,3565,3568,3585,3726,3728,3735,3749,3754,3914,3917,3927,3929,3933,3936,3937,3939,3941,3943,3945,3947,3969,4098,4100,4106,4108,4128,4136,4147,4175,4307,4328,4339,4343,4345,4346,4363,4507,4510,4515,4527,4529,4530,4533,4535,4537,4540,4568,4573,4577,4706,4707,4710,4712,4723,4726,4728,4730,4734,4744,4745,4746,4749,4751,4752,4758,4763,4769,4772,4778,4787,4788,4799,4919,4924,4926,4936,4940,4942,4944,4945,4946,4951,4953,4954,4957,4958,4960,4962,4968,4975,4979,4983,4985,4987,4995,5313,5316,5318,5321,5349,5352,5355,5495,5496,5504,5516,5523,5528,5533,5535,5537,5538,5541,5546,5548,5550,5554,5558,5560,5564,5568,5570,5579,5694,5849,5854,5868,5870,5871,5873,5874,5877,5880,5882,5886,5888,5889,5890,5893,5898,5901,5906,5907,5909,5910,5912,5914,5917,5918,5919,5922,5925,5928,5931,5935,5937,5940,5942,5944,5954,5959,5961,5963,5978,6062,6082,6086,6102,6110,6113,6215,6259,6262,6265,6277,6278,6279,6283,6293,6295,6298,6299,6301,6303,6306,6307,6308,6310,6313,6316,6319,6325,6326,6330,6347,6488,6491,6496,6501,6504,6507,6509,6513,6515,6518,6521,6527,6530,6533,6536,6537,6538,6540,6541,6545,6548,6728,6888,6895,6897,6900,6902,6907,6912,6917,6922,6923,7081,7084,7085,7091,7093,7094,7096,7101,7102,7110,7117,7129,7270,7274,7277,7282,7291,7298,7302,7304,7316,7326,7330,7339,7464,7470,7474,7479,7482,7484,7487,7498,7504,7509,7511,7514,7516,7518,7520,7522,7523,7527,7528,7531,7533,7535,7538,7545,7548,7551,7556,7562,7567,7691,7694,7696,7707,7710,7719,7721,7724,7731,7732,7733,7737,7739,7743,7747,7754,7881,7883,7886,7888,7894,7896,7897,7899,7905,7909,7911,7914,7916,7921,7923,7926,8049,8057,8059,8062,8078,8085,8086,8087,8088,8093,8096,8101,8110,8114,8235,8237,8239,8245,8248,8256,8260,8262,8264,8267,8270,8276,8280,8281,8285,8290,8293,8439,8446,8452,8454,8460,8463,8465,8466,8469,8471,8475,8478,8480,8484,8486,8492,8495,8499,8501,8506,8511,8517,8652,8659,8667,8672,8681,8684,8685,8688,8702,8710,8713,8717,8872,8874,8876,8878,8881,8886,8888,8891,8896,8898,8902,8909,9038,9043,9046,9051,9052,9055,9059,9061,9078,9084,9086,9096,9099,9102,9105,9107,9118,9124,9133,9254,9260,9297,9299,9305,9307,9321,9462,9464,9477,9486,9490,9609,9611,9615,9635,9641,9644,9647,9650,9657,9670,9672,9808,9812,9814,9829,9957,9980,9983,9987,9988,9989,10005,10011,10021,10178,10180,10182,10185,10320,10327,10330,10343,10356,10361,10363,10366,10368,10370,10373,10374,10378,10381,10384,10514,10519,10520,10527,10530,10533,10536,10537,10545,10548,10551,10553,10559,10566,10578,10586,10589,10601,10756,10759,10762,10763,10766,10767,10769,10773,10774,10776,10777,10778,10780,10783,10784,10790,10793,10795,11077,11088,11097,11107,11109,11112,11116,11120,11132,11275,11277,11280,11281,11284,11286,11288,11289,11293,11295,11297,11300,11302,11303,11305,11309,11312,11313,11315,11321,11325,11328,11470,11487,11615,11630,11639,11642,11646,11650,11652,11654,11657,11807,11811,11821,11823,11880,11975,11990,12316,12319,12324,12326,12330,12333,12339,12343,12345,12350,12356,12360,12363,12367,12372,12512,12533,12537,12557,12561,12741,12750,12754,12756,12813,12854,12925,12928,12931,12932,12936,12937,12939,12940,12943,12947,12951,12953,12968,13130,13131,13138,13142,13144,13147,13148,13155,13172,13346,13509,13515,13519,13524,13532,13539,13550,13696,13697,13699,13701,13704,13706,13710,13713,13715,13721,13725,13726,13733,13735,13744,13917,13920,13922,13927,13929,13932,13934,13936,13937,14079,14092,14095,14096,14100,14122,14127,14130,14134,14136,14288,14292,14295,14297,14300,14302,14307,14309,14310,14312,14328,14333,14436,14461,14472,14480,14482,14483,14486,14488,14489,14493,14498,14639,14644,14648,14656,14659,14661,14664,14670,14804,14819,14821,14824,14826,14835,14842,14844,14850,14856,14858,15007,15012,15015,15045,15047,15057,15060,15061,15063,15064,15228,15236,15237,15239,15244,15248,15251,15252,15256,15257,15260,15262,15263,15265,15269,15271,15422,15425,15430,15436,15438,15442,15443,15445,15447,15449,15452,15454,15456,15462,15622,15625,15629,15632,15639,15643,15648,15651,15653,15659,15815,15819,15826,15828,15833,15834,15842,15845,15850,15861,15868,15874,15880,15936,15937,16015,16020,16023,16025,16026,16031,16038,16044,16046,16054,16058,16061,16067,16073,16079,16083,16092,16243,16246,16249,16251,16255,16256,16258,16262,16288,16292,16436,16439,16440,16443,16445,16447,16449,16451,16453,16464,16468,16471,16474,16477,16478,16481,16487,16491,16647,16649,16653,16658,16665,16844,16850,16856,16858,16860,17035,17062,17214,17216,17230,17255,17400,17409,17415,17418,17420,17423,17428,17430,17431,17434,17439,17602,17608,17610,17613,17615,17618,17634,17790,17793,17966,17968,17970,17974,17984,18008,18009,18141,18149,18153,18157,18163,18169,18175,18181,18184,18185,18190,18192,18196,18199,18202,18206,18211,18213,18217,18220,18226,18246,18252,18255,18259,18373,18390,18397,18399,18401,18405,18409,18411,18412,18415,18419,18420,18422,18425,18428,18432,18434,18439,18442,18446,18448,18451,18453,18454,18459,18461,18464,18468,18471,18472,18624,18625,18627,18628,18635,18659,18663,18666,18670,18683,18820,18822,18824,18826,18828,18831,18835,18837,18841,18843,18845,18847,18850,18852,18854,18856,18857,18861,18864,18869,18882,18889,18988,18989,18991,18994,18998,19000,19002,19003,19006,19011,19012,19015,19017,19019,19021,19022,19028,19029,19034,19037,19041,19043,19045,19047,19051,19053,19054,19058,19066,19069,19070,19073,19075,19077,19084,19085,19087,19089,19091,19095,19098,19100,19103,19105,19109,19113,19117,19119,19120,19248,19250,19252,19281,19408,19417,19420,19431,19436,19440,19454,19581,19597,19600,19604,19617,20244,20247,20251,20253,20256,20260,20263,20264,20266,20267,20271,20275,20277,20281,20284,20285,20290,20297,20396,20418,20425,20429,20432,20434,20436,20439,20442,20446,20448,20452,20456,20459,20463,20466,20469,20470,20474,20477,20478,20479,20480,20483,20486,20490,20493,20498,20500,20502,20508,20512,20514,20517,20519,20524,20529,20656,20657,20659,20662,20665,20667,20668,20670,20674,20695,20701,20704,20807,20809,20811,20812,20813,20820,20825,20831,20837,20840,20843,20847,20848,20850,20853,20855,20856,20859,20861,20862,20866,20867,20872,20873,20876,20878,20880,20882,20883,20884,20893,20907,20909,20910,20913,20915,20919,20931,20935,20938, -chr19 47514094 47528406 m84039_230401_031619_s3/149820368/ccs 61,188,349,640,1793,2119,2331,2547,2709,2897,3190,3421,3553,3767,3922,4030,4334,4807,4991,5248,5464,5699,5875,6063,6290,6490,6676,6912,7138,7303,7526,7947,8083,8301,8419,8577,8738,8977,9096,9186,9285,9494,9720,9917,10148,10346,10493,10662,10925,11260,11600,11769,11925,12073,12312,12450,12582,12813,13022,13188,13597,13766,13936,14111, 113,132,114,87,107,94,100,110,118,105,121,101,126,115,77,178,159,133,151,124,116,90,111,113,116,151,126,112,91,116,114,93,98,109,136,121,143,102,89,98,161,142,93,147,101,127,106,131,120,147,90,118,126,167,127,131,177,120,117,156,111,124,139,105, 174,320,463,727,1900,2213,2431,2657,2827,3002,3311,3522,3679,3882,3999,4208,4493,4940,5142,5372,5580,5789,5986,6176,6406,6641,6802,7024,7229,7419,7640,8040,8181,8410,8555,8698,8881,9079,9185,9284,9446,9636,9813,10064,10249,10473,10599,10793,11045,11407,11690,11887,12051,12240,12439,12581,12759,12933,13139,13344,13708,13890,14075, 14,29,177,1066,219,118,116,52,70,188,110,31,88,40,31,126,314,51,106,92,119,86,77,114,84,35,110,114,74,107,307,43,120,9,22,40,96,17,1,1,48,84,104,84,97,20,63,132,215,193,79,38,22,72,11,1,54,89,49,253,58,46,36, 0,0,0,247,0,0,0,0,0,245,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,242,0,0,0,0,0,0,0,0,0,0,0,0,0, 1,4,10,15,18,21,23,25,28,31,35,37,40,42,46,49,56,57,60,103,126,174,176,180,183,187,264,320,322,324,335,346,348,375,412,463,467,476,521,534,548,551,561,573,577,579,580,586,588,592,596,601,603,605,610,612,617,618,620,625,632,639,727,746,754,759,761,763,764,767,770,772,776,778,784,786,787,788,793,799,806,808,814,815,820,853,861,882,952,955,959,970,974,975,982,985,986,989,992,996,1002,1007,1008,1011,1018,1021,1023,1036,1044,1046,1054,1057,1066,1076,1078,1080,1083,1085,1092,1093,1094,1100,1103,1105,1107,1110,1112,1113,1117,1123,1125,1127,1134,1135,1142,1147,1149,1151,1156,1161,1163,1165,1166,1169,1171,1174,1178,1181,1183,1187,1189,1192,1193,1197,1198,1199,1203,1205,1206,1217,1229,1233,1235,1236,1239,1242,1245,1246,1249,1252,1255,1258,1259,1260,1262,1265,1268,1273,1278,1284,1296,1302,1304,1310,1319,1320,1322,1324,1328,1330,1332,1334,1337,1339,1344,1346,1348,1350,1352,1355,1357,1359,1362,1371,1380,1384,1386,1388,1389,1391,1396,1398,1405,1420,1423,1425,1432,1434,1436,1439,1441,1442,1445,1446,1447,1452,1453,1454,1456,1460,1461,1462,1463,1466,1467,1468,1472,1475,1478,1492,1494,1496,1511,1523,1525,1530,1532,1533,1535,1537,1539,1541,1544,1545,1546,1548,1552,1554,1557,1562,1563,1565,1567,1568,1569,1571,1573,1576,1577,1578,1580,1581,1592,1595,1597,1607,1611,1615,1642,1695,1715,1741,1744,1748,1750,1752,1757,1760,1764,1767,1770,1772,1775,1779,1781,1783,1785,1792,1829,1900,1902,1908,1910,1927,1935,1944,1946,1948,1951,1970,1982,1985,1998,2037,2077,2079,2081,2084,2087,2090,2092,2096,2107,2108,2118,2213,2218,2230,2234,2241,2242,2245,2246,2248,2254,2256,2259,2261,2264,2266,2268,2270,2273,2275,2278,2284,2285,2286,2290,2291,2292,2295,2299,2300,2302,2304,2306,2309,2311,2316,2317,2327,2330,2390,2397,2431,2446,2455,2456,2458,2461,2478,2480,2484,2485,2487,2491,2493,2496,2498,2500,2501,2503,2504,2507,2509,2510,2513,2514,2518,2523,2524,2525,2527,2531,2534,2535,2538,2540,2545,2546,2657,2662,2665,2667,2675,2676,2680,2682,2687,2688,2690,2694,2695,2697,2698,2708,2827,2837,2840,2843,2844,2846,2848,2851,2856,2859,2861,2865,2867,2870,2874,2876,2883,2896,3002,3005,3009,3011,3013,3018,3020,3026,3028,3033,3035,3038,3042,3051,3053,3128,3140,3147,3166,3171,3174,3182,3189,3256,3311,3315,3317,3319,3321,3323,3325,3327,3329,3330,3339,3342,3343,3345,3346,3348,3351,3357,3360,3363,3367,3371,3372,3373,3374,3376,3383,3386,3417,3420,3480,3516,3522,3528,3529,3530,3535,3540,3550,3552,3650,3679,3690,3691,3693,3707,3708,3709,3712,3713,3719,3720,3724,3727,3728,3731,3732,3735,3736,3737,3738,3740,3742,3744,3746,3748,3751,3755,3762,3764,3766,3789,3864,3882,3888,3891,3892,3904,3907,3908,3910,3911,3914,3916,3918,3921,3999,4010,4014,4018,4020,4025,4029,4208,4211,4214,4215,4223,4228,4230,4232,4234,4242,4246,4249,4252,4258,4264,4273,4275,4276,4291,4292,4294,4296,4298,4306,4308,4310,4311,4312,4314,4318,4324,4333,4493,4494,4505,4508,4515,4563,4565,4566,4569,4571,4573,4574,4577,4581,4594,4627,4629,4688,4700,4703,4715,4716,4717,4731,4732,4734,4736,4737,4742,4744,4746,4749,4750,4752,4753,4758,4762,4765,4767,4770,4773,4776,4778,4784,4786,4789,4806,4940,4942,4946,4954,4969,4972,4990,5054,5142,5145,5147,5153,5156,5158,5159,5161,5164,5166,5171,5173,5177,5178,5179,5181,5182,5183,5185,5187,5190,5191,5193,5195,5199,5201,5202,5206,5207,5211,5214,5216,5219,5221,5223,5224,5225,5226,5231,5232,5234,5236,5242,5247,5372,5374,5381,5383,5387,5390,5393,5396,5400,5403,5407,5409,5411,5412,5413,5415,5418,5422,5424,5428,5431,5433,5437,5439,5443,5445,5446,5451,5453,5454,5456,5459,5460,5463,5536,5541,5580,5588,5590,5592,5596,5598,5603,5608,5611,5612,5613,5634,5635,5638,5640,5642,5643,5646,5652,5666,5676,5685,5690,5698,5789,5792,5794,5795,5796,5806,5809,5810,5812,5813,5818,5821,5822,5825,5827,5828,5831,5833,5835,5836,5838,5841,5844,5846,5847,5857,5871,5874,5986,5988,5995,6010,6011,6013,6016,6020,6023,6035,6038,6040,6042,6054,6058,6062,6176,6201,6203,6209,6210,6212,6216,6218,6222,6224,6226,6229,6230,6232,6242,6245,6247,6251,6253,6255,6256,6258,6264,6266,6274,6275,6277,6286,6287,6289,6406,6412,6418,6421,6424,6432,6434,6435,6442,6444,6445,6452,6455,6456,6457,6461,6463,6464,6470,6472,6489,6641,6645,6646,6648,6649,6650,6653,6661,6675,6802,6806,6817,6825,6827,6830,6837,6842,6848,6852,6856,6859,6861,6870,6885,6887,6889,6892,6893,6896,6904,6908,6911,7024,7028,7032,7039,7043,7045,7050,7056,7058,7067,7069,7075,7076,7080,7083,7089,7092,7094,7097,7104,7106,7110,7116,7125,7129,7132,7137,7229,7236,7248,7253,7254,7255,7256,7259,7261,7263,7267,7269,7270,7272,7278,7282,7284,7287,7289,7291,7294,7302,7419,7422,7430,7432,7435,7442,7447,7448,7451,7455,7458,7459,7461,7466,7469,7472,7474,7477,7478,7481,7483,7487,7494,7496,7498,7502,7515,7525,7555,7572,7640,7643,7646,7647,7649,7653,7654,7657,7658,7660,7663,7666,7676,7678,7680,7685,7689,7692,7693,7695,7698,7703,7704,7707,7711,7713,7717,7720,7722,7724,7725,7727,7730,7735,7737,7739,7744,7747,7751,7778,7825,7827,7841,7876,7890,7922,7926,7946,8040,8042,8045,8048,8050,8057,8058,8061,8066,8069,8082,8181,8188,8198,8200,8203,8205,8206,8216,8220,8221,8222,8225,8227,8229,8232,8236,8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-chr19 47514095 47525362 m84039_230401_031619_s3/45484832/ccs 141,306,429,602,1532,1769,1900,2098,2221,2378,2564,2814,3180,3384,3598,3718,3858,3979,4403,4597,4757,4876,4995,5543,5628,5739,5950,6137,6390,6526,6698,6900,7051,7225,7367,7493,7696,8059,8199,8329,8515,8626,8807,8971,9075,9214,9630,9769,9923,10137,10377,10492,10704,10904, 115,122,155,123,105,122,124,78,154,116,121,129,126,113,111,118,83,97,145,148,103,118,98,84,110,80,134,100,80,130,131,109,126,139,125,132,158,100,107,135,110,126,115,103,138,177,124,143,151,154,77,127,100,123, 256,428,584,725,1637,1891,2024,2176,2375,2494,2685,2943,3306,3497,3709,3836,3941,4076,4548,4745,4860,4994,5093,5627,5738,5819,6084,6237,6470,6656,6829,7009,7177,7364,7492,7625,7854,8159,8306,8464,8625,8752,8922,9074,9213,9391,9754,9912,10074,10291,10454,10619,10804,11027, 50,1,18,807,132,9,74,45,3,70,129,237,78,101,9,22,38,327,49,12,16,1,450,1,1,131,53,153,56,42,71,42,48,3,1,71,205,40,23,51,1,55,49,1,1,239,15,11,63,86,38,85,100,41, 0,0,0,247,0,0,0,0,0,0,0,0,0,0,0,0,0,246,0,0,0,0,247,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,248,0,0,0,0,0,0,0,0, 0,3,22,24,27,30,32,40,43,44,46,47,54,63,65,68,70,73,82,101,102,104,106,113,114,117,126,133,140,201,256,260,264,270,293,294,305,371,428,584,586,590,594,599,601,682,725,732,739,740,742,744,752,757,759,761,762,765,768,770,774,791,797,818,842,893,916,917,919,921,923,924,928,932,941,948,951,955,966,970,971,982,1014,1032,1040,1050,1053,1062,1072,1074,1076,1079,1081,1088,1089,1090,1096,1108,1109,1113,1114,1119,1122,1130,1131,1138,1141,1143,1145,1147,1152,1157,1159,1161,1162,1165,1167,1170,1174,1177,1179,1183,1185,1188,1189,1193,1194,1195,1199,1202,1225,1229,1231,1235,1238,1241,1242,1249,1253,1254,1256,1259,1262,1267,1272,1278,1290,1298,1303,1312,1313,1315,1317,1321,1323,1325,1327,1330,1332,1337,1339,1341,1343,1348,1350,1352,1355,1364,1372,1378,1380,1381,1383,1394,1397,1412,1415,1417,1424,1425,1427,1434,1436,1441,1442,1455,1456,1461,1500,1501,1513,1515,1520,1522,1523,1525,1527,1529,1531,1578,1637,1647,1650,1658,1661,1663,1669,1671,1683,1684,1686,1687,1694,1701,1703,1710,1712,1717,1718,1728,1730,1733,1737,1739,1744,1746,1749,1753,1756,1757,1759,1768,1891,1893,1899,2024,2028,2031,2032,2034,2036,2038,2040,2042,2074,2077,2097,2176,2178,2181,2184,2187,2190,2191,2194,2198,2200,2203,2205,2208,2217,2220,2345,2375,2377,2494,2499,2501,2502,2505,2515,2522,2525,2529,2531,2533,2536,2537,2542,2544,2545,2563,2685,2699,2702,2712,2714,2715,2717,2726,2735,2738,2759,2768,2812,2813,2888,2943,2981,2985,3043,3045,3072,3081,3102,3106,3112,3114,3118,3119,3122,3124,3129,3131,3137,3143,3152,3153,3157,3160,3161,3164,3168,3170,3172,3173,3178,3179,3306,3312,3316,3318,3321,3328,3330,3342,3348,3351,3363,3371,3379,3382,3383,3497,3499,3508,3520,3524,3526,3530,3539,3540,3542,3547,3550,3556,3557,3558,3561,3564,3570,3571,3573,3574,3577,3578,3591,3593,3597,3709,3717,3836,3857,3941,3950,3954,3969,3972,3978,4076,4079,4085,4092,4095,4097,4099,4101,4107,4112,4114,4117,4119,4120,4126,4127,4131,4133,4138,4141,4156,4157,4163,4164,4166,4168,4170,4176,4177,4181,4186,4187,4191,4197,4206,4216,4218,4220,4223,4228,4230,4232,4243,4249,4252,4253,4258,4260,4261,4266,4267,4268,4269,4272,4277,4279,4281,4291,4295,4297,4299,4302,4303,4306,4307,4309,4311,4312,4315,4318,4320,4321,4324,4325,4326,4327,4340,4342,4343,4346,4350,4373,4376,4402,4548,4549,4552,4554,4556,4562,4564,4574,4579,4582,4584,4588,4596,4686,4745,4748,4750,4756,4860,4875,4994,5093,5116,5156,5162,5165,5166,5173,5174,5176,5182,5184,5185,5190,5193,5194,5197,5199,5204,5207,5208,5209,5215,5217,5219,5222,5224,5225,5229,5230,5233,5238,5241,5244,5246,5250,5257,5262,5265,5273,5276,5278,5281,5282,5285,5291,5294,5298,5302,5305,5307,5309,5313,5315,5322,5326,5332,5336,5341,5415,5425,5441,5445,5449,5465,5473,5474,5476,5482,5488,5491,5494,5500,5504,5509,5512,5515,5518,5523,5531,5538,5541,5542,5627,5657,5720,5738,5819,5828,5848,5850,5852,5855,5869,5875,5877,5880,5883,5889,5892,5895,5898,5899,5901,5902,5904,5906,5909,5911,5920,5922,5925,5928,5934,5935,5937,5945,5949,6084,6090,6092,6102,6103,6106,6112,6115,6120,6122,6125,6128,6133,6136,6191,6234,6237,6251,6255,6268,6270,6278,6280,6283,6284,6286,6287,6288,6291,6298,6301,6302,6305,6306,6309,6312,6327,6331,6366,6389,6470,6482,6487,6489,6492,6494,6496,6498,6501,6504,6509,6517,6520,6525,6656,6664,6668,6674,6676,6685,6697,6743,6829,6833,6837,6840,6846,6848,6852,6861,6868,6870,6892,6896,6899,6977,7009,7031,7037,7048,7050,7111,7177,7188,7199,7224,7364,7365,7366,7492,7573,7625,7645,7648,7658,7662,7667,7671,7675,7695,7854,7858,7885,7892,7895,7898,7914,7972,7978,7981,7984,7986,8004,8007,8009,8040,8058,8091,8159,8170,8185,8198,8306,8328,8438,8464,8467,8472,8477,8478,8480,8483,8487,8493,8503,8508,8509,8511,8514,8597,8625,8699,8752,8775,8780,8783,8784,8787,8804,8806,8839,8854,8922,8930,8933,8937,8941,8944,8948,8950,8959,8962,8964,8968,8970,9041,9074,9146,9213,9391,9393,9403,9405,9407,9408,9410,9416,9433,9434,9436,9439,9442,9444,9445,9448,9451,9457,9458,9460,9463,9466,9476,9478,9481,9484,9487,9490,9491,9496,9500,9502,9504,9511,9515,9518,9528,9530,9532,9542,9543,9547,9549,9550,9551,9565,9567,9569,9573,9580,9584,9589,9592,9595,9598,9601,9603,9613,9618,9629,9659,9687,9754,9758,9768,9912,9922,9995,10074,10076,10077,10093,10102,10105,10109,10123,10130,10136,10187,10216,10274,10291,10302,10305,10307,10320,10371,10376,10454,10458,10462,10470,10474,10477,10480,10482,10485,10489,10491,10619,10623,10626,10635,10637,10639,10647,10651,10655,10671,10674,10676,10679,10684,10687,10694,10698,10703,10804,10815,10819,10823,10828,10830,10832,10838,10840,10844,10848,10852,10853,10854,10859,10865,10873,10876,10878,10880,10888,10892,10897,10901,10903,11027,11048,11052,11055,11067,11132,11218,11234,11238,11241,11242,11243,11244,11245,11246,11247, -chr19 47514312 47539335 m54329U_210810_004956/145688885/ccs 137,351,440,654,1333,1509,1728,1887,2213,2372,2587,2775,2963,3158,3325,3527,3714,4202,4340,4567,4823,5061,5255,5406,5624,5799,5959,6102,6282,6425,6768,6979,7149,7323,7545,7729,8198,8306,8576,8891,9207,9422,9613,9790,9960,10156,10406,10578,10716,10874,11104,11419,11592,11753,11965,12121,12311,12521,12723,12914,13090,13326,13494,13672,13886,14104,14266,14462,14658,14840,15038,15194,15396,15570,15770,15962,16132,16317,16520,16656,16881,17438,17643,17806,17978,18189,18379,18599,18777,18966,19155,19333,19491,19713,19921,20123,20361,20747,20906,21110,21345,21547,21742,21905,22114,22297,22504,22783,22985,23170,23395,23600,23899,24093,24235,24433,24634, 141,88,110,146,118,116,153,290,158,188,136,154,143,151,164,134,214,108,123,255,169,149,132,126,149,129,129,133,142,296,138,116,126,134,127,258,107,215,314,315,164,143,120,126,158,153,107,137,150,150,288,160,151,152,127,144,164,153,135,159,136,136,147,147,156,118,152,128,128,155,130,162,134,152,127,143,161,153,121,154,293,116,162,141,141,103,150,128,139,165,116,124,155,136,163,154,307,135,138,149,139,141,150,125,134,106,146,132,128,140,137,219,110,109,151,137,297, 82,278,439,550,800,1451,1625,1881,2177,2371,2560,2723,2929,3106,3309,3489,3661,3928,4310,4463,4822,4992,5210,5387,5532,5773,5928,6088,6235,6424,6721,6906,7095,7275,7457,7672,7987,8305,8521,8890,9206,9371,9565,9733,9916,10118,10309,10513,10715,10866,11024,11392,11579,11743,11905,12092,12265,12475,12674,12858,13073,13226,13462,13641,13819,14042,14222,14418,14590,14786,14995,15168,15356,15530,15722,15897,16105,16293,16470,16641,16810,17174,17554,17805,17947,18119,18292,18529,18727,18916,19131,19271,19457,19646,19849,20084,20277,20668,20882,21044,21259,21484,21688,21892,22030,22248,22403,22650,22915,23113,23310,23532,23819,24009,24202,24386,24570,24931, 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-chr19 47514327 47528440 m84039_230401_034725_s4/169282444/ccs 131,300,521,1342,1534,1748,1896,2124,2283,2476,2621,2770,2903,3009,3184,3391,3531,3682,4156,4463,4619,4830,5234,5530,5763,5935,6298,6513,6661,7071,7241,7412,7648,7785,7987,8168,8374,8494,8668,8838,9174,9630,9787,9976,10168,10360,10574,10856,10991,11173,11353,11559,11702,11909,12129,12307,12532,12682,12887,13081,13261,13444,13642,13835, 125,111,89,105,128,104,130,129,101,120,117,132,105,146,109,89,93,123,123,106,142,108,105,143,129,97,101,128,110,108,122,141,111,94,144,121,86,143,101,235,113,106,128,115,127,126,139,112,134,102,128,138,143,115,86,149,105,140,133,109,134,139,107,131, 256,411,610,1447,1662,1852,2026,2253,2384,2596,2738,2902,3008,3155,3293,3480,3624,3805,4279,4569,4761,4938,5339,5673,5892,6032,6399,6641,6771,7179,7363,7553,7759,7879,8131,8289,8460,8637,8769,9073,9287,9736,9915,10091,10295,10486,10713,10968,11125,11275,11481,11697,11845,12024,12215,12456,12637,12822,13020,13190,13395,13583,13749, 44,110,732,87,86,44,98,30,92,25,32,1,1,29,98,51,58,351,184,50,69,296,191,90,43,266,114,20,300,62,49,95,26,108,37,85,34,31,69,101,343,51,61,77,65,88,143,23,48,78,78,5,64,105,92,76,45,65,61,71,49,59,86, 0,0,248,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,247,0,0,0,244,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 1,3,6,27,31,42,45,47,53,60,61,63,65,74,76,80,81,85,87,89,91,96,97,99,102,106,107,108,109,113,115,118,121,125,126,128,130,256,258,263,288,293,299,411,416,424,427,429,433,440,447,450,454,458,460,462,465,469,472,474,476,481,484,493,498,518,520,610,611,623,627,631,634,642,650,654,658,659,661,663,665,671,684,685,687,689,691,692,702,711,721,736,740,741,784,802,810,812,820,823,842,846,849,851,858,859,860,866,868,869,871,876,900,901,908,911,915,917,922,927,929,931,935,937,940,944,947,949,953,955,958,959,963,964,969,971,972,983,995,999,1001,1002,1005,1008,1011,1012,1015,1018,1025,1026,1028,1031,1034,1039,1044,1050,1062,1068,1070,1076,1085,1088,1090,1094,1096,1098,1100,1103,1105,1110,1112,1114,1116,1118,1123,1128,1137,1150,1152,1154,1157,1162,1165,1171,1189,1191,1198,1199,1200,1202,1203,1205,1207,1212,1218,1219,1222,1232,1233,1234,1238,1241,1244,1284,1289,1291,1296,1298,1299,1301,1303,1305,1311,1319,1330,1341,1357,1407,1447,1450,1460,1462,1463,1468,1469,1470,1477,1480,1487,1488,1493,1498,1504,1506,1509,1513,1515,1525,1529,1533,1572,1662,1665,1667,1669,1673,1686,1687,1689,1691,1692,1693,1696,1699,1700,1709,1711,1713,1716,1721,1724,1725,1729,1732,1735,1747,1852,1861,1870,1872,1876,1885,1887,1893,1895,1922,1951,2021,2026,2029,2031,2033,2035,2040,2043,2049,2050,2051,2056,2060,2064,2065,2067,2069,2070,2071,2073,2074,2080,2081,2092,2095,2096,2107,2108,2118,2121,2123,2253,2255,2257,2260,2262,2271,2274,2277,2282,2384,2403,2415,2424,2426,2428,2429,2431,2433,2439,2440,2444,2446,2452,2454,2458,2472,2475,2551,2596,2597,2601,2604,2607,2620,2738,2741,2745,2749,2760,2766,2769,2902,2929,2955,3008,3043,3155,3160,3161,3164,3183,3293,3302,3311,3314,3318,3319,3320,3322,3328,3330,3338,3342,3343,3345,3349,3350,3351,3357,3362,3363,3369,3381,3390,3480,3484,3486,3487,3504,3506,3508,3511,3515,3517,3519,3523,3530,3624,3640,3648,3670,3671,3674,3676,3678,3681,3719,3805,3807,3811,3813,3815,3818,3820,3842,3847,3848,3851,3853,3857,3867,3869,3871,3875,3877,3878,3879,3884,3885,3886,3889,3891,3892,3898,3899,3903,3905,3910,3929,3935,4001,4003,4005,4008,4011,4016,4031,4034,4039,4040,4041,4046,4050,4052,4054,4056,4063,4064,4066,4068,4070,4072,4076,4079,4080,4082,4084,4088,4093,4098,4100,4102,4108,4109,4113,4115,4116,4122,4123,4125,4127,4131,4133,4135,4142,4146,4152,4155,4279,4304,4324,4325,4328,4330,4336,4340,4353,4364,4367,4368,4370,4372,4375,4377,4379,4382,4383,4386,4388,4392,4394,4397,4402,4405,4406,4411,4413,4417,4423,4427,4428,4431,4434,4439,4440,4443,4445,4448,4450,4462,4509,4562,4569,4570,4579,4589,4595,4598,4603,4618,4761,4763,4768,4770,4775,4776,4780,4781,4782,4786,4789,4791,4794,4796,4798,4803,4805,4815,4821,4827,4829,4938,4941,4944,4946,4949,4950,4952,4954,4958,4960,4961,4965,4966,4970,4973,4975,4978,4980,4983,4990,4991,4998,5001,5009,5017,5020,5022,5059,5099,5101,5130,5146,5149,5152,5155,5159,5162,5163,5166,5172,5174,5177,5181,5187,5190,5198,5202,5204,5205,5210,5212,5221,5233,5295,5339,5347,5349,5351,5355,5357,5362,5366,5370,5371,5372,5393,5448,5468,5472,5516,5520,5523,5525,5529,5673,5676,5677,5682,5684,5687,5696,5698,5700,5703,5706,5708,5712,5713,5715,5721,5723,5727,5728,5730,5732,5735,5737,5738,5743,5747,5751,5754,5762,5838,5892,5897,5899,5902,5905,5910,5913,5914,5916,5928,5934,6032,6057,6060,6063,6073,6075,6078,6082,6083,6086,6089,6092,6098,6104,6108,6166,6182,6185,6192,6238,6247,6254,6259,6264,6273,6297,6399,6404,6407,6411,6419,6426,6428,6429,6433,6435,6439,6444,6445,6449,6451,6453,6463,6467,6475,6479,6481,6482,6485,6487,6488,6490,6504,6509,6512,6577,6641,6643,6645,6660,6701,6771,6773,6778,6780,6784,6788,6799,6801,6806,6812,6814,6820,6823,6825,6831,6832,6836,6839,6850,6853,6860,6866,6869,6881,6883,6885,6888,6944,6951,6960,6965,6971,6974,6977,6980,6985,6986,6992,6998,7009,7010,7017,7043,7045,7065,7067,7070,7140,7151,7179,7181,7187,7189,7192,7199,7204,7205,7208,7212,7215,7216,7240,7278,7315,7363,7365,7367,7369,7371,7378,7385,7386,7387,7390,7392,7394,7397,7400,7411,7553,7570,7577,7583,7585,7593,7597,7633,7647,7759,7782,7784,7879,7881,7891,7934,7935,7938,7941,7945,7946,7951,7953,7957,7960,7962,7963,7982,7984,7986,8131,8134,8151,8154,8156,8157,8167,8289,8291,8312,8314,8316,8317,8320,8323,8327,8331,8333,8336,8340,8343,8344,8346,8347,8351,8352,8355,8357,8362,8365,8367,8368,8372,8373,8460,8478,8487,8493,8525,8637,8642,8643,8656,8659,8667,8737,8769,8785,8791,8794,8796,8800,8802,8806,8811,8813,8814,8817,8821,8834,8837,9073,9103,9104,9121,9123,9125,9134,9142,9152,9158,9160,9170,9173,9244,9287,9294,9298,9301,9313,9322,9324,9327,9331,9333,9335,9338,9339,9342,9343,9346,9355,9358,9364,9367,9369,9370,9372,9374,9375,9379,9384,9387,9395,9449,9453,9491,9526,9528,9534,9537,9548,9553,9560,9561,9563,9565,9570,9573,9575,9576,9579,9580,9584,9585,9587,9589,9592,9601,9608,9610,9615,9627,9629,9652,9726,9736,9743,9749,9752,9766,9768,9770,9772,9775,9778,9780,9783,9786,9874,9915,9918,9925,9936,9940,9943,9953,9956,9961,9964,9966,9975,10091,10109,10112,10126,10130,10133,10136,10137,10139,10144,10147,10149,10152,10160,10163,10167,10221,10295,10306,10309,10311,10313,10323,10326,10328,10331,10333,10335,10339,10345,10349,10351,10353,10357,10359,10419,10486,10488,10493,10495,10496,10498,10504,10511,10515,10519,10521,10522,10528,10529,10543,10545,10546,10549,10558,10564,10566,10568,10571,10572,10573,10713,10715,10716,10718,10726,10731,10736,10737,10739,10740,10742,10746,10751,10752,10754,10755,10758,10768,10770,10773,10806,10851,10855,10968,10974,10984,10985,10990,11125,11144,11157,11160,11172,11275,11300,11302,11316,11319,11327,11333,11341,11343,11346,11349,11352,11481,11489,11492,11496,11501,11502,11505,11513,11521,11523,11528,11530,11533,11535,11540,11556,11558,11670,11697,11698,11701,11845,11854,11863,11867,11869,11879,11883,11886,11894,11908,12024,12042,12045,12050,12057,12074,12078,12081,12082,12093,12095,12098,12100,12107,12119,12121,12128,12215,12228,12243,12244,12252,12255,12260,12261,12264,12268,12271,12274,12278,12285,12289,12290,12297,12299,12303,12305,12306,12456,12462,12466,12469,12470,12474,12475,12478,12481,12488,12491,12493,12505,12515,12531,12637,12662,12668,12677,12681,12822,12825,12833,12837,12838,12843,12845,12847,12848,12854,12856,12860,12863,12866,12869,12886,13020,13023,13026,13034,13037,13039,13041,13043,13046,13048,13049,13052,13069,13072,13076,13078,13080,13190,13203,13207,13211,13215,13236,13238,13240,13241,13244,13246,13248,13260,13301,13395,13405,13407,13410,13412,13417,13419,13427,13429,13434,13435,13438,13443,13470,13583,13591,13593,13594,13600,13604,13610,13618,13621,13625,13634,13641,13749,13764,13789,13791,13798,13799,13825,13830,13831,13834,13966,13968,13990,13992,13994,13996,13998,14001,14002,14004,14008,14043,14047,14087,14091, -chr19 47514355 47517971 m84008_230107_003043_s1/209457465/ccs 126,328,635,1131,1281,1504,1686,2266,2407,2618,2777,2936,3093, 139,248,140,119,116,145,579,140,136,100,110,150,138, 90,265,576,775,1250,1397,1649,2265,2406,2543,2718,2887,3086,3231, 36,63,59,356,31,107,37,1,1,75,59,49,7,1, 0,0,0,0,0,0,0,0,0,0,0,0,0,0, 90,93,97,98,100,102,108,110,114,118,125,265,266,272,277,279,283,285,287,290,294,298,300,301,312,316,318,319,325,327,576,583,584,592,594,595,596,600,602,604,609,615,617,621,623,627,631,632,634,698,775,805,833,873,881,884,886,888,890,895,900,902,905,908,910,913,917,920,922,926,928,978,1017,1023,1035,1041,1110,1119,1127,1130,1195,1211,1250,1252,1256,1257,1262,1264,1269,1280,1397,1400,1403,1405,1408,1410,1413,1419,1424,1437,1478,1480,1483,1487,1491,1499,1503,1649,1685,2265,2406,2543,2545,2550,2551,2553,2556,2564,2568,2573,2574,2578,2581,2584,2585,2587,2589,2590,2592,2597,2600,2611,2617,2718,2721,2724,2734,2737,2740,2743,2750,2754,2759,2767,2769,2771,2776,2887,2903,2907,2911,2912,2930,2935,3086,3092,3231,3604, -chr19 47514515 47519907 m84008_230107_003043_s1/130946739/ccs 153,314,1021,1340,1633,1845,1991,2153,2355,2520,2733,2904,3071,3309,3535,3694,3907,4074,4267,4417,4588,5024,5189, 84,118,318,281,155,111,152,162,155,140,103,138,188,147,137,159,142,133,109,132,134,132,136, 56,237,432,1339,1621,1788,1956,2143,2315,2510,2660,2836,3042,3259,3456,3672,3853,4049,4207,4376,4549,4722,5156, 97,77,589,1,12,57,35,10,40,10,73,68,29,50,79,22,54,25,60,41,39,302,33, 0,0,249,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 55,65,69,71,76,80,84,86,88,91,93,98,99,100,101,105,106,112,113,115,123,125,127,130,152,237,253,260,267,273,275,279,282,285,287,289,293,294,297,306,313,432,440,442,444,455,457,461,463,467,471,472,474,478,497,498,500,502,504,505,509,513,515,524,528,529,531,534,538,549,553,554,615,623,625,633,636,645,655,657,659,662,664,671,672,673,679,682,684,686,689,692,696,697,702,704,705,713,714,721,724,726,728,730,735,740,742,744,748,753,757,760,762,766,768,771,772,776,777,778,782,784,785,796,808,812,814,818,821,824,825,828,831,834,837,838,839,841,844,847,852,857,863,875,881,883,889,898,899,901,903,907,909,911,913,916,918,923,925,927,929,931,934,936,938,941,950,959,963,965,967,968,970,975,978,984,999,1002,1004,1020,1339,1621,1624,1626,1630,1632,1788,1790,1795,1797,1798,1799,1803,1804,1810,1818,1822,1844,1956,1962,1969,1981,1984,1987,1990,2143,2148,2152,2315,2317,2320,2324,2327,2330,2346,2354,2510,2516,2519,2660,2689,2691,2698,2699,2711,2718,2732,2836,2842,2849,2853,2855,2860,2863,2865,2868,2874,2876,2879,2883,2891,2895,2897,2901,2903,3042,3052,3056,3058,3060,3062,3064,3068,3070,3259,3262,3268,3270,3271,3273,3274,3278,3280,3285,3299,3308,3424,3456,3457,3460,3468,3471,3472,3475,3476,3488,3490,3491,3494,3496,3498,3526,3529,3534,3672,3674,3685,3688,3690,3693,3853,3855,3856,3871,3872,3874,3878,3886,3888,3890,3891,3898,3904,3906,4049,4052,4057,4068,4073,4207,4209,4218,4223,4226,4234,4239,4244,4249,4255,4266,4376,4383,4390,4403,4416,4549,4552,4559,4562,4566,4569,4570,4573,4575,4581,4582,4585,4587,4722,4725,4733,4736,4738,4741,4744,4746,4751,4753,4759,4761,4762,4765,4767,4770,4771,4773,4775,4779,4781,4782,4786,4787,4790,4791,4794,4796,4799,4801,4805,4806,4811,4812,4814,4816,4822,4826,4830,4838,4851,4859,4862,4915,4924,4937,4942,4944,4961,4963,4967,4970,4973,4976,4980,4983,4989,4993,4995,4998,5008,5011,5023,5156,5170,5172,5176,5178,5183,5188,5325,5341,5344,5346,5350,5372,5376,5377,5382, -chr19 47514810 47540310 m84008_230107_003043_s1/189797755/ccs 1049,1144,1332,1495,1642,1853,2007,2158,2350,2524,2871,3040,3203,3450,3768,3934,4124,4281,4451,4644,4914,5121,5318,5496,5665,5830,6015,6247,6498,6659,6872,7025,7231,7419,7673,7896,8110,8270,8453,8631,8775,8991,9174,9371,9571,9763,9971,10170,10352,10515,10721,10901,11071,11430,11609,11791,11989,12165,12366,12567,12753,12944,13141,13331,13546,13707,14061,14260,14470,14668,14870,15118,15273,15450,15656,15820,16016,16183,16375,16566,16772,16909,17136,17345,17569,17775,18159,18362,18531,18749,18916,19109,19302,19516,19751,19897,20074,20268,20475,20636,20836,21024,21211,21420,21563,21752,21925,22094,22358,22563,22723,22922,23103,23314,23474,23670,23865,24099,24292,24437,24622,24787,25012,25174, 94,142,109,143,129,153,116,135,173,290,131,126,165,296,138,189,137,140,172,269,147,116,125,133,153,135,168,136,99,115,143,175,134,157,94,112,84,124,147,131,172,147,160,152,180,151,129,118,144,205,134,122,300,142,139,179,175,178,138,123,121,116,104,131,133,316,146,123,142,149,134,140,129,138,112,155,166,131,145,148,134,148,150,145,176,339,156,130,154,149,141,144,151,141,121,151,155,137,146,172,153,165,169,142,144,140,132,157,117,101,147,134,148,140,154,141,141,122,121,154,145,155,128,154, 147,1143,1286,1441,1638,1771,2006,2123,2293,2523,2814,3002,3166,3368,3746,3906,4123,4261,4421,4623,4913,5061,5237,5443,5629,5818,5965,6183,6383,6597,6774,7015,7200,7365,7576,7767,8008,8194,8394,8600,8762,8947,9138,9334,9523,9751,9914,10100,10288,10496,10720,10855,11023,11371,11572,11748,11970,12164,12343,12504,12690,12874,13060,13245,13462,13679,14023,14207,14383,14612,14817,15004,15258,15402,15588,15768,15975,16182,16314,16520,16714,16906,17057,17286,17490,17745,18114,18315,18492,18685,18898,19057,19253,19453,19657,19872,20048,20229,20405,20621,20808,20989,21189,21380,21562,21707,21892,22057,22251,22475,22664,22870,23056,23251,23454,23628,23811,24006,24221,24413,24591,24767,24942,25140,25328, 902,1,46,54,4,82,1,35,57,1,57,38,37,82,22,28,1,20,30,21,1,60,81,53,36,12,50,64,115,62,98,10,31,54,97,129,102,76,59,31,13,44,36,37,48,12,57,70,64,19,1,46,48,59,37,43,19,1,23,63,63,70,81,86,84,28,38,53,87,56,53,114,15,48,68,52,41,1,61,46,58,3,79,59,79,30,45,47,39,64,18,52,49,63,94,25,26,39,70,15,28,35,22,40,1,45,33,37,107,88,59,52,47,63,20,42,54,93,71,24,31,20,70,34,38, 250,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,243,0,0,0,0,0,0,0, 11,18,147,160,166,168,172,176,177,179,183,202,203,205,207,209,210,214,218,229,233,236,239,243,254,258,259,266,269,278,280,286,291,292,295,302,305,307,320,328,338,341,350,360,364,367,369,376,378,384,418,419,426,429,431,433,440,445,449,453,458,462,465,467,471,473,476,477,481,482,483,489,501,513,517,519,523,526,529,530,533,536,539,543,546,549,552,562,568,586,588,594,603,604,606,608,612,614,616,618,621,646,655,664,668,670,672,675,689,716,718,720,723,725,729,730,746,747,750,752,759,795,809,816,817,819,821,823,825,828,829,830,836,838,840,841,843,851,855,857,860,864,872,876,878,879,881,899,901,906,908,910,911,915,918,920,922,926,932,942,945,947,950,953,955,956,960,969,979,981,989,996,998,1023,1048,1143,1286,1312,1327,1331,1441,1443,1463,1467,1470,1472,1475,1478,1481,1484,1485,1488,1494,1638,1641,1771,1777,1780,1791,1808,1811,1815,1818,1822,1824,1826,1829,1830,1833,1852,2006,2123,2126,2129,2139,2142,2148,2150,2153,2157,2293,2295,2300,2308,2310,2312,2315,2317,2320,2324,2330,2333,2335,2339,2341,2343,2347,2349,2523,2814,2831,2834,2838,2840,2870,3002,3006,3010,3018,3024,3039,3079,3166,3169,3191,3197,3199,3202,3368,3384,3387,3423,3425,3430,3434,3449,3746,3748,3751,3753,3767,3906,3922,3930,3933,4123,4261,4265,4268,4280,4421,4428,4432,4438,4443,4450,4502,4595,4623,4633,4643,4913,5061,5071,5073,5075,5076,5081,5083,5089,5099,5100,5104,5106,5109,5120,5237,5241,5243,5247,5250,5258,5262,5267,5271,5274,5275,5277,5279,5281,5295,5302,5304,5317,5443,5468,5470,5475,5476,5482,5489,5491,5495,5629,5662,5664,5714,5768,5796,5818,5823,5824,5829,5965,5966,5972,5984,5996,6006,6008,6009,6011,6013,6014,6183,6187,6190,6197,6200,6203,6208,6210,6219,6224,6226,6230,6233,6237,6240,6243,6246,6383,6404,6408,6411,6428,6433,6437,6440,6474,6488,6497,6597,6600,6626,6631,6647,6654,6658,6774,6790,6802,6805,6809,6815,6817,6827,6830,6835,6869,6871,6901,7015,7017,7019,7024,7200,7202,7206,7208,7222,7228,7230,7365,7369,7371,7376,7383,7386,7398,7400,7402,7404,7409,7418,7576,7580,7590,7591,7596,7609,7611,7617,7618,7621,7622,7627,7646,7657,7662,7666,7669,7672,7767,7770,7776,7778,7781,7785,7835,7837,7839,7849,7854,7856,7859,7863,7866,7867,7869,7874,7878,7880,7885,7887,7888,7891,7895,7978,8008,8030,8032,8039,8045,8052,8054,8057,8072,8073,8077,8080,8083,8084,8089,8109,8194,8198,8210,8211,8227,8230,8232,8234,8238,8241,8242,8243,8245,8247,8249,8254,8259,8261,8265,8269,8394,8396,8398,8404,8405,8406,8411,8452,8600,8604,8605,8621,8623,8626,8630,8762,8771,8774,8947,8950,8958,8963,8969,8972,8985,8990,9018,9138,9152,9155,9157,9162,9170,9173,9334,9336,9339,9352,9354,9356,9370,9523,9525,9527,9529,9541,9544,9547,9551,9552,9555,9557,9562,9567,9570,9751,9758,9762,9817,9914,9917,9919,9935,9937,9939,9967,9970,10100,10101,10103,10107,10114,10117,10121,10127,10129,10131,10153,10158,10169,10288,10301,10339,10351,10496,10514,10720,10855,10861,10872,10877,10882,10900,10966,10968,11023,11056,11061,11063,11068,11070,11371,11389,11395,11429,11572,11593,11602,11604,11607,11608,11748,11769,11778,11781,11786,11790,11970,11988,12164,12343,12352,12360,12365,12504,12515,12547,12550,12553,12564,12566,12690,12713,12716,12719,12733,12736,12752,12874,12879,12899,12901,12905,12909,12919,12924,12928,12933,12938,12943,13060,13062,13065,13067,13069,13073,13074,13075,13077,13080,13081,13083,13087,13093,13096,13098,13102,13104,13109,13119,13126,13140,13245,13248,13262,13266,13269,13272,13273,13278,13291,13294,13296,13299,13303,13319,13324,13325,13327,13330,13462,13465,13469,13471,13475,13478,13480,13488,13492,13494,13517,13519,13545,13679,13690,13692,13694,13697,13698,13700,13706,14023,14057,14060,14207,14209,14212,14233,14238,14259,14383,14389,14399,14401,14417,14446,14450,14451,14458,14461,14469,14612,14625,14634,14651,14656,14661,14662,14667,14708,14817,14824,14830,14837,14842,14845,14849,14851,14855,14860,14863,14866,14869,15004,15033,15034,15037,15040,15042,15043,15057,15061,15067,15070,15079,15089,15117,15258,15267,15272,15402,15426,15433,15436,15443,15449,15588,15593,15599,15602,15625,15628,15637,15642,15649,15655,15768,15786,15789,15791,15794,15819,15865,15975,15978,16015,16182,16314,16331,16333,16338,16351,16353,16362,16368,16374,16520,16526,16528,16531,16535,16537,16538,16546,16550,16565,16714,16732,16738,16739,16742,16744,16763,16771,16906,16908,16936,17057,17060,17069,17074,17077,17088,17099,17103,17107,17109,17118,17121,17127,17131,17133,17135,17286,17298,17301,17303,17305,17308,17310,17318,17323,17324,17326,17327,17332,17334,17339,17340,17344,17490,17492,17497,17505,17508,17514,17518,17519,17520,17525,17528,17530,17531,17537,17539,17546,17549,17550,17555,17559,17561,17564,17568,17745,17748,17752,17761,17765,17769,17774,18114,18130,18134,18135,18138,18154,18158,18315,18318,18332,18334,18337,18338,18340,18343,18344,18347,18353,18361,18492,18502,18506,18516,18522,18524,18528,18530,18685,18686,18691,18692,18728,18739,18748,18898,18901,18904,18909,18915,19057,19063,19068,19075,19081,19091,19095,19108,19253,19256,19262,19271,19301,19334,19453,19457,19474,19478,19480,19485,19487,19490,19492,19496,19498,19499,19504,19507,19513,19515,19657,19675,19679,19684,19698,19703,19710,19713,19724,19727,19737,19750,19872,19879,19888,19890,19893,19896,20048,20073,20229,20237,20250,20253,20256,20267,20405,20409,20414,20420,20436,20439,20455,20459,20469,20474,20589,20621,20623,20624,20635,20808,20810,20824,20829,20835,20989,20992,20996,21002,21009,21010,21014,21023,21189,21192,21199,21201,21210,21258,21380,21384,21390,21392,21393,21419,21562,21707,21714,21720,21725,21729,21745,21751,21892,21895,21899,21903,21912,21914,21919,21920,21922,21924,22057,22059,22060,22075,22077,22080,22083,22085,22087,22093,22251,22253,22258,22260,22268,22270,22272,22274,22279,22280,22282,22285,22287,22291,22292,22294,22295,22302,22303,22308,22315,22317,22325,22329,22352,22357,22475,22476,22480,22507,22508,22510,22512,22516,22518,22523,22529,22534,22538,22560,22562,22664,22675,22679,22680,22682,22683,22690,22695,22697,22716,22722,22870,22871,22876,22877,22900,22908,22916,22921,23056,23070,23074,23076,23081,23082,23085,23087,23094,23095,23100,23102,23251,23259,23268,23272,23276,23277,23279,23281,23283,23287,23289,23295,23299,23301,23303,23305,23313,23454,23462,23469,23473,23628,23631,23643,23646,23647,23649,23652,23655,23657,23660,23661,23663,23669,23811,23819,23822,23824,23834,23836,23838,23842,23847,23851,23854,23864,24006,24011,24014,24017,24020,24026,24028,24035,24038,24043,24050,24053,24055,24057,24060,24066,24069,24071,24073,24075,24076,24087,24089,24092,24093,24096,24098,24221,24235,24237,24239,24244,24248,24250,24253,24257,24267,24291,24413,24416,24419,24424,24430,24431,24436,24591,24594,24597,24601,24621,24767,24784,24786,24942,24947,24955,24956,24965,24972,24981,24986,24988,25011,25111,25140,25148,25151,25155,25162,25165,25167,25170,25173,25328,25334,25337,25340,25349,25357,25360,25365, -chr19 47514827 47529737 m84039_230404_003541_s3/181208974/ccs 894,1239,1538,1912,2234,2591,2779,3021,3134,3237,3440,3628,3942,4271,4461,4634,5117,5486,5869,6070,6278,6449,6645,6829,7024,7360,7595,7748,7910,8104,8257,8412,8616,8814,9048,9166,9392,9612,9784,9982,10140,10237,10355,10531,10766,10986,11174,11387,11585,11780,11982,12152,12230,12336,12692,12873,13063,13403,13576,13736,13941,14113,14318,14525, 136,284,349,296,350,144,197,112,84,171,150,305,299,151,124,453,355,359,147,150,149,159,127,148,307,154,139,140,193,148,154,180,197,128,117,178,170,138,127,139,96,78,140,222,188,187,212,175,171,191,169,77,86,349,165,162,287,164,155,164,151,170,192,168, 128,1030,1523,1887,2208,2584,2735,2976,3133,3218,3408,3590,3933,4241,4422,4585,5087,5472,5845,6016,6220,6427,6608,6772,6977,7331,7514,7734,7888,8103,8252,8411,8592,8813,8942,9165,9344,9562,9750,9911,10121,10236,10315,10495,10753,10954,11173,11386,11562,11756,11971,12151,12229,12316,12685,12857,13035,13350,13567,13731,13900,14092,14283,14510,14693, 766,209,15,25,26,7,44,45,1,19,32,38,9,30,39,49,30,14,24,54,58,22,37,57,47,29,81,14,22,1,5,1,24,1,106,1,48,50,34,71,19,1,40,36,13,32,1,1,23,24,11,1,1,20,7,16,28,53,9,5,41,21,35,15,39, 251,244,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 1,128,143,155,160,162,164,166,185,186,190,192,193,201,203,212,216,219,222,237,241,242,275,278,303,311,313,320,323,332,342,349,351,358,366,376,384,400,401,408,411,413,415,417,422,427,429,431,435,440,455,458,459,465,469,471,495,501,505,508,511,512,515,518,525,526,528,531,534,544,550,562,568,585,588,590,596,603,623,628,637,646,654,657,662,671,686,689,729,732,733,734,739,741,789,791,796,807,812,820,823,829,831,834,835,837,839,844,854,858,861,863,873,877,881,893,1030,1033,1034,1041,1047,1049,1051,1058,1062,1073,1076,1135,1143,1168,1170,1172,1200,1202,1203,1212,1214,1216,1219,1235,1238,1523,1525,1528,1530,1533,1537,1887,1889,1911,2208,2217,2220,2222,2228,2233,2584,2590,2735,2778,2976,2978,2981,2989,2993,2996,3011,3013,3020,3133,3218,3223,3232,3236,3408,3413,3438,3439,3590,3595,3627,3933,3938,3941,4241,4251,4255,4258,4259,4262,4270,4422,4440,4451,4460,4585,4587,4604,4613,4626,4633,5087,5116,5472,5478,5481,5485,5845,5859,5862,5868,6016,6024,6069,6220,6223,6227,6230,6233,6236,6244,6246,6259,6270,6277,6427,6445,6448,6608,6616,6625,6644,6772,6778,6792,6795,6799,6805,6812,6817,6821,6828,6977,6981,6983,6987,6990,6992,7000,7005,7007,7009,7014,7023,7331,7336,7339,7352,7355,7359,7514,7533,7538,7540,7544,7574,7594,7734,7741,7744,7747,7802,7888,7909,8103,8252,8256,8411,8592,8597,8615,8813,8942,8944,8950,8958,8961,8982,9038,9047,9165,9344,9346,9348,9362,9364,9391,9562,9581,9611,9750,9754,9762,9774,9777,9783,9911,9931,9939,9943,9946,9959,9962,9963,9975,9978,9981,10121,10129,10135,10139,10236,10315,10318,10326,10331,10339,10343,10346,10349,10354,10441,10495,10498,10500,10506,10523,10526,10527,10530,10753,10765,10954,10958,10961,10967,10968,10970,10977,10985,11173,11386,11562,11565,11569,11584,11756,11763,11771,11774,11779,11971,11981,12151,12229,12316,12335,12685,12691,12857,12859,12865,12872,13035,13062,13350,13360,13374,13377,13380,13391,13402,13567,13575,13731,13735,13900,13902,13929,13939,13940,14092,14112,14283,14294,14303,14316,14317,14510,14516,14524,14693,14710,14712,14731,14906,14907,14909,14911,14912, -chr19 47515224 47527520 m54329U_210323_190418/97651167/ccs 431,613,965,1168,1328,1480,1712,1959,2096,2273,2450,2647,2795,2971,3141,3324,3721,3955,4127,4340,4517,4740,4957,5183,5341,5539,5757,5958,6176,6330,6486,6676,6891,7084,7277,7478,7676,7877,8051,8224,8401,8607,8824,8973,9183,9372,9581,9927,10110,10275,10446,10623,10821,10953,11217,11356,11433,11766,11961, 120,257,117,151,151,116,98,127,130,135,118,137,127,135,153,139,134,94,108,116,114,122,129,118,115,133,121,121,110,150,101,131,136,106,107,129,133,134,154,147,162,124,130,159,120,114,281,105,124,166,129,131,128,119,138,76,219,97,128, 551,870,1082,1319,1479,1596,1810,2086,2226,2408,2568,2784,2922,3106,3294,3463,3855,4049,4235,4456,4631,4862,5086,5301,5456,5672,5878,6079,6286,6480,6587,6807,7027,7190,7384,7607,7809,8011,8205,8371,8563,8731,8954,9132,9303,9486,9862,10032,10234,10441,10575,10754,10949,11072,11355,11432,11652,11863,12089, 62,95,86,9,1,116,149,10,47,42,79,11,49,35,30,258,100,78,105,61,109,95,97,40,83,85,80,97,44,6,89,84,57,87,94,69,68,40,19,30,44,93,19,51,69,95,65,78,41,5,48,67,4,145,1,1,114,98,53, 0,0,0,0,0,0,246,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,242,0,0,0,0,0, 36,39,41,44,48,51,53,57,59,62,63,67,68,69,73,75,76,87,103,105,106,109,112,115,116,148,154,167,173,175,181,190,193,195,242,255,257,262,267,276,316,318,323,325,327,331,332,333,334,337,338,339,343,344,346,349,355,356,359,365,367,373,376,378,381,382,384,387,388,389,394,396,401,403,404,406,408,410,412,417,423,425,428,430,551,553,556,566,568,569,574,575,576,583,585,586,592,594,610,612,870,873,879,884,889,890,892,899,900,905,906,908,909,910,913,914,916,918,920,922,924,926,938,940,941,947,948,949,951,953,956,959,962,964,1082,1087,1089,1090,1092,1093,1095,1099,1100,1102,1106,1108,1109,1110,1113,1114,1117,1118,1120,1122,1126,1128,1131,1133,1136,1138,1140,1142,1148,1156,1158,1167,1319,1327,1479,1596,1597,1602,1603,1608,1613,1617,1619,1620,1623,1626,1629,1630,1631,1633,1634,1639,1641,1642,1644,1647,1649,1650,1652,1654,1656,1657,1660,1664,1667,1669,1671,1673,1675,1678,1680,1682,1685,1688,1701,1711,1810,1813,1814,1818,1820,1821,1822,1823,1825,1827,1830,1831,1833,1834,1838,1842,1844,1848,1851,1854,1855,1857,1859,1860,1862,1863,1867,1870,1873,1876,1879,1880,1883,1885,1887,1892,1894,1895,1900,1902,1904,1907,1909,1912,1916,1922,1924,1925,1927,1931,1933,1935,1939,1941,1958,2086,2095,2226,2232,2235,2238,2242,2246,2248,2251,2255,2258,2259,2261,2263,2266,2267,2272,2408,2424,2427,2431,2442,2446,2449,2568,2580,2582,2583,2584,2588,2595,2596,2600,2602,2603,2604,2607,2608,2612,2613,2614,2616,2618,2620,2622,2624,2627,2631,2633,2635,2638,2639,2640,2642,2646,2784,2786,2787,2792,2794,2922,2924,2930,2932,2935,2959,2964,2965,2970,3106,3108,3110,3113,3115,3118,3120,3122,3125,3128,3134,3140,3294,3296,3301,3306,3310,3317,3318,3323,3463,3470,3472,3475,3477,3481,3484,3485,3487,3489,3492,3496,3500,3503,3505,3509,3511,3514,3527,3530,3540,3544,3551,3612,3618,3622,3625,3626,3628,3634,3638,3641,3643,3646,3649,3652,3654,3657,3660,3662,3664,3665,3679,3681,3682,3685,3686,3687,3689,3692,3696,3699,3701,3708,3712,3715,3720,3855,3858,3862,3866,3877,3881,3883,3887,3890,3892,3893,3897,3898,3899,3903,3904,3906,3908,3911,3913,3915,3920,3922,3925,3926,3932,3938,3954,4049,4071,4077,4078,4082,4086,4087,4090,4092,4095,4097,4101,4102,4107,4108,4115,4118,4123,4126,4235,4247,4257,4276,4282,4283,4285,4287,4288,4289,4291,4294,4298,4300,4304,4307,4309,4313,4315,4319,4321,4322,4327,4329,4330,4335,4339,4456,4461,4464,4466,4468,4472,4479,4511,4516,4631,4637,4640,4642,4646,4665,4668,4671,4672,4673,4678,4679,4680,4682,4685,4686,4688,4689,4694,4696,4697,4698,4701,4703,4704,4707,4709,4711,4712,4714,4717,4719,4720,4722,4723,4733,4734,4739,4862,4864,4868,4871,4874,4876,4880,4886,4887,4889,4892,4896,4899,4901,4902,4908,4911,4915,4917,4923,4924,4925,4926,4927,4931,4935,4939,4947,4949,4950,4954,4956,4986,5086,5087,5089,5103,5106,5107,5109,5110,5113,5119,5122,5124,5127,5128,5130,5132,5133,5135,5137,5138,5143,5152,5154,5157,5159,5160,5163,5164,5166,5179,5182,5301,5311,5329,5340,5456,5470,5476,5481,5486,5489,5491,5498,5500,5506,5538,5672,5677,5679,5683,5694,5698,5702,5704,5724,5725,5729,5733,5736,5739,5744,5756,5878,5882,5885,5892,5894,5899,5901,5916,5943,5957,6079,6088,6093,6097,6099,6100,6102,6103,6108,6111,6114,6117,6120,6140,6146,6147,6152,6154,6175,6286,6288,6305,6309,6311,6313,6318,6319,6324,6329,6480,6485,6587,6601,6607,6616,6618,6621,6624,6629,6631,6633,6638,6641,6642,6645,6648,6651,6654,6657,6659,6661,6664,6666,6669,6675,6807,6810,6814,6816,6820,6822,6840,6842,6844,6846,6849,6850,6854,6855,6856,6869,6872,6884,6889,6890,7027,7035,7052,7056,7058,7059,7064,7072,7075,7078,7082,7083,7190,7194,7205,7218,7223,7225,7231,7232,7235,7236,7241,7248,7253,7254,7260,7266,7267,7271,7272,7276,7384,7390,7392,7395,7399,7428,7442,7445,7449,7451,7454,7457,7460,7464,7470,7473,7477,7607,7615,7617,7623,7626,7632,7639,7643,7647,7648,7649,7651,7654,7658,7660,7664,7667,7671,7672,7675,7809,7823,7825,7826,7829,7834,7842,7845,7849,7853,7856,7858,7860,7862,7864,7874,7876,8011,8013,8023,8035,8039,8042,8050,8205,8216,8223,8257,8371,8372,8387,8390,8400,8563,8566,8574,8579,8582,8585,8588,8590,8592,8596,8601,8606,8731,8733,8736,8745,8751,8752,8754,8758,8759,8762,8763,8764,8765,8768,8769,8771,8773,8778,8779,8782,8784,8786,8789,8792,8795,8798,8804,8810,8812,8823,8954,8964,8968,8970,8972,9132,9133,9137,9140,9142,9144,9146,9148,9161,9164,9168,9175,9182,9303,9305,9308,9312,9317,9318,9320,9321,9328,9333,9334,9336,9338,9339,9368,9371,9486,9490,9494,9496,9498,9500,9502,9527,9530,9531,9534,9536,9539,9540,9543,9545,9547,9548,9549,9552,9554,9559,9561,9564,9580,9862,9870,9875,9880,9881,9883,9890,9896,9899,9902,9912,9914,9926,10032,10034,10047,10049,10061,10062,10065,10067,10069,10073,10075,10077,10079,10081,10102,10109,10234,10241,10247,10249,10252,10253,10267,10269,10271,10274,10441,10445,10575,10578,10582,10589,10591,10594,10609,10615,10619,10622,10754,10759,10761,10762,10772,10773,10777,10792,10796,10798,10800,10801,10803,10806,10807,10808,10809,10812,10814,10816,10820,10949,10952,11072,11078,11080,11083,11087,11090,11092,11093,11095,11096,11100,11101,11103,11109,11113,11116,11123,11136,11141,11144,11148,11155,11160,111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-chr19 47515304 47543596 m54329U_210814_130637/78972153/ccs 343,470,740,893,1054,1248,1421,1579,1787,1933,2125,2546,2716,2893,3072,3305,3485,3833,4243,4651,5021,5220,5417,5597,5825,6014,6190,6382,6686,6887,7172,7311,7476,7706,7852,8019,8214,8401,8589,8746,8957,9141,9337,9532,9717,9892,10297,10533,10682,10885,11084,11305,11495,11682,11886,12070,12250,12443,12628,12841,13019,13191,13365,13558,13753,13939,14172,14295,14383,14509,14690,15171,15334,15609,15743,16337,16531,16677,16876,17109,17249,17769,17947,18299,18465,18657,19214,19438,19614,19820,20011,20234,20421,20601,20829,20987,21180,21379,21577,21780,21968,22186,22372,22569,22766,22941,23133,23324,23569,23725,23915,24113,24267,24484,24709,24900,25043,25276,25436,25751,26044,26258,26447,26699,27077,27255,27457,27634,27827, 126,127,134,145,176,149,136,153,134,191,376,111,167,112,181,143,308,409,397,355,179,174,179,200,176,154,153,303,165,139,129,126,151,139,166,178,147,152,156,189,172,147,149,156,166,398,210,148,172,175,199,110,159,173,136,176,192,171,165,151,164,173,192,141,152,158,105,87,87,136,480,159,274,133,572,150,140,158,131,119,487,126,332,150,164,552,223,175,163,169,158,137,161,154,138,172,159,155,173,145,160,121,113,109,108,131,160,117,129,130,122,130,149,117,124,125,156,130,144,290,158,158,174,377,149,185,176,141,176, 469,597,874,1038,1230,1397,1557,1732,1921,2124,2501,2657,2883,3005,3253,3448,3793,4242,4640,5006,5200,5394,5596,5797,6001,6168,6343,6685,6851,7026,7301,7437,7627,7845,8018,8197,8361,8553,8745,8935,9129,9288,9486,9688,9883,10290,10507,10681,10854,11060,11283,11415,11654,11855,12022,12246,12442,12614,12793,12992,13183,13364,13557,13699,13905,14097,14277,14382,14470,14645,15170,15330,15608,15742,16315,16487,16671,16835,17007,17228,17736,17895,18279,18449,18629,19209,19437,19613,19777,19989,20169,20371,20582,20755,20967,21159,21339,21534,21750,21925,22128,22307,22485,22678,22874,23072,23293,23441,23698,23855,24037,24243,24416,24601,24833,25025,25199,25406,25580,26041,26202,26416,26621,27076,27226,27440,27633,27775,28003, 1,143,19,16,18,24,22,55,12,1,45,59,10,67,52,37,40,1,11,15,20,23,1,28,13,22,39,1,36,146,10,39,79,7,1,17,40,36,1,22,12,49,46,29,9,7,26,1,31,24,22,80,28,31,48,4,1,14,48,27,8,1,1,54,34,75,18,1,39,45,1,4,1,1,22,44,6,41,102,21,33,52,20,16,28,5,1,1,43,22,65,50,19,74,20,21,40,43,30,43,58,65,84,88,67,61,31,128,27,60,76,24,68,108,67,18,77,30,171,3,56,31,78,1,29,17,1,52,28, 0,246,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,249,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,249,0,0,0,0,0,0,0,0,0,0, 7,19,29,32,35,36,39,42,44,47,48,49,51,54,57,62,67,73,84,90,92,98,107,108,110,112,116,118,122,125,134,138,140,143,184,186,187,193,208,211,213,220,224,227,233,234,235,240,241,242,244,248,251,254,260,263,266,272,276,280,282,284,290,292,293,295,298,299,301,304,311,313,318,323,329,342,424,469,597,600,609,617,619,620,623,627,629,632,634,641,653,657,659,663,665,687,688,690,692,715,716,723,739,874,883,892,1038,1041,1043,1053,1230,1245,1247,1397,1400,1403,1404,1409,1418,1420,1557,1559,1562,1565,1570,1574,1575,1578,1732,1744,1746,1749,1750,1752,1757,1761,1770,1774,1786,1921,1927,1932,2124,2501,2503,2507,2513,2514,2518,2525,2526,2536,2538,2542,2545,2657,2682,2689,2704,2705,2710,2712,2715,2883,2892,3005,3022,3029,3032,3037,3039,3047,3055,3062,3068,3071,3253,3263,3265,3266,3268,3273,3276,3289,3304,3448,3450,3459,3463,3464,3466,3470,3484,3793,3825,3832,4242,4640,4650,5006,5020,5200,5212,5219,5394,5416,5596,5797,5824,6001,6013,6168,6175,6189,6343,6381,6685,6851,6879,6886,7026,7029,7031,7040,7044,7057,7059,7062,7064,7067,7068,7072,7074,7078,7083,7085,7087,7088,7092,7095,7096,7100,7104,7106,7108,7115,7120,7130,7133,7135,7141,7142,7146,7152,7159,7171,7301,7303,7310,7437,7444,7473,7475,7627,7635,7637,7639,7645,7646,7647,7649,7652,7653,7655,7656,7665,7670,7674,7676,7679,7681,7684,7689,7692,7694,7705,7845,7847,7851,8018,8197,8213,8361,8364,8378,8387,8397,8400,8553,8558,8564,8566,8574,8575,8588,8745,8935,8956,9129,9133,9140,9288,9292,9304,9307,9310,9312,9315,9319,9336,9486,9496,9499,9502,9504,9521,9526,9529,9531,9688,9706,9711,9712,9716,9883,9886,9891,10290,10292,10296,10507,10517,10522,10532,10681,10854,10865,10884,11060,11073,11083,11283,11304,11415,11416,11418,11464,11466,11469,11471,11474,11494,11654,11656,11681,11855,11862,11882,11885,12022,12049,12067,12069,12246,12249,12442,12614,12627,12793,12799,12809,12812,12815,12820,12833,12840,12992,13003,13007,13009,13018,13183,13186,13190,13364,13557,13699,13730,13732,13742,13750,13752,13905,13910,13922,13929,13933,13938,14097,14099,14118,14119,14123,14126,14144,14148,14153,14171,14277,14294,14382,14470,14473,14481,14483,14487,14502,14508,14553,14645,14648,14655,14675,14683,14686,14687,14689,15170,15330,15333,15608,15742,16315,16331,16336,16487,16497,16499,16501,16504,16509,16511,16514,16517,16530,16671,16676,16835,16850,16854,16872,16875,17007,17020,17022,17035,17039,17041,17054,17057,17077,17079,17088,17092,17095,17099,17108,17179,17228,17230,17236,17243,17248,17736,17741,17745,17747,17751,17754,17760,17766,17768,17866,17895,17898,17904,17908,17910,17915,17920,17922,17946,18279,18289,18294,18298,18380,18449,18460,18464,18629,18632,18636,18642,18646,18649,18653,18656,19209,19213,19437,19613,19777,19781,19785,19798,19801,19804,19808,19813,19819,19989,19991,19995,19996,19997,20000,20002,20006,20008,20010,20169,20171,20196,20197,20202,20206,20208,20211,20212,20214,20233,20371,20382,20406,20413,20414,20417,20420,20582,20588,20590,20600,20755,20777,20791,20803,20806,20825,20828,20967,20971,20986,21159,21179,21339,21342,21343,21349,21350,21356,21375,21378,21534,21554,21576,21750,21754,21779,21925,21938,21939,21946,21951,21957,21967,22128,22132,22135,22136,22142,22156,22162,22167,22171,22185,22307,22312,22316,22332,22338,22350,22363,22371,22485,22492,22495,22498,22500,22501,22525,22544,22549,22551,22554,22558,22568,22678,22684,22695,22702,22727,22731,22733,22735,22737,22741,22748,22752,22755,22757,22765,22809,22856,22874,22881,22888,22889,22891,22894,22897,22901,22909,22911,22915,22917,22920,22927,22933,22940,23027,23072,23076,23100,23102,23105,23109,23112,23114,23117,23129,23132,23293,23295,23300,23306,23315,23323,23441,23445,23451,23475,23478,23481,23487,23490,23493,23496,23500,23509,23513,23521,23526,23568,23669,23698,23704,23719,23720,23724,23855,23860,23866,23878,23885,23891,23894,23897,23903,23907,23914,24037,24043,24055,24059,24062,24064,24067,24069,24074,24084,24086,24088,24112,24243,24246,24257,24264,24266,24294,24416,24422,24441,24443,24445,24449,24452,24458,24459,24469,24472,24483,24601,24606,24608,24613,24615,24621,24623,24625,24626,24630,24633,24640,24644,24646,24649,24652,24667,24669,24683,24687,24689,24691,24693,24697,24698,24701,24705,24708,24833,24835,24840,24844,24846,24852,24859,24863,24867,24869,24884,24892,24899,25025,25029,25042,25199,25204,25218,25219,25221,25228,25230,25234,25237,25240,25265,25269,25271,25275,25406,25435,25580,25584,25587,25601,25619,25621,25622,25627,25628,25634,25640,25646,25650,25653,25655,25658,25669,25670,25672,25675,25676,25679,25682,25683,25685,25688,25692,25694,25696,25697,25703,25704,25714,25719,25729,25733,25750,26041,26043,26202,26215,26232,26234,26236,26238,26240,26243,26247,26249,26254,26257,26416,26420,26424,26428,26446,26621,26622,26632,26651,26654,26657,26662,26696,26698,27076,27226,27250,27254,27440,27446,27451,27456,27633,27775,27780,27800,27808,27814,27822,27826,28003,28005,28018,28030, -chr19 47515325 47525397 m64076_210328_012155/64620793/ccs 315,745,1096,1234,1386,1525,1738,1936,2353,2746,2939,3096,3293,3483,3629,3807,3955,4109,4337,4732,4908,5063,5234,5480,5602,5830,6013,6217,6389,6554,6748,6921,7070,7218,7430,7612,7771,7939,8136,8321,8503,8686,8869,9005,9235,9398,9592,9781, 101,197,122,117,129,129,123,107,107,124,81,129,134,145,133,109,153,107,81,106,101,121,132,99,86,103,98,77,108,145,134,123,134,91,96,116,134,162,147,138,152,129,132,165,116,138,139,118, 416,942,1218,1351,1515,1654,1861,2043,2460,2870,3020,3225,3427,3628,3762,3916,4108,4216,4418,4838,5009,5184,5366,5579,5688,5933,6111,6294,6497,6699,6882,7044,7204,7309,7526,7728,7905,8101,8283,8459,8655,8815,9001,9170,9351,9536,9731,9899, 329,154,16,35,10,84,75,310,286,69,76,68,56,1,45,39,1,121,314,70,54,50,114,23,142,80,106,95,57,49,39,26,14,121,86,43,34,35,38,44,31,54,4,65,47,56,50,77, 0,0,0,0,0,0,0,243,0,0,0,0,0,0,0,0,0,0,244,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 8,11,14,15,18,21,24,27,28,31,34,37,42,47,53,66,73,75,81,93,95,123,128,133,142,155,157,159,162,167,170,172,176,195,197,204,205,206,208,209,211,213,217,218,219,228,232,233,234,235,238,239,240,244,245,247,250,251,252,253,254,256,257,260,264,266,268,274,276,277,279,282,283,285,288,289,290,296,303,305,308,310,312,314,416,433,436,439,441,444,446,447,449,451,453,455,457,460,469,470,472,473,478,479,480,487,489,490,492,497,498,503,514,516,519,523,525,527,530,532,535,542,617,620,622,629,635,637,639,641,643,645,647,648,649,651,653,670,671,674,676,677,679,681,685,687,698,699,703,704,705,709,712,721,723,725,744,942,956,963,968,971,974,976,977,981,985,987,990,992,994,995,996,998,1000,1001,1002,1004,1005,1007,1011,1013,1014,1015,1018,1019,1022,1023,1025,1027,1028,1033,1036,1038,1041,1043,1045,1047,1053,1062,1063,1064,1068,1069,1070,1073,1080,1095,1218,1225,1233,1351,1374,1385,1515,1520,1524,1654,1656,1663,1668,1676,1683,1689,1699,1709,1720,1721,1725,1737,1861,1863,1865,1867,1868,1870,1872,1873,1884,1885,1886,1890,1892,1894,1895,1896,1899,1900,1902,1904,1908,1909,1912,1914,1917,1919,1921,1924,1927,1928,1933,1935,1970,2043,2053,2054,2056,2059,2061,2064,2066,2069,2075,2077,2080,2084,2088,2090,2092,2093,2096,2106,2110,2132,2198,2201,2204,2210,2211,2213,2216,2218,2223,2225,2226,2227,2229,2233,2235,2237,2240,2241,2243,2247,2251,2253,2255,2257,2259,2261,2263,2265,2268,2269,2271,2286,2288,2290,2291,2292,2295,2296,2297,2298,2303,2304,2309,2310,2311,2313,2314,2316,2328,2330,2331,2333,2337,2338,2341,2344,2345,2348,2352,2460,2471,2472,2474,2475,2476,2479,2482,2483,2484,2486,2488,2489,2490,2493,2494,2500,2501,2505,2507,2508,2509,2512,2513,2518,2523,2525,2527,2529,2532,2536,2538,2540,2543,2545,2547,2553,2619,2623,2625,2645,2657,2658,2661,2665,2666,2669,2672,2673,2676,2677,2683,2684,2685,2688,2689,2691,2692,2695,2696,2697,2699,2702,2728,2731,2736,2745,2870,2874,2876,2878,2887,2890,2892,2894,2898,2901,2902,2903,2922,2934,2938,3020,3027,3029,3032,3035,3041,3043,3047,3050,3051,3052,3053,3056,3058,3059,3070,3075,3077,3079,3081,3089,3093,3095,3225,3226,3230,3231,3234,3236,3239,3248,3251,3253,3256,3258,3261,3262,3264,3265,3267,3269,3270,3272,3273,3277,3278,3281,3283,3284,3286,3289,3292,3427,3438,3448,3452,3453,3455,3456,3459,3463,3466,3468,3470,3472,3473,3475,3479,3482,3628,3762,3765,3777,3787,3797,3799,3804,3805,3806,3916,3925,3936,3947,3949,3954,4108,4216,4220,4222,4226,4228,4229,4231,4234,4236,4237,4238,4240,4243,4244,4246,4247,4251,4255,4258,4267,4268,4273,4275,4276,4278,4280,4284,4286,4288,4290,4293,4294,4296,4297,4302,4306,4309,4311,4315,4317,4320,4325,4332,4336,4418,4422,4433,4436,4442,4444,4445,4450,4473,4476,4479,4493,4541,4554,4576,4578,4581,4586,4587,4588,4590,4593,4594,4596,4602,4604,4605,4606,4609,4611,4612,4614,4615,4617,4619,4620,4622,4625,4627,4628,4630,4631,4641,4642,4647,4651,4653,4655,4658,4662,4663,4664,4665,4667,4670,4672,4674,4678,4686,4695,4698,4701,4702,4704,4705,4707,4709,4712,4714,4715,4719,4721,4723,4728,4731,4838,4842,4846,4855,4857,4858,4859,4862,4864,4865,4868,4869,4894,4907,5009,5011,5014,5015,5017,5026,5029,5030,5032,5035,5036,5038,5040,5041,5043,5045,5046,5051,5060,5062,5184,5187,5190,5192,5195,5196,5199,5200,5202,5205,5208,5211,5216,5218,5228,5230,5233,5366,5367,5369,5371,5374,5377,5380,5382,5383,5388,5393,5394,5396,5398,5399,5405,5410,5412,5413,5415,5416,5418,5423,5425,5429,5430,5432,5433,5434,5437,5440,5441,5445,5449,5450,5452,5454,5459,5461,5465,5467,5477,5479,5579,5584,5601,5688,5690,5708,5713,5719,5721,5725,5729,5731,5735,5737,5738,5740,5742,5745,5757,5759,5761,5766,5768,5769,5774,5777,5778,5780,5782,5785,5789,5792,5793,5799,5806,5808,5812,5816,5829,5933,5938,5942,5948,5950,5954,5955,5960,5970,5971,5973,5975,5980,5982,5985,5989,5991,5992,5995,6000,6003,6012,6111,6114,6116,6122,6124,6128,6132,6141,6143,6145,6146,6147,6150,6153,6155,6156,6157,6160,6164,6168,6169,6170,6172,6174,6176,6178,6180,6183,6184,6197,6201,6203,6205,6215,6216,6294,6301,6303,6307,6308,6311,6315,6319,6321,6333,6336,6337,6341,6344,6347,6349,6353,6356,6357,6358,6359,6363,6365,6366,6368,6372,6375,6380,6382,6385,6388,6407,6426,6497,6506,6508,6511,6513,6516,6521,6523,6525,6530,6533,6539,6549,6551,6553,6699,6702,6706,6708,6712,6714,6718,6732,6734,6736,6747,6882,6886,6889,6901,6904,6920,7044,7049,7050,7054,7069,7121,7204,7209,7210,7213,7217,7309,7314,7315,7320,7343,7348,7351,7354,7357,7358,7362,7364,7367,7371,7375,7377,7382,7383,7386,7388,7393,7395,7396,7398,7399,7403,7404,7406,7411,7414,7416,7417,7419,7420,7429,7526,7545,7548,7552,7554,7558,7561,7563,7565,7566,7569,7573,7582,7586,7589,7590,7592,7593,7611,7665,7728,7736,7739,7743,7747,7750,7752,7754,7756,7762,7765,7770,7905,7924,7933,7936,7938,8101,8102,8107,8112,8116,8117,8119,8133,8135,8283,8286,8309,8320,8459,8462,8470,8475,8478,8481,8484,8486,8488,8492,8502,8655,8664,8682,8685,8815,8818,8820,8823,8826,8831,8840,8854,8864,8866,8868,9001,9004,9170,9173,9176,9177,9179,9182,9184,9187,9189,9192,9194,9198,9200,9203,9207,9213,9215,9216,9221,9222,9228,9229,9231,9233,9234,9351,9361,9366,9368,9371,9373,9375,9379,9381,9384,9389,9391,9393,9395,9397,9536,9544,9551,9553,9555,9557,9559,9561,9562,9565,9566,9568,9569,9573,9586,9589,9591,9731,9739,9745,9749,9753,9755,9756,9758,9761,9763,9766,9780,9899,9906,9909,9912,9915,9921,9923,9927,9930,9938,9940,9943,9945,9952,9965,9975, -chr19 47515526 47530633 m64076_210328_012155/70713469/ccs 110,243,659,1164,1400,1629,1798,1959,2203,2360,2546,2727,2886,3079,3233,3399,3593,3778,3930,4139,4334,4506,4687,4882,5097,5292,5439,5647,5867,6037,6177,6386,6548,6724,6950,7096,7240,7397,7598,7743,7940,8094,8313,8519,8743,8832,9049,9302,9483,9667,9856,10069,10224,10448,10583,10798,10983,11172,11417,11602,11788,12208,12418,12579,12786,12978,13121,13370,13554,13752,13971,14172,14375,14523,14733,14913, 116,415,498,215,224,163,137,135,127,158,123,156,138,142,160,149,136,120,140,139,114,180,135,125,129,107,148,131,124,139,143,128,142,147,145,89,127,143,135,149,127,165,117,135,88,179,176,117,110,109,112,123,149,132,153,133,157,176,104,91,137,129,143,148,125,132,130,132,136,94,125,105,101,178,146,153, 226,658,1157,1379,1624,1792,1935,2094,2330,2518,2669,2883,3024,3221,3393,3548,3729,3898,4070,4278,4448,4686,4822,5007,5226,5399,5587,5778,5991,6176,6320,6514,6690,6871,7095,7185,7367,7540,7733,7892,8067,8259,8430,8654,8831,9011,9225,9419,9593,9776,9968,10192,10373,10580,10736,10931,11140,11348,11521,11693,11925,12337,12561,12727,12911,13110,13251,13502,13690,13846,14096,14277,14476,14701,14879,15066, 17,1,7,21,5,6,24,109,30,28,58,3,55,12,6,45,49,32,69,56,58,1,60,90,66,40,60,89,46,1,66,34,34,79,1,55,30,58,10,48,27,54,89,89,1,38,77,64,74,80,101,32,75,3,62,52,32,69,81,95,283,81,18,59,67,11,119,52,62,125,76,98,47,32,34,16, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,250,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 40,41,43,46,50,53,56,59,61,63,69,72,74,77,78,79,81,84,85,86,91,93,103,105,109,226,229,234,237,239,242,658,1157,1159,1163,1379,1399,1624,1628,1792,1797,1935,1948,1952,1955,1958,2094,2099,2106,2108,2116,2125,2129,2130,2131,2133,2136,2137,2140,2144,2147,2151,2153,2154,2156,2160,2161,2164,2174,2183,2193,2199,2200,2202,2330,2332,2335,2336,2337,2339,2342,2343,2354,2356,2358,2359,2518,2521,2524,2542,2545,2669,2670,2673,2680,2683,2685,2687,2691,2693,2700,2702,2703,2705,2707,2714,2719,2721,2726,2883,2885,3024,3028,3029,3030,3036,3043,3047,3048,3050,3052,3078,3221,3232,3393,3398,3548,3553,3555,3558,3562,3565,3566,3569,3578,3581,3583,3585,3587,3592,3729,3732,3739,3747,3749,3753,3754,3755,3758,3759,3761,3766,3767,3769,3771,3774,3777,3898,3900,3902,3906,3929,4018,4070,4072,4076,4082,4088,4098,4101,4103,4109,4112,4117,4121,4122,4125,4128,4132,4138,4278,4284,4285,4311,4313,4315,4317,4328,4331,4333,4448,4451,4460,4465,4479,4484,4485,4488,4491,4494,4502,4505,4686,4822,4824,4828,4830,4832,4833,4835,4837,4838,4839,4841,4843,4846,4847,4851,4852,4853,4854,4855,4858,4860,4861,4864,4865,4867,4874,4877,4881,5007,5025,5032,5044,5045,5051,5061,5087,5089,5096,5226,5227,5230,5231,5235,5237,5238,5242,5248,5252,5265,5269,5272,5273,5275,5277,5287,5291,5399,5407,5409,5413,5430,5434,5438,5587,5597,5604,5606,5610,5621,5625,5627,5646,5703,5778,5784,5790,5791,5793,5794,5805,5808,5811,5813,5814,5829,5831,5837,5838,5840,5843,5845,5847,5848,5850,5851,5853,5854,5856,5866,5991,5996,6002,6004,6009,6015,6017,6020,6036,6176,6320,6324,6350,6352,6355,6356,6357,6360,6376,6378,6385,6514,6518,6528,6532,6534,6536,6538,6541,6542,6547,6690,6693,6695,6699,6705,6716,6723,6790,6871,6878,6882,6942,6949,7095,7185,7186,7189,7191,7196,7198,7201,7202,7207,7208,7210,7215,7224,7228,7231,7233,7239,7367,7369,7373,7390,7394,7396,7433,7540,7543,7545,7547,7551,7552,7554,7555,7558,7560,7566,7567,7569,7572,7574,7578,7581,7597,7733,7740,7742,7892,7905,7910,7912,7920,7925,7936,7939,8067,8071,8086,8089,8092,8093,8259,8262,8265,8276,8284,8287,8289,8291,8295,8302,8305,8312,8430,8432,8435,8444,8451,8453,8457,8458,8461,8462,8463,8464,8467,8470,8472,8477,8481,8483,8485,8488,8491,8494,8497,8503,8506,8509,8518,8654,8661,8665,8667,8669,8671,8675,8678,8681,8683,8685,8688,8704,8714,8721,8725,8735,8742,8831,9011,9025,9026,9027,9032,9033,9035,9037,9048,9225,9231,9237,9244,9246,9248,9249,9253,9255,9257,9260,9263,9265,9272,9275,9281,9285,9288,9289,9296,9301,9419,9425,9430,9432,9433,9435,9445,9447,9449,9455,9457,9458,9461,9477,9480,9482,9593,9602,9609,9615,9617,9627,9629,9642,9645,9647,9653,9658,9666,9776,9778,9780,9782,9784,9803,9806,9808,9810,9813,9816,9817,9823,9824,9825,9826,9828,9834,9835,9838,9840,9841,9846,9852,9855,9968,9969,9970,9972,9975,9980,9991,9994,9997,10002,10007,10021,10022,10027,10028,10040,10042,10044,10046,10048,10051,10052,10054,10066,10068,10192,10200,10205,10210,10214,10216,10220,10223,10373,10378,10380,10383,10385,10388,10390,10392,10398,10400,10402,10406,10408,10410,10414,10416,10447,10580,10582,10736,10753,10756,10761,10763,10766,10769,10771,10774,10775,10785,10787,10790,10794,10797,10931,10956,10972,10978,10982,11140,11145,11149,11152,11154,11160,11161,11163,11166,11167,11171,11348,11362,11366,11368,11373,11377,11379,11381,11384,11388,11391,11392,11394,11395,11397,11398,11400,11416,11521,11537,11538,11555,11558,11561,11562,11565,11567,11569,11571,11573,11577,11580,11589,11590,11594,11598,11601,11693,11701,11716,11719,11722,11724,11733,11735,11739,11741,11742,11745,11748,11749,11751,11753,11754,11758,11760,11763,11765,11766,11769,11778,11781,11783,11784,11785,11787,11925,11930,11932,11934,11936,11938,11939,11942,11944,11946,11950,11954,11957,11959,11962,11964,11967,11971,11972,11974,11975,11979,11981,11982,11983,11986,11990,11991,11993,11996,11999,12000,12001,12004,12006,12007,12011,12015,12019,12022,12024,12033,12035,12036,12039,12046,12059,12062,12092,12094,12096,12097,12104,12110,12111,12120,12123,12125,12126,12129,12131,12134,12135,12139,12142,12145,12147,12150,12157,12163,12171,12174,12175,12190,12194,12202,12207,12337,12340,12347,12352,12356,12357,12359,12363,12366,12367,12372,12376,12377,12384,12392,12395,12397,12417,12561,12571,12575,12578,12727,12731,12734,12738,12742,12743,12746,12753,12762,12768,12770,12785,12911,12917,12924,12933,12934,12936,12939,12943,12945,12949,12973,12977,13110,13116,13119,13120,13154,13251,13255,13256,13258,13267,13270,13273,13275,13276,13282,13284,13286,13287,13291,13293,13296,13299,13301,13302,13304,13305,13307,13310,13312,13324,13330,13332,13334,13336,13337,13339,13341,13343,13345,13347,13350,13354,13356,13360,13363,13365,13369,13502,13520,13522,13523,13525,13527,13529,13530,13535,13538,13540,13543,13545,13553,13690,13692,13695,13697,13698,13702,13709,13711,13714,13726,13728,13731,13733,13740,13747,13751,13846,13849,13852,13855,13861,13864,13867,13872,13874,13876,13880,13882,13886,13887,13888,13891,13893,13897,13899,13905,13906,13909,13912,13913,13917,13919,13920,13923,13925,13926,13927,13929,13939,13941,13943,13945,13946,13951,13954,13957,13959,13965,13968,13970,14096,14104,14106,14110,14113,14116,14118,14120,14124,14129,14131,14143,14146,14148,14149,14151,14155,14158,14164,14171,14277,14281,14287,14301,14304,14305,14318,14320,14323,14325,14327,14329,14331,14346,14348,14350,14353,14357,14364,14374,14476,14479,14482,14500,14513,14515,14517,14520,14522,14701,14705,14709,14715,14721,14729,14732,14879,14881,14907,14912,15066,15082, -chr19 47515617 47528492 m84039_230404_003541_s3/134221345/ccs 148,325,767,1029,1213,1473,1670,1883,2025,2138,2338,2677,2911,3047,3249,3380,3577,3776,3962,4111,4318,4488,4650,4840,4982,5310,5651,5815,6022,6237,6420,6599,6744,6951,7097,7298,7454,7636,7814,7988,8171,8363,8623,8862,9010,9192,9367,9524,9727,9895,10069,10239,10390,10620,10922,11067,11248,11464,11650,11859,12055,12293,12396,12575, 111,119,109,172,128,85,100,124,112,173,92,112,123,111,130,79,75,136,104,114,111,137,154,139,128,113,102,122,102,122,134,138,142,100,155,124,131,143,131,113,98,126,117,97,101,126,116,119,116,162,115,150,124,144,121,112,163,106,150,130,114,102,149,143, 112,259,444,876,1201,1341,1558,1770,2007,2137,2311,2430,2789,3034,3158,3379,3459,3652,3912,4066,4225,4429,4625,4804,4979,5110,5423,5753,5937,6124,6359,6554,6737,6886,7051,7252,7422,7585,7779,7945,8101,8269,8489,8740,8959,9111,9318,9483,9643,9843,10057,10184,10389,10514,10764,11043,11179,11411,11570,11800,11989,12169,12395,12545,12718, 36,66,323,153,12,132,112,113,18,1,27,247,122,13,91,1,118,124,50,45,93,59,25,36,3,200,228,62,85,113,61,45,7,65,46,46,32,51,35,43,70,94,134,122,51,81,49,41,84,52,12,55,1,106,158,24,69,53,80,59,66,124,1,30,33, 0,0,0,0,0,242,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,246,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,2,19,112,136,147,217,259,261,263,278,288,291,294,307,310,313,317,324,444,447,450,455,460,462,465,466,470,471,478,481,487,492,526,528,585,600,622,623,625,626,643,645,649,651,653,659,663,668,671,674,677,680,683,684,688,690,693,695,697,698,707,710,714,716,718,721,722,725,726,728,730,731,746,748,750,764,766,833,876,877,886,896,899,923,933,934,935,946,964,970,972,975,977,986,1008,1021,1025,1028,1201,1212,1341,1343,1346,1350,1352,1356,1358,1364,1372,1376,1377,1379,1404,1406,1412,1415,1416,1420,1424,1425,1427,1429,1432,1433,1440,1444,1446,1450,1457,1469,1472,1558,1581,1585,1591,1594,1595,1599,1604,1609,1612,1619,1622,1623,1628,1630,1632,1634,1637,1638,1642,1646,1649,1655,1657,1664,1669,1730,1757,1770,1773,1777,1785,1789,1791,1793,1797,1799,1801,1804,1819,1820,1868,1882,2007,2008,2024,2137,2311,2313,2321,2334,2337,2430,2439,2442,2455,2458,2464,2468,2471,2475,2490,2492,2495,2514,2518,2520,2531,2591,2604,2610,2617,2626,2630,2633,2635,2636,2640,2641,2647,2648,2652,2654,2655,2658,2662,2666,2671,2676,2789,2795,2804,2806,2807,2810,2815,2825,2827,2828,2831,2835,2837,2852,2863,2866,2878,2881,2887,2889,2910,3034,3046,3158,3162,3165,3168,3170,3173,3177,3199,3201,3202,3204,3206,3207,3212,3214,3219,3232,3240,3243,3248,3379,3459,3467,3513,3522,3523,3531,3534,3545,3547,3551,3574,3576,3652,3662,3670,3675,3683,3685,3688,3690,3693,3694,3708,3711,3716,3719,3721,3722,3724,3727,3730,3732,3736,3740,3743,3748,3756,3759,3760,3762,3767,3768,3769,3772,3775,3912,3914,3922,3928,3929,3936,3953,3961,4066,4073,4078,4081,4083,4104,4105,4110,4150,4225,4227,4240,4262,4264,4266,4267,4272,4273,4274,4276,4279,4280,4283,4288,4292,4295,4297,4301,4317,4429,4433,4449,4455,4457,4459,4466,4484,4487,4625,4643,4649,4685,4804,4819,4823,4837,4839,4943,4979,4981,5110,5122,5134,5143,5144,5147,5149,5152,5155,5158,5163,5177,5189,5193,5195,5196,5201,5202,5204,5210,5219,5221,5223,5224,5225,5227,5233,5235,5243,5248,5250,5253,5271,5273,5288,5291,5309,5357,5423,5426,5430,5433,5435,5439,5455,5456,5461,5464,5465,5467,5469,5472,5476,5479,5521,5563,5568,5596,5600,5603,5605,5608,5617,5620,5625,5632,5635,5637,5638,5650,5753,5755,5758,5765,5767,5770,5772,5773,5778,5780,5782,5798,5800,5808,5810,5814,5937,5940,5945,5948,5949,5954,5967,5969,5970,5992,5996,6000,6021,6092,6113,6124,6127,6130,6133,6146,6150,6155,6159,6162,6163,6165,6167,6173,6174,6177,6181,6183,6187,6190,6192,6194,6195,6197,6200,6205,6207,6209,6221,6223,6224,6230,6232,6234,6236,6269,6359,6361,6364,6379,6382,6385,6389,6391,6395,6397,6401,6411,6415,6417,6419,6554,6558,6560,6564,6565,6569,6572,6575,6584,6587,6589,6595,6598,6737,6743,6886,6891,6895,6901,6910,6911,6915,6918,6924,6926,6950,7051,7055,7068,7073,7075,7076,7078,7079,7083,7086,7091,7094,7096,7218,7252,7268,7271,7272,7289,7297,7422,7426,7430,7433,7435,7447,7449,7453,7480,7585,7591,7611,7614,7616,7622,7625,7635,7702,7779,7785,7786,7813,7945,7946,7949,7959,7961,7964,7987,8101,8104,8108,8112,8137,8140,8156,8159,8162,8164,8166,8170,8269,8288,8291,8294,8297,8298,8302,8305,8307,8310,8314,8319,8326,8328,8332,8333,8339,8342,8343,8345,8362,8489,8490,8492,8496,8497,8500,8503,8507,8508,8522,8523,8525,8528,8541,8543,8545,8549,8561,8562,8578,8588,8591,8599,8601,8609,8622,8740,8759,8764,8793,8795,8837,8861,8959,8966,8969,8971,8978,8984,8987,8991,9003,9006,9009,9111,9124,9126,9128,9140,9143,9146,9156,9159,9162,9167,9172,9175,9178,9186,9189,9191,9318,9332,9334,9342,9346,9350,9353,9366,9483,9487,9512,9523,9550,9643,9647,9649,9651,9653,9671,9676,9678,9681,9691,9693,9696,9700,9701,9702,9707,9719,9726,9843,9847,9860,9873,9876,9894,10057,10060,10062,10065,10068,10184,10208,10211,10227,10229,10238,10275,10389,10514,10517,10538,10541,10544,10573,10619,10764,10794,10837,10847,10849,10898,10921,11043,11045,11056,11061,11062,11066,11179,11183,11218,11220,11221,11223,11232,11234,11236,11240,11247,11348,11411,11412,11414,11415,11418,11420,11422,11424,11436,11440,11445,11447,11456,11458,11460,11462,11463,11518,11570,11593,11602,11611,11613,11625,11635,11637,11639,11647,11649,11675,11800,11806,11810,11813,11820,11823,11835,11847,11857,11858,11989,12000,12008,12025,12032,12036,12048,12052,12054,12169,12173,12186,12195,12198,12201,12205,12214,12221,12224,12230,12241,12257,12261,12271,12275,12292,12335,12395,12545,12559,12571,12574,12617,12674,12704,12718,12728,12740,12750,12841,12855,12856,12857,12859,12860,12861, -chr19 47515639 47536773 m64076_210328_012155/69403730/ccs 86,252,496,722,915,1116,1281,1673,1869,2108,2384,2886,3255,3358,3537,3991,4135,4299,4484,4653,4896,5062,5241,5458,5648,5843,6267,6413,6639,6844,6998,7138,7281,7690,7822,7997,8217,8432,8657,8896,9053,9222,9405,9614,9775,9971,10164,10333,10521,10715,10902,11066,11219,11406,11607,11796,11960,12125,12338,12531,12860,13037,13208,13452,13648,13841,14015,14247,14416,14592,14698,14834,15019,15193,15335,15534,15715,15866,16062,16659,16868,17058,17291,17483,17643,17797,18031,18246,18437,18643,18845,19053,19203,19390,19555,19752,19982,20168,20516,20655,20825,20997, 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-chr19 47516423 47523540 m84008_230107_003043_s1/127407090/ccs 215,368,528,692,860,1068,1258,1410,1584,1837,1988,2163,2359,2479,2676,2869,3099,3274,3436,3621,3807,4008,4209,4397,4596,4789,5007,5177,5313,5570,5851,6075,6263,6561, 126,136,138,160,140,141,133,167,127,105,163,122,112,175,172,147,146,146,140,175,136,142,138,166,133,147,114,121,175,131,97,131,262,354, 132,341,504,666,852,1000,1209,1391,1577,1711,1942,2151,2285,2471,2654,2848,3016,3245,3420,3576,3796,3943,4150,4347,4563,4729,4936,5121,5298,5488,5701,5948,6206,6525,6915, 83,27,24,26,8,68,49,19,7,126,46,12,74,8,22,21,83,29,16,45,11,65,59,50,33,60,71,56,15,82,150,127,57,36,1, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 131,158,162,164,169,195,198,207,210,212,214,341,347,352,354,356,362,367,504,508,511,514,515,527,666,669,672,675,681,683,691,852,859,1000,1021,1049,1053,1057,1060,1067,1209,1225,1227,1257,1391,1409,1577,1578,1583,1711,1723,1741,1747,1748,1753,1754,1757,1759,1763,1769,1772,1774,1803,1804,1809,1812,1836,1942,1953,1960,1972,1976,1978,1987,2151,2162,2285,2291,2305,2310,2331,2347,2353,2356,2358,2471,2478,2654,2657,2669,2673,2675,2848,2852,2858,2868,3016,3023,3058,3065,3068,3078,3080,3083,3098,3214,3245,3255,3257,3261,3263,3273,3420,3426,3431,3435,3462,3576,3579,3581,3582,3587,3611,3618,3620,3796,3801,3803,3806,3943,3947,3948,3950,3957,3982,3986,3992,3996,4001,4003,4007,4150,4157,4162,4169,4176,4181,4208,4347,4375,4390,4396,4563,4566,4570,4573,4576,4595,4729,4730,4748,4764,4770,4774,4788,4936,4948,4950,4953,4961,4969,4975,4981,5006,5121,5127,5129,5132,5149,5165,5176,5298,5312,5488,5508,5522,5526,5530,5533,5534,5543,5549,5551,5554,5566,5569,5701,5722,5738,5744,5746,5748,5753,5779,5783,5787,5789,5792,5803,5811,5819,5843,5850,5948,5952,5959,5990,5998,6010,6017,6021,6023,6046,6048,6050,6074,6152,6206,6211,6214,6225,6227,6230,6234,6237,6238,6245,6251,6262,6525,6560,6915,7048,7064, -chr19 47516482 47530674 m84039_230401_031619_s3/178849005/ccs 69,305,438,665,752,894,1104,1243,1384,1580,1995,2124,2316,2416,2573,2723,2863,3058,3216,3365,3541,3720,3898,4091,4288,4467,4650,4859,4995,5187,5363,5534,5746,5912,6083,6451,6596,6804,6963,7169,7540,7714,8103,8464,8690,8871,9040,9258,9422,9571,9803,10152,10343,10539,10718,10901,11072,11338,11472,11617,11777,11990,12163,12441,12551,12775,12969,13162,13315,13495,13670,13850, 117,113,114,75,141,145,104,112,110,130,111,93,92,136,144,139,171,119,148,110,124,102,118,118,117,88,85,103,93,77,120,106,111,132,87,109,128,118,125,85,131,110,92,101,125,142,140,105,113,144,80,128,140,110,150,94,265,101,144,76,127,111,117,87,146,121,105,110,101,125,79,120, 186,418,552,740,893,1039,1208,1355,1494,1710,2106,2217,2408,2552,2717,2862,3034,3177,3364,3475,3665,3822,4016,4209,4405,4555,4735,4962,5088,5264,5483,5640,5857,6044,6170,6560,6724,6922,7088,7254,7671,7824,8195,8565,8815,9013,9180,9363,9535,9715,9883,10280,10483,10649,10868,10995,11337,11439,11616,11693,11904,12101,12280,12528,12697,12896,13074,13272,13416,13620,13749,13970, 119,20,113,12,1,65,35,29,86,285,18,99,8,21,6,1,24,39,1,66,55,76,75,79,62,95,124,33,99,99,51,106,55,39,281,36,80,41,81,286,43,279,269,125,56,27,78,59,36,88,269,63,56,69,33,77,1,33,1,84,86,62,161,23,78,73,88,43,79,50,101,45, 0,0,0,0,0,0,0,0,0,251,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,3,4,6,11,57,58,68,132,167,186,199,218,220,223,225,226,227,230,232,234,235,238,240,241,243,244,247,249,250,253,256,259,262,265,268,271,272,276,279,281,283,304,418,426,429,435,436,437,552,553,564,566,569,570,572,577,583,587,590,594,601,606,609,615,618,624,631,639,664,740,751,779,893,1039,1048,1050,1055,1058,1061,1065,1067,1069,1073,1075,1079,1085,1087,1089,1093,1097,1101,1103,1170,1201,1208,1213,1214,1220,1224,1231,1233,1240,1242,1355,1357,1359,1361,1364,1370,1377,1379,1383,1454,1494,1504,1520,1522,1523,1526,1528,1530,1533,1546,1556,1558,1561,1562,1566,1570,1572,1575,1579,1710,1717,1720,1722,1728,1731,1732,1737,1738,1744,1745,1751,1752,1756,1758,1763,1766,1767,1771,1772,1774,1776,1777,1781,1782,1788,1789,1791,1793,1795,1796,1799,1800,1802,1803,1805,1806,1807,1810,1812,1817,1820,1823,1826,1827,1829,1835,1836,1840,1842,1844,1846,1849,1851,1854,1856,1858,1861,1864,1872,1876,1879,1880,1885,1887,1888,1893,1899,1903,1904,1906,1908,1910,1914,1918,1920,1922,1923,1924,1926,1930,1933,1934,1936,1938,1945,1947,1948,1951,1952,1953,1954,1956,1962,1963,1964,1967,1970,1973,1977,1981,1994,2106,2111,2117,2120,2123,2217,2220,2239,2250,2254,2255,2258,2263,2266,2270,2283,2284,2287,2298,2301,2315,2408,2415,2552,2554,2558,2572,2717,2722,2862,2924,3008,3034,3049,3055,3057,3177,3192,3200,3208,3210,3215,3364,3475,3495,3498,3500,3511,3519,3520,3526,3529,3530,3537,3540,3665,3669,3673,3682,3687,3713,3719,3790,3813,3822,3839,3840,3843,3844,3846,3855,3857,3861,3863,3865,3866,3868,3876,3885,3886,3887,3892,3897,4016,4018,4022,4026,4028,4031,4037,4038,4042,4044,4052,4054,4055,4059,4062,4067,4071,4073,4074,4080,4082,4085,4090,4209,4224,4231,4233,4236,4239,4241,4255,4260,4263,4276,4287,4405,4416,4427,4430,4435,4437,4458,4466,4555,4557,4568,4571,4574,4577,4585,4587,4594,4595,4600,4603,4604,4606,4611,4615,4618,4619,4625,4627,4642,4649,4735,4742,4744,4747,4756,4761,4764,4768,4771,4774,4776,4777,4780,4786,4789,4795,4796,4800,4805,4807,4810,4814,4816,4819,4820,4828,4831,4834,4837,4846,4858,4932,4957,4962,4978,4985,4994,5088,5094,5113,5119,5126,5132,5133,5136,5140,5144,5146,5148,5153,5161,5162,5169,5178,5186,5264,5265,5274,5277,5287,5289,5291,5296,5300,5304,5306,5309,5318,5322,5324,5328,5331,5333,5335,5336,5341,5346,5348,5350,5355,5362,5483,5487,5491,5495,5501,5506,5531,5533,5571,5620,5640,5659,5665,5677,5680,5696,5700,5707,5711,5714,5717,5726,5729,5733,5737,5745,5857,5869,5874,5879,5881,5885,5892,5894,5895,5905,5911,6044,6054,6058,6061,6067,6069,6082,6170,6176,6179,6180,6193,6199,6205,6210,6215,6217,6221,6225,6228,6233,6242,6246,6249,6251,6253,6295,6341,6347,6375,6384,6387,6390,6394,6402,6407,6410,6411,6413,6414,6419,6431,6442,6444,6446,6450,6513,6560,6568,6575,6577,6579,6586,6589,6591,6595,6623,6724,6726,6728,6738,6765,6773,6782,6803,6922,6932,6936,6937,6939,6944,6949,6952,6953,6955,6958,6962,7001,7088,7093,7094,7101,7103,7106,7116,7125,7127,7129,7140,7144,7146,7157,7160,7165,7168,7254,7269,7276,7279,7282,7290,7293,7298,7301,7304,7306,7308,7312,7317,7319,7322,7329,7330,7332,7337,7339,7342,7346,7349,7350,7354,7356,7359,7361,7369,7371,7379,7430,7440,7452,7461,7467,7468,7470,7474,7475,7481,7484,7485,7489,7494,7495,7496,7498,7500,7502,7505,7508,7511,7514,7523,7524,7526,7528,7534,7539,7671,7674,7678,7684,7686,7688,7694,7702,7713,7824,7829,7835,7845,7848,7852,7855,7857,7859,7861,7866,7868,7873,7874,7876,7879,7883,7884,7887,7889,7890,7897,7899,7907,7909,7918,7920,7925,7929,7932,7943,7951,8002,8007,8018,8020,8023,8027,8033,8036,8041,8043,8048,8049,8051,8054,8063,8081,8083,8086,8094,8102,8195,8201,8209,8211,8213,8217,8238,8240,8242,8249,8251,8254,8269,8271,8276,8279,8286,8289,8346,8356,8361,8364,8371,8373,8375,8379,8381,8382,8388,8389,8391,8401,8403,8406,8409,8411,8415,8418,8419,8424,8426,8428,8431,8433,8435,8439,8443,8446,8447,8449,8450,8453,8454,8457,8459,8461,8463,8471,8496,8565,8569,8573,8576,8578,8581,8583,8586,8591,8593,8599,8600,8602,8606,8611,8614,8615,8618,8620,8622,8626,8628,8630,8632,8633,8642,8651,8655,8658,8660,8671,8679,8683,8686,8689,8815,8828,8835,8836,8838,8840,8845,8846,8849,8851,8857,8863,8870,9013,9021,9027,9031,9033,9039,9180,9188,9194,9205,9207,9210,9213,9215,9218,9220,9221,9224,9229,9230,9233,9245,9255,9257,9363,9374,9382,9384,9389,9391,9394,9396,9401,9403,9417,9421,9535,9554,9556,9559,9561,9570,9715,9724,9728,9730,9735,9740,9744,9747,9764,9769,9771,9774,9777,9782,9783,9793,9795,9802,9883,9885,9896,9900,9903,9906,9907,9911,9915,9918,9926,9928,9931,9935,9937,9939,9942,9943,9954,9956,9959,9961,9964,9968,9974,9982,9984,9986,9992,10049,10069,10078,10083,10084,10089,10096,10098,10104,10105,10112,10113,10116,10121,10122,10125,10129,10142,10146,10150,10151,10280,10314,10317,10320,10323,10327,10330,10331,10342,10441,10483,10485,10486,10493,10498,10506,10513,10523,10538,10649,10656,10663,10669,10672,10674,10677,10679,10681,10683,10686,10688,10694,10698,10699,10704,10706,10715,10717,10789,10868,10884,10887,10895,10900,10995,11020,11027,11033,11051,11057,11064,11067,11068,11071,11337,11400,11402,11439,11471,11616,11693,11716,11722,11733,11737,11740,11748,11759,11765,11774,11776,11904,11906,11914,11916,11922,11937,11939,11941,11943,11944,11948,11950,11962,11964,11965,11978,11980,11989,12015,12057,12101,12105,12117,12121,12124,12125,12137,12151,12154,12157,12159,12162,12280,12284,12296,12298,12301,12304,12309,12312,12315,12316,12329,12335,12337,12339,12341,12342,12344,12346,12348,12350,12355,12359,12361,12365,12368,12370,12374,12386,12393,12401,12418,12420,12439,12440,12528,12530,12540,12543,12545,12548,12550,12697,12702,12703,12707,12711,12714,12717,12719,12720,12726,12733,12735,12736,12738,12743,12745,12747,12752,12756,12774,12859,12896,12908,12915,12916,12923,12926,12928,12932,12940,12942,12944,12946,12949,12960,12968,13023,13074,13077,13091,13094,13096,13098,13099,13103,13107,13113,13116,13119,13121,13123,13127,13134,13146,13149,13161,13272,13278,13290,13292,13296,13298,13304,13307,13314,13416,13418,13441,13443,13444,13450,13451,13454,13460,13470,13476,13479,13482,13485,13494,13620,13622,13626,13631,13641,13649,13653,13654,13657,13659,13666,13669,13749,13774,13802,13811,13817,13821,13831,13833,13837,13842,13846,13849,13970,13980,13982,13986,13987,13999,14014,14179,14181,14185,14187, -chr19 47516511 47535109 m84039_230404_003541_s3/246354145/ccs 396,525,752,1160,1337,1556,1845,2105,2288,2664,2877,3017,3228,3599,3771,3974,4145,4227,4320,4533,4740,4923,5089,5290,5507,5702,6091,6301,6389,6572,7119,7292,7483,7663,7862,8024,8186,8384,8566,8758,8927,9205,9378,9897,10241,10407,10718,11178,11348,11664,11886,12046,12133,12240,12618,12802,12971,13167,13372,13541,13738,13882,15008,15131,15221,15396,15726,15889,16099,16468,16833,17383,17596,17781,17885,17989,18396, 128,179,366,153,112,75,157,161,334,152,139,156,321,150,192,147,81,75,169,149,121,135,160,168,145,272,208,84,149,458,127,166,175,163,161,159,197,163,115,137,277,132,518,343,165,246,453,169,315,182,145,86,77,332,139,160,159,147,160,116,143,1107,122,89,120,266,120,118,348,339,549,212,179,103,100,406,136, 351,524,704,1118,1313,1449,1631,2002,2266,2622,2816,3016,3173,3549,3749,3963,4121,4226,4302,4489,4682,4861,5058,5249,5458,5652,5974,6299,6385,6538,7030,7246,7458,7658,7826,8023,8183,8383,8547,8681,8895,9204,9337,9896,10240,10406,10653,11171,11347,11663,11846,12031,12132,12210,12572,12757,12962,13130,13314,13532,13657,13881,14989,15130,15220,15341,15662,15846,16007,16447,16807,17382,17595,17775,17884,17985,18395, 45,1,48,42,24,107,214,103,22,42,61,1,55,50,22,11,24,1,18,44,58,62,31,41,49,50,117,2,4,34,89,46,25,5,36,1,3,1,19,77,32,1,41,1,1,1,65,7,1,1,40,15,1,30,46,45,9,37,58,9,81,1,19,1,1,55,64,43,92,21,26,1,1,6,1,4,1, 0,0,0,0,0,0,250,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 0,1,2,4,5,351,359,395,524,704,713,716,718,723,725,737,739,751,1118,1141,1145,1151,1159,1313,1321,1336,1449,1473,1496,1501,1506,1531,1534,1543,1545,1548,1552,1555,1631,1633,1639,1641,1644,1672,1673,1676,1678,1682,1689,1735,1738,1739,1743,1754,1761,1763,1765,1767,1768,1771,1774,1778,1784,1785,1789,1792,1795,1798,1799,1844,2002,2004,2009,2010,2014,2025,2026,2030,2031,2034,2049,2054,2056,2058,2061,2064,2067,2069,2072,2077,2081,2083,2086,2089,2104,2266,2270,2273,2279,2282,2287,2622,2624,2638,2639,2653,2655,2663,2784,2816,2817,2831,2832,2835,2838,2840,2843,2846,2852,2859,2864,2867,2876,3016,3173,3181,3219,3223,3227,3549,3554,3564,3577,3580,3596,3598,3749,3755,3761,3765,3770,3963,3968,3970,3973,4121,4143,4144,4226,4302,4308,4319,4489,4491,4496,4500,4509,4514,4520,4532,4682,4690,4701,4705,4710,4714,4717,4719,4739,4861,4867,4872,4879,4881,4884,4886,4887,4892,4922,4984,5058,5060,5063,5067,5069,5088,5249,5266,5271,5275,5289,5458,5476,5499,5506,5652,5655,5668,5671,5675,5686,5689,5692,5701,5974,6035,6043,6049,6053,6056,6059,6062,6083,6090,6299,6300,6385,6388,6538,6571,7030,7075,7077,7118,7246,7264,7272,7275,7282,7286,7291,7397,7458,7461,7463,7479,7482,7658,7662,7826,7829,7831,7857,7861,8023,8183,8185,8383,8547,8555,8565,8681,8689,8706,8732,8737,8739,8746,8757,8895,8910,8911,8926,9204,9337,9363,9368,9370,9373,9375,9377,9896,10240,10406,10653,10656,10664,10668,10717,11171,11177,11347,11663,11846,11850,11853,11855,11860,11867,11873,11875,11883,11885,12031,12036,12039,12042,12045,12132,12210,12212,12232,12237,12239,12572,12574,12578,12579,12591,12593,12596,12600,12617,12662,12757,12772,12774,12775,12786,12801,12962,12965,12970,13130,13155,13157,13166,13314,13329,13331,13338,13346,13348,13371,13495,13532,13534,13540,13657,13677,13687,13697,13701,13706,13711,13715,13718,13737,13881,14989,15000,15006,15007,15130,15220,15341,15342,15344,15346,15350,15354,15366,15369,15395,15662,15680,15697,15699,15701,15704,15725,15846,15868,15870,15873,15875,15877,15885,15886,15888,16007,16028,16029,16042,16064,16068,16075,16078,16083,16098,16447,16467,16807,16814,16820,16822,16824,16828,16832,17382,17595,17775,17780,17884,17985,17988,18395,18532,18540,18544,18546,18548,18560,18567,18574,18582,18585, -chr19 47516658 47520871 m84039_230401_034725_s4/172757415/ccs 186,335,523,722,929,1065,1256,1431,1698,1949,2208,2492,2729,2901,3104,3285,3461,3668,3850,4017, 117,121,119,96,134,137,128,95,216,152,283,200,141,132,127,147,186,127,145,107, 149,303,456,642,818,1063,1202,1384,1526,1914,2101,2491,2692,2870,3033,3231,3432,3647,3795,3995, 37,32,67,80,111,2,54,47,172,35,107,1,37,31,71,54,29,21,55,22, 0,0,0,0,0,0,0,0,247,0,0,0,0,0,0,0,0,0,0,0, 0,1,3,4,6,51,149,159,161,162,164,168,173,175,178,182,184,185,303,312,321,326,334,456,464,466,471,473,476,480,486,489,491,495,497,499,501,503,505,520,522,642,649,663,667,670,674,679,688,698,707,710,711,713,716,718,721,818,824,835,839,843,851,855,858,861,867,870,873,875,880,882,883,886,890,892,894,897,898,900,904,908,910,912,914,916,918,920,922,925,926,928,1063,1064,1202,1204,1208,1220,1223,1227,1239,1247,1249,1255,1302,1384,1387,1392,1398,1401,1405,1408,1416,1421,1430,1526,1529,1531,1535,1542,1545,1549,1553,1555,1557,1567,1569,1570,1576,1577,1581,1583,1588,1591,1592,1596,1599,1601,1606,1607,1614,1616,1618,1621,1624,1630,1631,1635,1642,1645,1648,1651,1652,1654,1657,1660,1697,1914,1930,1934,1942,1945,1948,2101,2112,2117,2123,2132,2137,2140,2160,2169,2171,2173,2174,2179,2181,2186,2187,2189,2195,2199,2202,2204,2207,2491,2692,2695,2698,2700,2704,2708,2711,2716,2719,2728,2870,2880,2883,2888,2890,2891,2896,2900,3033,3045,3071,3072,3075,3080,3083,3089,3103,3231,3247,3255,3258,3262,3264,3268,3270,3275,3281,3283,3284,3360,3432,3447,3448,3450,3453,3460,3647,3649,3667,3795,3812,3816,3820,3826,3830,3831,3843,3845,3849,3907,3995,4013,4016,4078,4112,4124,4142,4146,4154,4164,4166,4171,4172,4184,4188,4192,4198,4200,4206,4207,4208,4209,4211, -chr19 47516680 47530390 m84008_230107_003043_s1/83759496/ccs 204,357,501,716,854,1098,1239,1732,2068,2172,2331,2482,2674,2857,3054,3233,3421,3590,3760,3944,4158,4379,4525,4740,4947,5108,5280,5465,5667,5838,6016,6214,6385,6553,6750,6940,7184,7389,7550,7746,7929,8135,8323,8502,8706,8890,9004,9090,9458,9619,9764,9961,10135,10441,10632,10833,10991,11212,11387,11729,11905,12155,12377,12556,12731,12940,13137,13284,13459, 148,141,146,126,145,140,133,275,81,130,112,144,137,130,102,165,158,161,183,179,151,145,160,129,116,160,155,163,152,160,144,136,152,130,168,168,108,135,176,158,150,130,146,203,179,113,85,333,101,139,157,144,305,171,144,147,157,109,93,172,167,92,117,134,148,154,128,162,150, 176,352,498,647,842,999,1238,1372,2007,2149,2302,2443,2626,2811,2987,3156,3398,3579,3751,3943,4123,4309,4524,4685,4869,5063,5268,5435,5628,5819,5998,6160,6350,6537,6683,6918,7108,7292,7524,7726,7904,8079,8265,8469,8705,8885,9003,9089,9423,9559,9758,9921,10105,10440,10612,10776,10980,11148,11321,11480,11901,12072,12247,12494,12690,12879,13094,13265,13446, 28,5,3,69,12,99,1,360,61,23,29,39,48,46,67,77,23,11,9,1,35,70,1,55,78,45,12,30,39,19,18,54,35,16,67,22,76,97,26,20,25,56,58,33,1,5,1,1,35,60,6,40,30,1,20,57,11,64,66,249,4,83,130,62,41,61,43,19,13, 0,0,0,0,0,0,0,250,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 7,22,25,29,34,37,38,43,176,182,184,187,190,199,203,352,355,356,498,500,582,647,649,661,664,676,685,688,689,691,715,842,853,999,1003,1008,1011,1017,1019,1023,1026,1027,1034,1042,1049,1065,1066,1070,1072,1079,1094,1097,1238,1372,1392,1397,1400,1402,1406,1410,1413,1415,1417,1421,1422,1424,1428,1437,1443,1449,1451,1452,1454,1456,1458,1460,1462,1466,1468,1470,1473,1475,1489,1502,1507,1511,1518,1521,1539,1542,1546,1552,1557,1564,1567,1568,1572,1575,1578,1583,1590,1592,1594,1597,1600,1601,1606,1608,1613,1614,1621,1624,1628,1665,1704,1719,1723,1725,1731,2007,2009,2012,2014,2026,2029,2040,2064,2065,2067,2149,2171,2302,2305,2318,2319,2323,2330,2443,2448,2450,2457,2469,2475,2481,2626,2628,2631,2633,2636,2643,2654,2659,2670,2673,2811,2818,2839,2842,2850,2856,2987,2991,3007,3009,3046,3053,3156,3166,3168,3175,3181,3193,3200,3203,3205,3207,3208,3229,3231,3232,3398,3420,3579,3585,3589,3751,3755,3759,3943,4123,4153,4157,4309,4311,4316,4323,4334,4336,4342,4346,4350,4352,4359,4361,4363,4366,4369,4372,4378,4524,4685,4692,4705,4714,4717,4720,4723,4728,4739,4869,4875,4881,4886,4907,4920,4925,4926,4946,5063,5066,5079,5081,5083,5088,5095,5096,5100,5107,5228,5268,5279,5435,5439,5443,5445,5448,5451,5460,5461,5464,5628,5630,5632,5666,5819,5822,5837,5998,5999,6002,6015,6160,6169,6178,6181,6184,6188,6213,6350,6365,6368,6370,6382,6384,6537,6552,6683,6685,6701,6713,6718,6743,6744,6746,6749,6918,6939,7108,7113,7128,7130,7133,7135,7137,7140,7141,7144,7146,7153,7163,7169,7177,7178,7183,7292,7298,7310,7313,7314,7318,7324,7329,7351,7353,7357,7366,7370,7380,7382,7388,7495,7524,7527,7528,7532,7534,7541,7549,7726,7728,7733,7741,7745,7839,7904,7907,7913,7917,7920,7924,7928,8079,8089,8095,8097,8100,8105,8134,8265,8283,8305,8322,8469,8476,8479,8497,8500,8501,8705,8885,8889,8926,9003,9089,9423,9452,9457,9559,9579,9592,9595,9598,9600,9608,9614,9618,9758,9763,9921,9933,9938,9941,9943,9949,9960,10105,10109,10112,10121,10124,10131,10134,10440,10612,10627,10631,10776,10782,10786,10787,10790,10793,10796,10798,10808,10814,10821,10825,10829,10832,10980,10990,11148,11151,11157,11177,11190,11192,11211,11321,11323,11345,11362,11386,11480,11494,11497,11505,11511,11518,11522,11526,11546,11552,11569,11574,11637,11657,11661,11664,11666,11669,11671,11679,11686,11698,11709,11718,11721,11723,11724,11728,11901,11904,12072,12076,12078,12081,12084,12086,12119,12121,12128,12132,12135,12148,12150,12154,12247,12253,12305,12307,12308,12312,12315,12328,12330,12333,12338,12356,12368,12373,12376,12494,12517,12519,12526,12532,12533,12537,12555,12690,12696,12701,12704,12707,12709,12710,12721,12723,12727,12730,12879,12888,12894,12897,12900,12904,12927,12930,12935,12939,13094,13108,13110,13112,13114,13125,13129,13131,13136,13183,13265,13283,13446,13455,13458,13609,13611,13617,13620,13661,13672, -chr19 47516962 47536525 m84008_230107_003043_s1/80221888/ccs 219,413,625,827,1029,1273,1443,1655,1870,2209,2412,2592,2799,2980,3187,3613,3849,4033,4385,4555,4762,4951,5107,5361,5550,5719,5936,6090,6290,6477,6677,6878,7087,7225,7420,7577,7736,7911,8070,8263,8464,8698,8874,9192,9314,9513,9707,9919,10128,10315,10543,10723,10920,11093,11265,11430,11641,11800,12013,12236,12418,12610,12812,13019,13185,13401,13607,13976,14195,14313,14584,14776,14962,15281,15501,15730,15916,16070,16230,16384,16553,16755,16990,17159,17336,17506,17681,17900,18101,18271,18391,18681,18877,19039,19235, 119,101,125,144,122,101,130,131,292,100,101,136,151,138,124,103,77,126,111,163,160,155,139,117,138,103,106,157,147,199,120,129,113,145,101,126,129,93,130,168,143,109,285,121,149,153,130,142,151,159,116,134,142,124,127,147,90,108,102,98,108,102,112,122,150,130,96,118,97,150,91,111,249,109,117,81,114,123,147,129,90,132,116,136,123,116,160,120,114,119,172,120,117,132,129, 217,338,514,750,971,1151,1374,1573,1786,2162,2309,2513,2728,2950,3118,3311,3716,3926,4159,4496,4718,4922,5106,5246,5478,5688,5822,6042,6247,6437,6676,6797,7007,7200,7370,7521,7703,7865,8004,8200,8431,8607,8807,9159,9313,9463,9666,9837,10061,10279,10474,10659,10857,11062,11217,11392,11577,11731,11908,12115,12334,12526,12712,12924,13141,13335,13531,13703,14094,14292,14463,14675,14887,15211,15390,15618,15811,16030,16193,16377,16513,16643,16887,17106,17295,17459,17622,17841,18020,18215,18390,18563,18801,18994,19171,19364, 2,75,111,77,58,122,69,82,84,47,103,79,71,30,69,302,133,107,226,59,44,29,1,115,72,31,114,48,43,40,1,81,80,25,50,56,33,46,66,63,33,91,67,33,1,50,41,82,67,36,69,64,63,31,48,38,64,69,105,121,84,84,100,95,44,66,76,273,101,21,121,101,75,70,111,112,105,40,37,7,40,112,103,53,41,47,59,59,81,56,1,118,76,45,64,84, 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-chr19 47517039 47534671 m54329U_210323_190418/91883686/ccs 204,389,611,792,980,1172,1483,1880,2058,2242,2486,2653,2791,2984,3139,3343,3505,3627,3854,4043,4260,4418,4584,4774,5010,5316,5593,5729,5876,6072,6271,6558,6735,6926,7050,7224,7408,7595,7747,7900,8064,8223,8444,8661,8848,8981,9164,9386,9612,9797,9971,10174,10352,10573,10721,10913,11072,11242,11414,11631,11824,11955,12164,12360,12467,12700,12883,13075,13258,13441,13623,13868,13981,14201,14437,14635,14788,14965,15172,15348,15529,15713,16111,16264,16416,16634,16816,17003,17203,17410, 121,148,156,129,157,246,144,123,140,118,76,115,103,154,140,111,115,136,127,125,79,111,118,126,268,209,117,146,153,110,144,129,103,123,166,154,127,94,116,138,120,112,123,117,105,126,102,131,121,125,125,86,154,115,100,127,128,117,121,102,89,132,139,106,182,128,147,141,135,110,149,107,143,152,119,88,125,103,88,124,134,127,105,141,157,126,108,149,132,143, 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-chr19 47518014 47541411 m84039_230404_003541_s3/70320442/ccs 186,365,574,783,929,1121,1322,1476,1651,1851,2050,2239,2502,2631,2815,3017,3185,3381,3532,3746,3913,4094,4344,4636,4839,4983,5145,5313,5406,5723,5866,6069,6258,6442,6611,6818,6985,7206,7308,7566,7792,7994,8189,8387,8893,9124,9285,9487,9677,9851,10009,10174,10353,10567,10746,10951,11111,11337,11529,11734,11919,12102,12275,12424,12637,13163,13262,13469,13692,13893,14123,14350,14531,14720,14939,15133,15294,15459,15620,15780,16008,16201,16401,16563,16697,16884,17104,17269,17473,17677,17894,18055,18210,18428,18615,18806,19028,19195,19392,19745,19886,20082,20296,20469,20667,20899,21070,21218,21412,21566,21750,21981,22201,22339,22710,22868,23081, 146,179,156,132,159,121,138,141,131,166,155,161,95,153,151,154,140,110,169,126,156,156,291,202,119,115,134,92,206,137,147,120,141,139,132,140,164,101,253,133,148,140,126,494,178,160,89,143,129,146,139,140,150,151,148,120,180,154,137,125,159,121,78,153,525,90,166,147,146,192,138,133,167,163,150,131,107,147,140,147,144,147,135,130,165,137,143,159,139,173,126,126,144,107,145,145,147,131,306,128,155,129,122,120,145,127,84,137,140,123,107,138,106,350,157,148,134, 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-chr19 47518445 47532680 m84039_230401_031619_s3/104336502/ccs 148,280,476,653,788,912,1073,1575,1763,2129,2455,2664,2847,3019,3221,3401,3592,3815,3995,4176,4482,4658,4829,5067,5276,5472,5848,6028,6243,6421,6623,6797,6948,7128,7266,7460,7722,7884,8083,8665,8899,9077,9257,9649,10189,10417,10575,10988,11383,11560,12116,12298,12444,12624,12794,13347,13525,13881,14065, 89,120,89,91,109,109,94,132,130,188,84,116,108,145,86,120,123,130,107,85,110,101,130,120,112,122,115,126,104,95,106,146,179,134,155,142,103,116,110,128,124,117,137,105,141,100,100,96,128,123,103,122,117,134,119,103,112,131,99, 100,237,400,565,744,897,1021,1167,1707,1893,2317,2539,2780,2955,3164,3307,3521,3715,3945,4102,4261,4592,4759,4959,5187,5388,5594,5963,6154,6347,6516,6729,6943,7127,7262,7421,7602,7825,8000,8193,8793,9023,9194,9394,9754,10330,10517,10675,11084,11511,11683,12219,12420,12561,12758,12913,13450,13637,14012, 48,43,76,88,44,15,52,408,56,236,138,125,67,64,57,94,71,100,50,74,221,66,70,108,89,84,254,65,89,74,107,68,5,1,4,39,120,59,83,472,106,54,63,255,435,87,58,313,299,49,433,79,24,63,36,434,75,244,53, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 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1514,11517,11521,11522,11526,11527,11534,11535,11549,11551,11554,11559,11656,11683,11684,11687,11691,11696,11700,11705,11734,11736,11738,11742,11744,11745,11748,11754,11758,11767,11772,11776,11777,11779,11798,11853,11867,11870,11876,11905,11911,11913,11918,11926,11934,11938,11941,11943,11962,11965,12026,12047,12063,12065,12070,12082,12086,12088,12091,12093,12096,12097,12101,12102,12105,12106,12113,12114,12115,12219,12238,12243,12245,12252,12255,12262,12270,12273,12275,12281,12297,12352,12420,12422,12427,12430,12433,12441,12443,12498,12561,12573,12575,12580,12583,12586,12589,12590,12594,12598,12604,12613,12615,12618,12620,12623,12758,12760,12764,12766,12773,12789,12792,12793,12913,12923,12925,12932,12934,12937,12939,12943,12947,12952,12957,12958,12960,12964,12971,12973,12999,13008,13014,13018,13089,13094,13099,13111,13113,13116,13119,13121,13123,13124,13127,13130,13138,13146,13149,13150,13154,13158,13162,13167,13168,13179,13184,13185,13215,13217,13261,13266,13288,13290,13294,13303,13308,13309,13311,13314,13318,13320,13322,13325,13327,13330,13335,13338,13343,13346,13368,13376,13450,13461,13483,13494,13498,13500,13502,13508,13512,13524,13569,13591,13637,13652,13660,13664,13671,13674,13678,13680,13682,13731,13734,13773,13822,13824,13837,13842,13843,13850,13852,13854,13856,13858,13859,13863,13866,13880,13939,14012,14030,14035,14037,14042,14044,14046,14052,14059,14064,14164,14180,14186,14202,14209,14211,14213,14214,14215,14216,14217,14218,14219, -chr19 47518637 47538004 m54329U_210326_192251/117572610/ccs 76,249,490,696,927,1139,1300,1497,1689,1892,2121,2287,2492,2709,2904,3120,3353,3524,3744,3968,4102,4440,4614,4787,5011,5178,5405,5615,5811,5990,6200,6421,6599,6687,6788,6964,7069,7166,7343,7542,7697,7849,8037,8214,8386,8578,8766,8983,9178,9344,9549,9752,9955,10247,10414,10612,10809,10970,11170,11395,11600,11777,11954,12176,12371,12559,12768,12980,13177,13420,13614,13809,14001,14189,14443,14636,14808,15001,15206,15396,15582,15770,15985,16162,16351,16600,16792,17003,17211,17384,17578,17750,17938,18169,18373,18550,18771,19001, 141,146,148,144,127,115,146,165,163,157,133,165,144,119,139,122,104,138,136,133,330,152,172,155,123,107,121,134,134,117,106,140,87,85,175,101,76,153,128,109,129,152,135,169,132,159,159,137,122,136,164,126,128,125,143,156,125,119,104,124,146,146,149,114,129,153,126,114,155,149,173,147,159,128,121,140,140,162,136,151,168,138,124,157,160,143,133,139,145,168,152,151,142,125,139,151,143,107, 217,395,638,840,1054,1254,1446,1662,1852,2049,2254,2452,2636,2828,3043,3242,3457,3662,3880,4101,4432,4592,4786,4942,5134,5285,5526,5749,5945,6107,6306,6561,6686,6772,6963,7065,7145,7319,7471,7651,7826,8001,8172,8383,8518,8737,8925,9120,9300,9480,9713,9878,10083,10372,10557,10768,10934,11089,11274,11519,11746,11923,12103,12290,12500,12712,12894,13094,13332,13569,13787,13956,14160,14317,14564,14776,14948,15163,15342,15547,15750,15908,16109,16319,16511,16743,16925,17142,17356,17552,17730,17901,18080,18294,18512,18701,18914,19108, 32,95,58,87,85,46,51,27,40,72,33,40,73,76,77,111,67,82,88,1,8,22,1,69,44,120,89,62,45,93,115,38,1,16,1,4,21,24,71,46,23,36,42,3,60,29,58,58,44,69,39,77,164,42,55,41,36,81,121,81,31,31,73,81,59,56,86,83,88,45,22,45,29,126,72,32,53,43,54,35,20,77,53,32,89,49,78,69,28,26,20,37,89,79,38,70,87,85, 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22,24,28,30,32,33,36,38,40,46,53,55,58,60,75,217,221,224,226,229,232,235,237,240,245,248,395,399,401,405,412,413,420,427,428,431,434,438,441,445,448,449,452,453,454,455,457,460,463,464,466,473,489,638,640,641,644,649,658,660,661,664,665,666,670,673,675,678,680,684,685,691,695,840,842,846,852,855,859,865,866,870,872,874,877,881,883,887,892,896,898,902,904,910,913,918,922,926,1054,1061,1066,1070,1071,1073,1093,1098,1100,1101,1104,1106,1107,1110,1116,1124,1134,1138,1254,1264,1267,1276,1279,1283,1285,1286,1289,1291,1293,1294,1299,1446,1450,1452,1453,1456,1458,1460,1461,1462,1468,1469,1471,1474,1478,1481,1493,1496,1662,1671,1675,1677,1681,1682,1683,1688,1852,1858,1859,1862,1865,1867,1871,1875,1877,1880,1883,1887,1891,2049,2073,2120,2254,2259,2261,2276,2286,2452,2460,2464,2473,2474,2476,2481,2483,2487,2491,2564,2636,2639,2640,2645,2648,2650,2655,2657,2660,2664,2666,2667,2669,2670,2675,2678,2681,2684,2687,2702,2707,2708,2828,2839,2840,2843,2844,2845,2847,2851,2853,2855,2858,2859,2867,2872,2876,2878,2880,2883,2885,2886,2891,2896,2903,2963,3043,3047,3050,3052,3055,3057,3060,3063,3065,3067,3069,3071,3073,3075,3077,3079,3082,3089,3096,3098,3101,3114,3115,3119,3242,3248,3250,3252,3254,3255,3257,3261,3268,3269,3274,3286,3288,3290,3293,3294,3296,3297,3299,3300,3303,3309,3310,3313,3315,3329,3334,3338,3346,3352,3457,3458,3461,3476,3482,3484,3487,3491,3494,3502,3504,3507,3510,3512,3513,3519,3520,3523,3662,3684,3687,3689,3691,3694,3698,3700,3701,3703,3706,3708,3710,3712,3725,3730,3732,3743,3880,3885,3889,3895,3900,3905,3909,3912,3914,3918,3920,3926,3933,3936,3939,3947,3952,3958,3967,4101,4432,4439,4592,4604,4608,4611,4613,4786,4942,4946,4952,4956,4958,4961,4976,4980,5007,5010,5134,5137,5145,5148,5153,5156,5159,5161,5163,5167,5172,5174,5177,5285,5288,5290,5307,5316,5323,5325,5329,5330,5340,5344,5349,5350,5351,5353,5355,5357,5360,5363,5366,5375,5381,5383,5394,5404,5526,5529,5533,5537,5539,5541,5543,5547,5550,5553,5566,5576,5586,5589,5593,5597,5599,5614,5749,5754,5762,5764,5775,5776,5782,5787,5793,5806,5810,5945,5949,5961,5964,5965,5967,5969,5972,5976,5978,5982,5985,5989,6107,6110,6111,6114,6118,6123,6125,6127,6132,6133,6135,6139,6142,6143,6145,6149,6155,6158,6159,6161,6163,6164,6166,6171,6174,6177,6181,6185,6188,6193,6199,6306,6311,6313,6315,6317,6319,6330,6331,6333,6335,6337,6339,6340,6341,6345,6346,6347,6349,6352,6357,6360,6363,6365,6367,6370,6371,6375,6379,6384,6388,6400,6404,6411,6420,6561,6564,6568,6572,6573,6575,6576,6583,6589,6598,6686,6772,6779,6787,6963,7065,7068,7145,7156,7157,7159,7163,7165,7319,7321,7342,7471,7482,7484,7485,7500,7501,7504,7505,7507,7520,7522,7541,7651,7653,7656,7660,7663,7669,7682,7686,7687,7696,7826,7844,7848,8001,8005,8009,8014,8017,8019,8023,8025,8026,8028,8031,8032,8036,8172,8182,8186,8189,8190,8193,8195,8208,8211,8213,8383,8385,8518,8523,8527,8529,8532,8534,8537,8539,8543,8546,8554,8558,8559,8566,8575,8577,8737,8742,8745,8748,8756,8761,8763,8765,8925,8928,8929,8932,8933,8937,8955,8958,8960,8963,8966,8968,8982,9120,9127,9132,9134,9139,9149,9157,9165,9177,9300,9305,9313,9315,9316,9319,9321,9322,9340,9343,9480,9506,9508,9509,9512,9514,9515,9516,9521,9522,9524,9526,9527,9543,9548,9713,9715,9717,9719,9721,9724,9727,9729,9731,9737,9744,9746,9751,9878,9880,9890,9893,9896,9902,9906,9909,9911,9912,9917,9920,9922,9923,9925,9928,9930,9932,9933,9936,9943,9950,9954,10083,10089,10092,10094,10095,10097,10103,10116,10117,10120,10121,10123,10125,10127,10128,10130,10132,10138,10141,10147,10149,10151,10152,10155,10156,10158,10161,10164,10166,10167,10169,10170,10172,10175,10176,10177,10180,10186,10188,10194,10195,10197,10199,10201,10204,10206,10207,10210,10212,10215,10219,10221,10225,10228,10230,10234,10242,10246,10372,10387,10388,10390,10394,10395,10400,10403,10405,10408,10410,10413,10557,10560,10562,10563,10567,10571,10574,10576,10577,10580,10586,10591,10595,10596,10598,10605,10611,10768,10769,10775,10776,10780,10783,10786,10790,10792,10800,10804,10808,10934,10945,10951,10969,11089,11093,11098,11102,11104,11112,11114,11121,11123,11127,11129,11130,11132,11134,11136,11140,11142,11146,11152,11160,11166,11169,11274,11275,11278,11280,11284,11286,11288,11291,11292,11299,11303,11305,11306,11309,11312,11313,11316,11322,11326,11332,11338,11341,11343,11344,11347,11351,11352,11356,11357,11365,11387,11390,11394,11519,11537,11540,11546,11547,11548,11566,11568,11570,11572,11574,11576,11580,11594,11599,11746,11751,11768,11773,11776,11923,11937,11939,11944,11953,12103,12120,12127,12135,12148,12154,12158,12175,12290,12293,12313,12321,12326,12327,12338,12340,12342,12344,12346,12349,12351,12354,12370,12396,12500,12505,12510,12513,12530,12532,12538,12544,12558,12712,12715,12717,12726,12728,12731,12735,12737,12738,12739,12745,12746,12750,12751,12753,12756,12758,12767,12894,12897,12914,12922,12927,12929,12932,12938,12939,12942,12944,12946,12949,12952,12954,12956,12957,12963,12971,12979,13094,13102,13106,13108,13111,13115,13121,13122,13127,13129,13130,13133,13135,13136,13138,13141,13142,13144,13147,13151,13153,13155,13158,13160,13163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-chr19 47518754 47532290 m84008_230107_003043_s1/9245284/ccs 116,295,490,693,861,1035,1200,1405,1645,1818,2026,2210,2371,2570,2779,2973,3157,3343,3549,3726,4547,4753,4939,5084,5333,5550,5685,5886,6060,6249,6424,6602,6810,6991,7161,7384,7559,7760,7966,8178,8362,8774,8945,9135,9329,9475,9660,9856,10105,10287,10487,10663,10865,11072,11269,11473,11644,11832,12009,12193,12416,12589,12799,13008,13207, 136,129,168,167,147,151,153,140,118,145,143,125,150,159,150,148,132,165,160,792,139,145,144,169,138,126,138,106,143,140,135,157,125,136,161,121,129,138,135,141,318,135,156,176,134,146,187,130,137,143,119,141,117,137,118,139,124,141,152,134,151,140,139,120,108, 46,252,424,658,860,1008,1186,1353,1545,1763,1963,2169,2335,2521,2729,2929,3121,3289,3508,3709,4518,4686,4898,5083,5253,5471,5676,5823,5992,6203,6389,6559,6759,6935,7127,7322,7505,7688,7898,8101,8319,8680,8909,9101,9311,9463,9621,9847,9986,10242,10430,10606,10804,10982,11209,11387,11612,11768,11973,12161,12327,12567,12729,12938,13128,13315, 70,43,66,35,1,27,14,52,100,55,63,41,36,49,50,44,36,54,41,17,29,67,41,1,80,79,9,63,68,46,35,43,51,56,34,62,54,72,68,77,43,94,36,34,18,12,39,9,119,45,57,57,61,90,60,86,32,64,36,32,89,22,70,70,79,75, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,243,0,0,0,0,0,0,243,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 45,71,73,76,78,79,86,92,94,100,104,107,109,112,115,252,274,278,282,294,424,445,452,461,473,475,484,487,489,658,669,673,677,680,682,686,692,860,1008,1027,1032,1034,1160,1186,1199,1353,1380,1400,1404,1545,1554,1558,1564,1566,1568,1571,1572,1574,1587,1589,1592,1595,1597,1598,1600,1602,1608,1613,1617,1618,1619,1624,1629,1639,1641,1644,1763,1786,1794,1800,1803,1805,1806,1812,1814,1817,1963,1968,1971,1995,1999,2003,2010,2025,2169,2189,2190,2194,2198,2201,2203,2209,2335,2343,2347,2364,2366,2370,2521,2527,2528,2532,2539,2548,2552,2557,2560,2563,2566,2569,2729,2731,2733,2735,2737,2740,2741,2749,2754,2758,2760,2762,2773,2778,2929,2932,2934,2939,2942,2953,2964,2972,3121,3136,3143,3156,3208,3289,3295,3318,3338,3339,3342,3508,3520,3524,3527,3531,3532,3537,3539,3545,3546,3548,3709,3721,3725,4518,4522,4524,4528,4539,4546,4686,4688,4691,4695,4713,4732,4734,4748,4750,4752,4898,4916,4925,4930,4938,5083,5253,5256,5261,5272,5274,5282,5286,5294,5296,5297,5309,5313,5314,5321,5323,5325,5329,5331,5332,5471,5477,5484,5492,5498,5501,5503,5512,5518,5549,5676,5684,5823,5827,5835,5839,5842,5845,5847,5850,5854,5856,5860,5863,5865,5867,5875,5879,5885,5992,5997,6001,6003,6005,6011,6013,6017,6021,6023,6033,6036,6039,6044,6049,6055,6059,6203,6205,6208,6225,6227,6230,6245,6248,6389,6392,6394,6397,6400,6413,6423,6559,6569,6571,6579,6580,6597,6601,6759,6766,6769,6786,6792,6807,6809,6935,6937,6943,6946,6948,6951,6953,6954,6955,6957,6959,6962,6963,6966,6969,6974,6978,6988,6990,7127,7129,7132,7136,7142,7144,7146,7150,7152,7154,7158,7160,7322,7347,7366,7377,7383,7505,7511,7532,7536,7558,7688,7702,7712,7716,7718,7720,7724,7726,7758,7759,7898,7902,7906,7921,7927,7928,7932,7937,7938,7942,7948,7951,7955,7963,7965,8101,8109,8110,8114,8118,8124,8130,8147,8149,8160,8177,8319,8323,8325,8330,8334,8336,8338,8343,8361,8680,8684,8688,8691,8693,8696,8698,8705,8713,8716,8720,8724,8725,8730,8733,8735,8738,8741,8744,8746,8749,8756,8762,8767,8773,8909,8913,8923,8925,8929,8931,8937,8942,8944,9101,9107,9112,9119,9130,9132,9134,9311,9314,9322,9328,9463,9467,9470,9474,9621,9640,9644,9646,9648,9652,9659,9847,9854,9855,9986,9993,10005,10010,10017,10021,10025,10026,10028,10031,10034,10036,10039,10042,10045,10047,10056,10058,10065,10067,10069,10071,10082,10085,10089,10091,10095,10098,10104,10169,10242,10255,10257,10258,10260,10270,10273,10278,10280,10286,10430,10432,10441,10444,10447,10449,10456,10458,10460,10461,10463,10465,10466,10468,10473,10475,10481,10482,10486,10517,10606,10610,10626,10632,10638,10642,10645,10646,10653,10656,10660,10662,10804,10821,10824,10828,10829,10833,10843,10846,10849,10851,10853,10857,10864,10982,10983,10989,10991,10997,11000,11002,11004,11008,11010,11014,11020,11026,11034,11038,11051,11058,11060,11062,11064,11071,11167,11209,11212,11215,11219,11224,11225,11246,11248,11250,11253,11255,11258,11268,11387,11396,11400,11405,11407,11408,11414,11434,11436,11438,11440,11442,11444,11448,11450,11452,11458,11462,11465,11467,11472,11612,11615,11617,11622,11631,11643,11768,11770,11775,11779,11790,11793,11800,11810,11818,11823,11831,11973,11986,12005,12008,12161,12164,12168,12178,12192,12327,12341,12343,12345,12347,12353,12355,12358,12359,12362,12373,12376,12389,12393,12409,12415,12567,12588,12729,12740,12751,12757,12759,12765,12768,12769,12788,12798,12938,12945,12948,12953,12959,12962,12965,12966,12970,12973,12977,12979,12982,13007,13128,13131,13140,13145,13148,13152,13154,13157,13159,13160,13167,13170,13174,13177,13178,13182,13198,13202,13206,13315,13333,13363,13365,13369,13376,13383,13389,13522, -chr19 47518837 47521124 m84039_230404_003541_s3/117772968/ccs 152,462,703,898,1085,1407,1628,1783,1955, 278,132,194,127,299,169,154,151,152, 151,430,594,897,1025,1384,1576,1782,1934,2107, 1,32,109,1,60,23,52,1,21,1, 0,0,0,0,0,0,0,0,0,0, 1,2,3,5,24,26,151,430,438,441,449,450,461,594,609,613,616,618,621,623,631,633,646,702,897,1025,1029,1051,1069,1077,1084,1384,1393,1398,1400,1406,1576,1579,1580,1584,1587,1590,1593,1597,1599,1611,1625,1627,1782,1934,1942,1952,1954,2107,2261,2265,2282,2284, -chr19 47518978 47534929 m84039_230401_034725_s4/237175162/ccs 88,217,328,512,715,832,965,1047,1161,1249,1370,1531,1794,1872,2043,2244,2408,2542,2678,2813,3042,3142,3483,4023,4133,4510,4807,4932,5240,5489,5788,5927,6129,6259,6382,6542,6644,6934,7025,7142,7297,7502,7634,7899,7993,8126,8407,8502,8659,8844,8961,9148,9250,9429,9670,9992,10295,10439,10663,10746,11047,11160,11340,11497,11802,11930,12070,12323,12566,12767,12931,13416,13628,13785,13878,13983,14064,14175,14332,14420,14558,14676,14807,15017,15147,15458, 108,110,183,202,116,132,76,109,87,120,156,143,77,170,200,158,133,135,134,228,99,293,522,109,303,296,80,307,171,298,138,157,129,122,157,101,217,86,116,154,204,131,167,93,82,280,94,156,168,101,186,101,162,235,275,162,143,209,82,300,112,114,156,262,127,139,252,175,183,163,484,141,101,92,104,80,110,154,87,135,117,130,170,129,308,383, 87,196,327,511,714,831,964,1041,1156,1248,1369,1526,1674,1871,2042,2243,2402,2541,2677,2812,3041,3141,3435,4005,4132,4436,4806,4887,5239,5411,5787,5926,6084,6258,6381,6539,6643,6861,7020,7141,7296,7501,7633,7801,7992,8075,8406,8501,8658,8827,8945,9147,9249,9412,9664,9945,10154,10438,10648,10745,11046,11159,11274,11496,11759,11929,12069,12322,12498,12749,12930,13415,13557,13729,13877,13982,14063,14174,14329,14419,14555,14675,14806,14977,15146,15455,15841, 1,21,1,1,1,1,1,6,5,1,1,5,120,1,1,1,6,1,1,1,1,1,48,18,1,74,1,45,1,78,1,1,45,1,1,3,1,73,5,1,1,1,1,98,1,51,1,1,1,17,16,1,1,17,6,47,141,1,15,1,1,1,66,1,43,1,1,1,68,18,1,1,71,56,1,1,1,1,3,1,3,1,1,40,1,3,1, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,244,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 4,5,87,116,196,216,327,511,714,831,964,1041,1046,1156,1160,1248,1369,1526,1530,1674,1697,1759,1767,1768,1793,1871,2042,2243,2402,2405,2407,2541,2677,2812,3041,3141,3435,3443,3482,4005,4019,4022,4071,4132,4436,4440,4466,4495,4509,4806,4887,4888,4931,5239,5411,5428,5488,5787,5926,6036,6084,6128,6258,6323,6335,6381,6439,6539,6541,6643,6861,6929,6933,7020,7024,7102,7141,7296,7501,7575,7633,7801,7836,7837,7875,7876,7878,7898,7992,8075,8079,8115,8125,8406,8501,8658,8827,8843,8945,8960,9147,9249,9412,9416,9428,9664,9669,9945,9991,10046,10154,10163,10234,10241,10262,10266,10294,10364,10365,10438,10648,10662,10745,11046,11159,11238,11274,11277,11280,11337,11339,11430,11496,11759,11762,11769,11801,11897,11929,11989,12069,12322,12498,12565,12626,12749,12762,12766,12930,13415,13557,13621,13627,13683,13729,13731,13742,13744,13746,13759,13770,13784,13877,13982,14063,14174,14329,14331,14419,14469,14555,14557,14614,14675,14806,14977,15016,15146,15455,15457,15841,15888,15941,15942,15943,15944,15946,15947, -chr19 47519260 47541371 m84008_230107_003043_s1/164959873/ccs 99,306,479,686,881,1073,1248,1431,1636,1845,2021,2188,2366,2568,2739,2955,3107,3363,3541,3720,4182,4339,4578,4771,4960,5096,5265,5465,5621,5805,6009,6174,6352,6569,6734,6956,7206,7375,7603,7791,8003,8261,8432,8656,8783,8981,9205,9374,9529,9759,10123,10266,10473,10691,10866,10970,11187,11340,11535,11909,12120,12272,12457,12679,12880,13061,13274,13418,13688,13886,14071,14222,14392,14544,14762,14953,15110,15336,15554,15751,15915,16102,16253,16508,16676,16855,17071,17266,17462,17628,17827,18000,18213,18410,18574,18734,19385,19631,19830,19990,20193,20374,20551,20759,21083,21250,21479,21702, 88,112,129,138,143,132,105,111,117,119,108,117,128,120,127,139,143,139,128,391,115,121,121,121,118,143,142,131,105,112,124,136,132,130,168,146,113,152,132,95,94,134,104,97,154,111,108,134,161,283,118,144,128,144,85,142,123,136,306,118,134,148,160,147,116,148,143,165,83,140,133,97,151,164,119,132,148,148,178,128,155,124,199,153,163,170,123,108,106,144,152,130,104,100,144,645,194,142,126,137,121,157,124,94,154,152,114,97, 187,418,608,824,1024,1205,1353,1542,1753,1964,2129,2305,2494,2688,2866,3094,3250,3502,3669,4111,4297,4460,4699,4892,5078,5239,5407,5596,5726,5917,6133,6310,6484,6699,6902,7102,7319,7527,7735,7886,8097,8395,8536,8753,8937,9092,9313,9508,9690,10042,10241,10410,10601,10835,10951,11112,11310,11476,11841,12027,12254,12420,12617,12826,12996,13209,13417,13583,13771,14026,14204,14319,14543,14708,14881,15085,15258,15484,15732,15879,16070,16226,16452,16661,16839,17025,17194,17374,17568,17772,17979,18130,18317,18510,18718,19379,19579,19773,19956,20127,20314,20531,20675,20853,21237,21402,21593,21799, 119,61,78,57,49,43,78,94,92,57,59,61,74,51,89,13,113,39,51,71,42,118,72,68,18,26,58,25,79,92,41,42,85,35,54,104,56,76,56,117,164,37,120,30,44,113,61,21,69,81,25,63,90,31,19,75,30,59,68,93,18,37,62,54,65,65,1,105,115,45,18,73,1,54,72,25,78,70,19,36,32,27,56,15,16,46,72,88,60,55,21,83,93,64,16,6,52,57,34,66,60,20,84,230,13,77,109,95, 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37,47,52,53,56,58,68,73,76,78,79,84,89,95,98,187,208,218,233,237,259,265,268,270,274,280,283,288,290,305,418,434,441,446,473,478,608,620,627,630,634,635,642,644,647,648,650,651,656,658,659,660,665,669,671,673,676,679,681,682,684,685,824,826,830,833,834,848,849,851,854,858,861,863,870,873,878,880,1024,1030,1036,1042,1048,1049,1051,1055,1057,1063,1065,1069,1072,1205,1211,1214,1217,1218,1222,1224,1227,1232,1239,1242,1245,1247,1353,1377,1382,1387,1391,1395,1396,1399,1400,1403,1413,1422,1424,1427,1430,1542,1554,1560,1589,1591,1597,1599,1608,1616,1635,1753,1756,1759,1772,1776,1780,1782,1793,1796,1799,1802,1843,1844,1964,1967,1969,1972,1989,1993,1996,1999,2001,2002,2005,2011,2020,2129,2136,2142,2153,2156,2157,2161,2162,2164,2166,2174,2187,2305,2310,2313,2317,2319,2330,2332,2335,2338,2340,2346,2347,2361,2365,2494,2497,2500,2513,2515,2517,2522,2526,2530,2532,2535,2541,2548,2550,2554,2559,2562,2564,2567,2688,2690,2700,2711,2713,2717,2721,2727,2729,2732,2733,2738,2866,2885,2894,2895,2898,2903,2906,2911,2916,2918,2921,2925,2931,2932,2951,2954,3094,3099,3104,3106,3250,3253,3258,3259,3262,3266,3273,3278,3282,3285,3289,3293,3297,3314,3317,3320,3322,3325,3327,3340,3362,3502,3504,3509,3510,3512,3526,3530,3535,3540,3669,3675,3683,3685,3691,3695,3698,3700,3706,3709,3711,3719,4111,4115,4117,4144,4150,4151,4155,4159,4162,4178,4181,4297,4310,4313,4323,4325,4328,4338,4460,4472,4476,4482,4497,4500,4503,4507,4511,4538,4540,4543,4553,4558,4560,4570,4571,4575,4577,4699,4700,4702,4705,4706,4708,4710,4715,4719,4723,4726,4729,4732,4733,4735,4745,4747,4749,4770,4892,4895,4903,4905,4907,4909,4952,4959,5078,5082,5084,5089,5095,5123,5239,5241,5244,5257,5264,5407,5409,5412,5416,5420,5425,5426,5434,5436,5438,5464,5596,5601,5604,5607,5608,5610,5620,5726,5728,5732,5733,5737,5746,5750,5752,5757,5762,5766,5769,5771,5773,5781,5799,5804,5917,5924,5928,5932,5946,5949,5952,5956,5958,5960,5962,5964,5965,5967,5982,5985,5989,5994,5995,5998,6004,6008,6133,6137,6147,6166,6168,6173,6310,6350,6351,6484,6502,6522,6568,6699,6702,6707,6709,6715,6722,6726,6727,6731,6733,6902,6906,6924,6939,6943,6950,6955,7102,7121,7122,7133,7143,7154,7157,7161,7169,7171,7174,7175,7176,7179,7183,7205,7319,7322,7327,7328,7331,7336,7337,7340,7343,7348,7361,7366,7367,7371,7374,7527,7532,7538,7542,7547,7548,7552,7553,7556,7566,7571,7581,7583,7586,7587,7589,7594,7602,7735,7740,7742,7745,7747,7752,7758,7759,7761,7762,7765,7766,7769,7776,7779,7780,7782,7783,7786,7788,7790,7886,7905,7925,7928,7931,7932,7934,7941,7946,7947,7948,7955,7957,7961,7963,7964,7967,7970,7975,7976,7980,7982,7985,7988,8002,8097,8100,8103,8114,8118,8120,8121,8123,8125,8126,8131,8146,8149,8155,8162,8167,8171,8178,8183,8192,8203,8214,8220,8222,8225,8232,8260,8360,8395,8396,8399,8402,8404,8409,8411,8417,8423,8428,8431,8536,8549,8558,8561,8573,8577,8580,8584,8587,8593,8598,8599,8602,8604,8605,8606,8613,8616,8618,8631,8649,8655,8753,8755,8757,8762,8782,8937,8955,8957,8959,8963,8967,8974,8980,9092,9106,9113,9114,9121,9123,9129,9154,9156,9159,9169,9179,9204,9313,9315,9323,9336,9369,9373,9508,9511,9514,9517,9522,9528,9690,9693,9695,9696,9698,9699,9701,9704,9707,9710,9717,9720,9740,9741,9743,9746,9747,9748,9756,9758,10042,10044,10045,10048,10053,10059,10061,10062,10065,10066,10071,10072,10075,10078,10091,10103,10122,10241,10258,10260,10265,10374,10410,10413,10419,10420,10422,10425,10428,10430,10434,10443,10455,10459,10460,10466,10468,10472,10601,10611,10614,10627,10629,10631,10633,10648,10654,10657,10661,10667,10670,10676,10682,10684,10687,10690,10835,10842,10857,10863,10865,10951,10969,11112,11116,11119,11132,11135,11140,11142,11143,11146,11156,11172,11186,11310,11333,11336,11339,11476,11483,11488,11489,11494,11496,11497,11504,11534,11841,11846,11851,11854,11856,11858,11860,11879,11881,11885,11887,11888,11891,11893,11899,11906,11908,12027,12033,12034,12039,12049,12052,12053,12055,12066,12068,12084,12085,12092,12095,12118,12119,12161,12254,12262,12267,12269,12271,12420,12423,12427,12430,12445,12447,12450,12454,12456,12617,12621,12623,12626,12628,12629,12634,12636,12643,12647,12651,12656,12661,12667,12673,12675,12678,12826,12828,12848,12856,12858,12863,12866,12867,12869,12872,12874,12879,12996,12998,13000,13004,13024,13028,13033,13048,13054,13056,13058,13060,13209,13211,13242,13248,13260,13264,13270,13273,13417,13583,13595,13599,13611,13615,13616,13620,13625,13629,13632,13641,13643,13645,13646,13650,13657,13659,13661,13662,13668,13671,13675,13679,13681,13682,13684,13685,13687,13771,13776,13793,13808,13849,13856,13859,13862,13865,13870,13873,13875,13881,13884,13885,14026,14027,14034,14039,14041,14048,14066,14070,14204,14210,14212,14221,14319,14334,14353,14358,14383,14384,14386,14391,14543,14594,14708,14727,14746,14755,14761,14881,14886,14893,14898,14900,14903,14913,14929,14934,14947,14952,15085,15087,15088,15091,15093,15109,15258,15284,15290,15294,15299,15301,15306,15308,15311,15316,15321,15329,15335,15484,15486,15492,15525,15528,15531,15544,15551,15553,15732,15735,15750,15879,15884,15890,15914,15945,16070,16079,16098,16101,1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-chr19 47519556 47545267 m84008_230107_003043_s1/169083681/ccs 1044,1229,1468,1749,2121,2327,2513,3666,4252,4525,4665,4825,5196,5647,6182,6621,7132,7352,7579,7782,7941,8134,8844,9011,9137,9343,9591,9809,9967,10173,10420,10624,10807,10999,11166,11561,12163,12334,12564,12765,12973,13315,13561,13758,13898,14523,15095,16311,16509,16729,16918,17117,17473,17832,18032,18387,18603,18780,19004,19306,19817,20252,20675,21698,22181,22557,22913,23123,23286,23505,23670,24092,24256,24687,24854,25254, 184,201,268,352,135,135,1140,585,272,139,141,272,371,534,438,483,194,213,164,158,167,700,166,125,166,247,161,157,205,212,203,177,191,161,394,547,137,199,183,182,341,205,135,139,624,571,1213,197,214,188,166,355,358,171,323,182,176,223,284,510,434,148,1022,305,375,256,189,162,218,164,367,148,376,163,306,140, 1012,1228,1430,1736,2101,2256,2462,3653,4251,4524,4664,4806,5097,5567,6181,6620,7104,7326,7565,7743,7940,8108,8834,9010,9136,9303,9590,9752,9966,10172,10385,10623,10801,10998,11160,11560,12108,12300,12533,12747,12947,13314,13520,13696,13897,14522,15094,16308,16508,16723,16917,17084,17472,17831,18003,18355,18569,18779,19003,19288,19816,20251,20400,21697,22003,22556,22813,23102,23285,23504,23669,24037,24240,24632,24850,25160,25394, 32,1,38,13,20,71,51,13,1,1,1,19,99,80,1,1,28,26,14,39,1,26,10,1,1,40,1,57,1,1,35,1,6,1,6,1,55,34,31,18,26,1,41,62,1,1,1,3,1,6,1,33,1,1,29,32,34,1,1,18,1,1,275,1,178,1,100,21,1,1,1,55,16,55,4,94,96, 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,251,0,248,0,0,0,0,0,0,0,0,0,0,0,243, 1012,1029,1038,1043,1228,1430,1437,1467,1736,1742,1745,1748,2101,2107,2110,2120,2256,2260,2265,2268,2292,2293,2298,2299,2321,2326,2462,2469,2482,2506,2512,3653,3657,3662,3665,4251,4524,4664,4806,4824,5097,5147,5195,5567,5579,5606,5644,5646,6181,6620,7104,7131,7326,7351,7565,7578,7743,7776,7781,7904,7940,8108,8133,8834,8837,8843,9010,9136,9234,9303,9342,9590,9752,9757,9758,9789,9808,9966,10172,10385,10419,10623,10801,10804,10806,10998,11160,11165,11560,12108,12118,12121,12129,12135,12138,12142,12162,12300,12303,12307,12309,12312,12315,12333,12533,12536,12540,12549,12552,12553,12555,12561,12563,12747,12757,12764,12947,12972,13314,13520,13522,13523,13537,13541,13547,13550,13553,13560,13696,13704,13709,13711,13729,13733,13739,13743,13747,13751,13755,13757,13897,14522,15094,16308,16310,16508,16723,16728,16917,17084,17094,17111,17116,17472,17831,18003,18005,18031,18355,18386,18569,18575,18579,18587,18589,18595,18602,18779,19003,19288,19291,19305,19816,20251,20400,20421,20423,20427,20431,20435,20437,20439,20442,20457,20462,20467,20470,20472,20488,20532,20536,20579,20581,20614,20641,20643,20652,20668,20671,20674,21697,22003,22004,22033,22038,22041,22072,22095,22100,22102,22129,22132,22151,22153,22157,22169,22174,22176,22180,22556,22813,22883,22886,22889,22891,22893,22909,22912,23102,23122,23285,23504,23669,24037,24039,24047,24054,24061,24069,24071,24087,24091,24240,24243,24247,24254,24255,24632,24686,24850,24853,25160,25162,25171,25179,25184,25208,25211,25213,25217,25225,25239,25244,25249,25250,25253,25394,25399,25402,25404,25405,25450,25463,25468,25474,25477,25478,25481,25484,25490, -chr19 47519636 47531246 m54329U_210323_190418/64947030/ccs 167,390,576,749,896,1126,1510,1672,2138,2267,2475,2756,2922,3115,3271,3431,3702,3883,4100,4240,4436,4646,4817,4986,5145,5334,5534,5853,6025,6213,6396,6621,6725,6946,7157,7326,7559,7812,7975,8303,8489,8694,8841,9021,9236,9427,9765,9992,10238,10370,10542,10751,10957,11148,11321,11469, 115,133,93,80,123,144,114,242,108,117,260,130,135,120,147,252,157,133,139,139,155,117,137,125,93,111,295,167,129,137,133,103,128,107,111,116,126,149,287,97,158,122,142,138,127,254,109,124,94,122,156,156,117,98,126,95, 129,282,523,669,829,1019,1270,1624,1914,2246,2384,2735,2886,3057,3235,3418,3683,3859,4016,4239,4379,4591,4763,4954,5111,5238,5445,5829,6020,6154,6350,6529,6724,6853,7053,7268,7442,7685,7961,8262,8400,8647,8816,8983,9159,9363,9681,9874,10116,10332,10492,10698,10907,11074,11246,11447, 38,108,53,80,67,107,240,48,224,21,91,21,36,58,36,13,19,24,84,1,57,55,54,32,34,96,89,24,5,59,46,92,1,93,104,58,117,127,14,41,89,47,25,38,77,64,84,118,122,38,50,53,50,74,75,22, 0,0,0,0,0,0,0,0,253,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, 129,133,134,135,137,141,142,144,146,150,151,153,156,163,166,282,283,286,288,289,291,292,294,296,299,304,307,318,319,324,328,330,335,347,349,351,355,357,363,369,375,379,382,386,389,523,535,537,569,575,669,675,678,682,684,688,690,692,695,696,698,702,717,721,722,730,732,734,743,748,829,831,840,843,848,874,886,889,892,895,1019,1026,1031,1034,1035,1037,1041,1045,1046,1048,1050,1051,1052,1054,1056,1059,1062,1065,1067,1068,1072,1073,1076,1078,1079,1083,1084,1090,1095,1101,1111,1115,1116,1118,1120,1123,1125,1270,1274,1276,1293,1295,1355,1386,1389,1392,1417,1431,1434,1437,1441,1442,1443,1445,1447,1455,1463,1475,1478,1479,1494,1498,1509,1624,1628,1631,1634,1636,1637,1640,1641,1642,1646,1655,1656,1660,1665,1671,1914,1923,1931,1933,1938,1941,1944,1946,1949,1950,1953,1955,1958,1961,1962,1963,1965,1967,1969,1970,1973,1975,1976,1977,1979,1981,1982,1986,1988,1989,1992,1993,1996,2000,2004,2006,2008,2018,2022,2038,2041,2043,2044,2046,2048,2050,2053,2057,2060,2065,2067,2070,2073,2077,2079,2083,2085,2087,2089,2092,2100,2101,2104,2106,2108,2111,2114,2117,2118,2120,2124,2125,2129,2131,2134,2137,2246,2266,2384,2387,2391,2393,2397,2399,2403,2417,2419,2421,2423,2426,2431,2432,2433,2469,2472,2474,2735,2739,2741,2754,2755,2886,2889,2894,2898,2914,2918,2921,3057,3064,3068,3075,3077,3080,3081,3085,3088,3093,3096,3098,3099,3103,3107,3110,3112,3114,3235,3242,3244,3247,3250,3270,3418,3423,3430,3683,3687,3701,3859,3862,3864,3866,3867,3868,3869,3871,3874,3878,3880,3882,4016,4047,4053,4055,4058,4059,4066,4094,4099,4239,4379,4404,4408,4420,4435,4591,4594,4597,4598,4601,4602,4604,4609,4611,4612,4618,4619,4625,4628,4630,4633,4639,4645,4763,4779,4781,4788,4804,4812,4816,4954,4976,4985,5111,5127,5132,5134,5136,5144,5238,5254,5268,5271,5274,5280,5289,5291,5293,5296,5302,5304,5305,5310,5311,5314,5318,5321,5323,5325,5327,5333,5445,5450,5461,5464,5471,5477,5479,5480,5483,5485,5491,5494,5496,5498,5499,5509,5522,5525,5527,5530,5531,5533,5829,5831,5834,5835,5839,5846,5848,5850,5851,5852,5904,6020,6024,6068,6154,6157,6161,6162,6165,6172,6178,6179,6182,6183,6185,6190,6194,6196,6200,6203,6207,6212,6350,6366,6373,6377,6378,6382,6395,6529,6545,6547,6550,6557,6562,6565,6573,6582,6591,6595,6597,6602,6607,6613,6620,6724,6818,6853,6883,6885,6889,6892,6895,6901,6906,6909,6910,6912,6914,6915,6916,6918,6925,6927,6930,6932,6935,6937,6940,6944,6945,7053,7070,7076,7078,7080,7083,7087,7089,7090,7092,7095,7097,7101,7112,7115,7116,7117,7119,7121,7122,7123,7124,7128,7133,7136,7138,7150,7156,7268,7282,7293,7295,7300,7305,7310,7312,7318,7319,7321,7325,7442,7447,7450,7453,7454,7461,7465,7468,7470,7472,7474,7477,7482,7488,7493,7495,7497,7498,7504,7508,7510,7520,7522,7527,7531,7533,7534,7536,7538,7545,7547,7550,7552,7558,7685,7701,7707,7709,7712,7718,7732,7734,7739,7745,7748,7751,7753,7766,7769,7771,7773,7774,7777,7778,7779,7783,7784,7785,7786,7787,7788,7794,7797,7803,7805,7808,7810,7811,7961,7964,7966,7967,7970,7972,7974,8262,8264,8266,8277,8286,8291,8294,8296,8302,8400,8423,8429,8438,8442,8445,8453,8457,8459,8463,8470,8472,8475,8477,8480,8487,8488,8647,8656,8661,8668,8670,8673,8674,8676,8677,8679,8685,8687,8691,8693,8816,8831,8840,8983,8986,8987,9016,9020,9159,9162,9165,9170,9173,9187,9196,9198,9200,9202,9203,9205,9207,9208,9211,9213,9220,9222,9226,9229,9235,9363,9365,9373,9386,9388,9389,9391,9395,9401,9404,9406,9409,9411,9426,9681,9694,9695,9697,9702,9708,9713,9716,9717,9720,9721,9726,9727,9730,9733,9738,9740,9742,9746,9747,9753,9756,9764,9874,9880,9882,9894,9904,9905,9907,9908,9909,9916,9918,9921,9928,9929,9932,9935,9937,9940,9944,9945,9946,9953,9955,9958,9960,9962,9963,9967,9968,9969,9977,9980,9983,9985,9991,10116,10123,10126,10132,10133,10135,10137,10139,10143,10145,10149,10155,10161,10163,10164,10169,10172,10173,10194,10196,10198,10200,10207,10211,10222,10226,10237,10332,10345,10348,10351,10369,10492,10499,10515,10519,10532,10536,10541,10698,10700,10716,10750,10907,10909,10917,10925,10928,10929,10936,10945,10948,10956,11074,11083,11088,11091,11095,11096,11103,11105,11112,11114,11117,11122,11129,11132,11136,11141,11144,11147,11246,11253,11255,11266,11269,11271,11276,11280,11285,11287,11294,11300,11302,11305,11310,11313,11315,11320,11447,11449,11456,11463,11465,11468,11564,11566,11577,11579,11585,11593,11595,11598,11602,11604,11606,11610,11612,11613,11614,11617,11619, +#ct st en fiber nuc_starts nuc_lengths msp_starts msp_lengths fire_starts fire_lengths fire_qual m6a +chr19 47480179 47512478 m54329U_210814_130637/54723395/ccs 57,268,452,643,818,1024,1305,1522,1660,1847,2039,2276,2398,2583,2764,2919,3076,3270,3418,3558,3860,4238,4590,4761,4937,5123,5326,5510,5670,5861,5992,6129,6806,7087,7256,7498,7703,7921,8095,8277,8465,8634,9043,9384,9560,9750,10049,10189,10330,10571,10777,10957,11115,11300,11525,11697,11880,12091,12246,12435,12628,12859,13236,13583,13783,14139,14300,14503,14672,14859,15048,15175,15376,15630,15984,16087,16268,16464,16623,16784,16955,17141,17514,17762,17886,18057,18227,18437,18651,18904,19033,19231,19409,19620,19784,20036,20185,20363,20541,20758,20910,21132,21316,21497,21645,21870,22205,22399,22589,22775,23124,23291,23507,23719,23900,24068,24232,24465,24681,24878,25075,25264,25448,25651,25881,26228,26394,26641,26801,27025,27223,27457,27598,27723,27964,28168,28415,28623,28759,28938,29127,29697,29968,30121,30322,30515,30714,30889,31087,31311,31683,31894, 210,136,119,100,145,133,128,122,135,118,130,93,151,125,144,129,120,108,101,142,279,197,117,134,162,149,159,125,155,130,91,511,115,131,103,116,138,112,141,138,125,257,111,126,128,259,139,130,125,103,114,110,142,136,122,144,141,106,132,146,148,92,116,150,144,122,145,151,125,116,121,145,169,108,102,127,133,144,154,150,142,136,124,88,138,121,152,161,131,88,151,142,137,163,154,84,116,118,112,99,142,145,148,147,132,292,139,148,141,121,108,136,121,148,155,163,143,141,139,164,106,144,135,125,84,131,146,159,148,127,135,128,106,116,112,106,105,76,109,188,116,195,152,150,153,148,129,158,79,120,145,95, 56,267,404,571,743,963,1157,1433,1644,1795,1965,2169,2369,2549,2708,2908,3048,3196,3378,3519,3700,4139,4435,4707,4895,5099,5272,5485,5635,5825,5991,6083,6640,6921,7218,7359,7614,7841,8033,8236,8415,8590,8891,9154,9510,9688,10009,10188,10319,10455,10674,10891,11067,11257,11436,11647,11841,12021,12197,12378,12581,12776,12951,13352,13733,13927,14261,14445,14654,14797,14975,15169,15320,15545,15738,16086,16214,16401,16608,16777,16934,17097,17277,17638,17850,18024,18178,18379,18598,18782,18992,19184,19373,19546,19783,19938,20120,20301,20481,20653,20857,21052,21277,21464,21644,21777,22162,22344,22547,22730,22896,23232,23427,23628,23867,24055,24231,24375,24606,24820,25042,25181,25408,25583,25776,25965,26359,26540,26800,26949,27152,27358,27585,27704,27839,28076,28274,28520,28699,28868,29126,29243,29892,30120,30271,30475,30663,30843,31047,31166,31431,31828, 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+chr19 47492987 47512813 m84039_230401_031619_s3/197857390/ccs 175,392,610,777,1103,1263,1684,1863,1983,2193,2368,2812,3060,3274,3438,3535,3708,3848,4215,4421,4689,5037,5174,5283,5375,5592,5806,5971,6230,6433,6670,6795,6940,7044,7259,7775,7903,8036,8214,8439,8675,8854,9063,9235,9340,9431,9596,9685,9977,10134,10414,10558,10710,10912,11128,11330,11569,11710,11997,12137,12636,12913,13280,13524,13673,13894,14202,14308,14489,14669,14788,14907,15002,15087,15320,15499,15642,15865,15982,16069,16456,16748,17017,17132,17259,17471,17650,17748,18032,18425,18555,18847,19246, 146,179,166,140,158,375,178,118,146,147,124,247,213,159,92,109,108,345,145,190,294,136,79,91,121,170,164,128,202,207,110,104,103,136,154,127,110,177,224,162,167,146,169,104,90,164,88,291,155,108,126,151,171,155,195,224,140,286,139,262,276,303,242,148,144,185,105,97,179,111,79,94,84,169,135,121,190,114,86,304,169,256,114,75,103,175,93,278,357,114,237,398,346, 138,321,571,776,917,1261,1638,1862,1981,2129,2340,2492,3059,3273,3433,3530,3644,3816,4193,4360,4611,4983,5173,5253,5374,5496,5762,5970,6099,6432,6640,6780,6899,7043,7180,7413,7902,8013,8213,8438,8601,8842,9000,9232,9339,9430,9595,9684,9976,10132,10242,10540,10709,10881,11067,11323,11554,11709,11996,12136,12399,12912,13216,13522,13672,13817,14079,14307,14405,14668,14780,14867,15001,15086,15256,15455,15620,15832,15979,16068,16373,16625,17004,17131,17207,17362,17646,17743,18026,18389,18539,18792,19245,19592, 37,71,39,1,186,2,46,1,2,64,28,320,1,1,5,5,64,32,22,61,78,54,1,30,1,96,44,1,131,1,30,15,41,1,79,362,1,23,1,1,74,12,63,3,1,1,1,1,1,2,172,18,1,31,61,7,15,1,1,1,237,1,64,2,1,77,123,1,84,1,8,40,1,1,64,44,22,33,3,1,83,123,13,1,52,109,4,5,6,36,16,55,1,1, . . . 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+chr19 47495527 47524428 m54329U_210813_020940/25756168/ccs 189,575,752,1148,1338,1549,1759,1961,2143,2311,2507,2699,2875,3064,3259,3449,3580,3778,3992,4175,4505,4693,5030,5400,5764,5953,6153,6314,6527,6725,6888,7122,7302,7458,7662,8034,8221,8433,8626,8815,8984,9138,9341,9482,9665,9892,10099,10227,10407,10569,10760,10934,11118,11334,11528,11682,11963,12237,12403,12596,12750,12924,13103,13295,13467,13655,13853,14474,14648,14821,14996,15174,15369,15523,15739,15897,16099,16282,16434,16538,16976,17154,17318,17476,17815,18016,18156,18538,18834,18999,19176,20134,20286,20388,20525,20706,20833,20980,21143,21556,21749,21966,22148,22399,22572,22953,23182,23370,23520,23666,23918,24092,24305,24457,24647,24862,25179,25350,25716,25861,26002,26180,26302,26507,26662,26946,27218,27359,27666,28179,28354,28515,28662, 385,176,391,180,205,162,201,120,158,141,135,149,149,151,182,130,195,162,163,326,162,310,339,355,149,178,156,173,138,162,192,126,155,181,356,169,151,159,148,146,151,202,134,182,145,123,127,144,141,140,152,149,148,172,130,146,273,159,166,145,153,157,174,144,158,192,580,120,152,174,173,167,153,215,134,151,150,145,103,430,168,163,157,333,160,139,325,295,138,152,240,115,101,83,139,126,143,162,360,148,132,150,154,130,251,187,164,141,145,174,101,125,118,165,147,273,154,321,119,140,114,117,156,145,128,250,140,281,454,143,131,129,164, 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+chr19 47496001 47518986 m84039_230401_031619_s3/137303312/ccs 154,281,496,697,832,972,1089,1326,1494,1674,1887,2062,2180,2532,2659,2795,2913,3022,3224,3484,3635,4020,4105,4181,4325,4489,4611,4814,4902,5042,5312,5470,5624,5769,6004,6143,6400,6483,6615,6839,7230,7420,7774,8014,8339,8626,9112,9261,9423,9637,9903,10023,10139,10292,10532,10740,10892,11314,11450,11571,11784,11926,12319,12532,12682,12851,12962,13119,13393,13590,13886,14491,14893,15030,15112,15432,15580,15749,16544,16850,16965,17222,17496,17729,17952,18094,18250,18384,18526,18736,18845,18983,19369,19569,19733,20079,20272,20354,20453,20779,20943,21130,21246,21625,21711,21833,21957,22085,22248,22423,22515,22680, 126,125,121,117,114,111,96,167,147,205,113,104,309,126,113,117,108,201,211,150,384,84,75,143,89,121,183,76,138,166,157,83,100,171,138,123,79,83,161,177,151,218,146,86,208,483,145,161,206,265,118,115,116,239,204,151,395,131,120,146,141,357,212,88,162,110,156,273,89,295,604,390,136,81,272,147,168,715,305,114,200,273,232,222,141,153,133,107,205,106,137,356,199,163,345,100,79,98,259,163,186,99,355,85,121,99,123,162,174,91,111,148, 129,280,406,617,814,946,1083,1185,1493,1641,1879,2000,2166,2489,2658,2772,2912,3021,3223,3435,3634,4019,4104,4180,4324,4414,4610,4794,4890,5040,5208,5469,5553,5724,5940,6142,6266,6479,6566,6776,7016,7381,7638,7920,8100,8547,9109,9257,9422,9629,9902,10021,10138,10255,10531,10736,10891,11287,11445,11570,11717,11925,12283,12531,12620,12844,12961,13118,13392,13482,13885,14490,14881,15029,15111,15384,15579,15748,16464,16849,16964,17165,17495,17728,17951,18093,18247,18383,18491,18731,18842,18982,19339,19568,19732,20078,20179,20351,20452,20712,20942,21129,21229,21601,21710,21832,21932,22080,22247,22422,22514,22626, 25,1,90,80,18,26,6,141,1,33,8,62,14,43,1,23,1,1,1,49,1,1,1,1,1,75,1,20,12,2,104,1,71,45,64,1,134,4,49,63,214,39,136,94,239,79,3,4,1,8,1,2,1,37,1,4,1,27,5,1,67,1,36,1,62,7,1,1,1,108,1,1,12,1,1,48,1,1,80,1,1,57,1,1,1,1,3,1,35,5,3,1,30,1,1,1,93,3,1,67,1,1,17,24,1,1,25,5,1,1,1,54, . . . 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+chr19 47496027 47511981 m84008_230107_003043_s1/182523563/ccs 166,336,571,741,942,1143,1321,1516,1693,1890,2096,2249,2418,2641,2837,3034,3236,3400,3593,3763,3929,4110,4335,4485,4722,4923,5107,5292,5467,5646,5807,6006,6200,6391,6594,6784,7004,7142,7350,7535,7704,7864,8049,8218,8353,8432,8573,9055,9403,9606,9954,10114,10304,10503,10686,10860,11044,11221,11456,11673,11835,12039,12255,12405,12584,12794,12950,13098,13494,13685,13849,14073,14226,14464,14614,14830,15015,15219,15423,15651, 119,153,99,110,108,105,129,109,123,127,130,152,164,160,156,130,136,149,127,101,155,173,132,189,144,94,184,144,141,129,175,149,187,172,156,157,113,140,145,107,127,109,119,108,78,100,481,314,153,297,130,142,133,136,125,142,143,137,115,113,124,137,89,137,146,128,147,334,151,121,150,139,200,119,190,151,176,133,153,120, 83,285,489,670,851,1050,1248,1450,1625,1816,2017,2226,2401,2582,2801,2993,3164,3372,3549,3720,3864,4084,4283,4467,4674,4866,5017,5291,5436,5608,5775,5982,6155,6387,6563,6750,6941,7117,7282,7495,7642,7831,7973,8168,8326,8431,8532,9054,9369,9556,9903,10084,10256,10437,10639,10811,11002,11187,11358,11571,11786,11959,12176,12344,12542,12730,12922,13097,13432,13645,13806,13999,14212,14426,14583,14804,14981,15191,15352,15576,15771, 83,51,82,71,91,93,73,66,68,74,79,23,17,59,36,41,72,28,44,43,65,26,52,18,48,57,90,1,31,38,32,24,45,4,31,34,63,25,68,40,62,33,76,50,27,1,41,1,34,50,51,30,48,66,47,49,42,34,98,102,49,80,79,61,42,64,28,1,62,40,43,74,14,38,31,26,34,28,71,75,86, . . . 82,91,97,100,112,117,127,131,134,140,149,156,158,160,165,285,286,290,294,301,303,308,309,312,313,316,322,326,328,335,364,489,498,503,521,525,532,536,538,543,545,550,551,556,558,570,670,673,675,684,686,690,695,696,700,707,717,722,726,729,732,734,736,740,851,862,865,875,882,888,901,904,906,908,910,916,919,927,931,935,939,941,1050,1056,1077,1081,1084,1086,1089,1091,1094,1097,1100,1103,1105,1110,1112,1123,1135,1142,1248,1251,1256,1260,1263,1267,1272,1275,1278,1285,1291,1294,1298,1300,1304,1306,1309,1312,1320,1450,1463,1466,1471,1475,1477,1479,1482,1484,1490,1495,1497,1502,1515,1625,1637,1644,1645,1652,1656,1675,1676,1692,1774,1816,1826,1829,1834,1837,1838,1840,1862,1866,1867,1869,1871,1887,1889,1981,2017,2023,2034,2037,2042,2046,2048,2052,2054,2058,2060,2063,2066,2071,2076,2078,2095,2226,2229,2233,2243,2248,2401,2409,2410,2415,2417,2468,2582,2587,2606,2608,2617,2622,2623,2629,2630,2633,2640,2677,2801,2807,2813,2817,2819,2836,2993,2997,2998,3000,3004,3030,3033,3164,3170,3174,3187,3190,3195,3200,3202,3217,3223,3225,3235,3372,3387,3391,3393,3398,3399,3549,3556,3559,3564,3577,3581,3584,3586,3592,3720,3731,3734,3736,3740,3755,3762,3864,3866,3898,3904,3906,3928,4046,4084,4109,4283,4285,4301,4305,4307,4322,4334,4467,4480,4484,4674,4677,4680,4686,4689,4691,4712,4721,4866,4868,4872,4877,4878,4881,4883,4885,4888,4890,4893,4897,4900,4915,4922,5017,5041,5045,5047,5070,5073,5082,5085,5088,5090,5091,5092,5093,5095,5096,5103,5106,5291,5436,5438,5439,5445,5446,5449,5457,5463,5466,5574,5608,5610,5611,5614,5615,5618,5620,5623,5626,5633,5637,5639,5642,5645,5775,5780,5803,5806,5982,5990,5997,6003,6005,6155,6170,6175,6177,6180,6184,6189,6191,6193,6197,6199,6387,6390,6563,6565,6567,6569,6585,6593,6750,6758,6763,6765,6768,6775,6783,6941,6948,6951,6958,6963,6972,6974,6977,6979,6984,6989,7003,7117,7119,7128,7131,7135,7138,7141,7282,7309,7320,7325,7327,7329,7331,7337,7340,7349,7495,7497,7531,7534,7642,7646,7650,7675,7678,7688,7690,7692,7703,7802,7831,7833,7844,7847,7853,7856,7861,7863,7973,7989,7991,7993,8012,8013,8016,8040,8048,8168,8184,8190,8194,8204,8217,8326,8344,8348,8352,8431,8532,8537,8554,8556,8572,9054,9369,9387,9389,9394,9402,9556,9567,9569,9571,9578,9589,9591,9595,9601,9605,9903,9907,9915,9917,9921,9926,9927,9929,9953,10084,10089,10104,10108,10113,10256,10263,10296,10298,10303,10390,10437,10447,10463,10476,10482,10488,10493,10496,10502,10639,10665,10685,10811,10814,10817,10819,10830,10854,10856,10859,11002,11008,11014,11017,11019,11022,11030,11038,11043,11187,11189,11197,11199,11201,11207,11210,11217,11220,11358,11368,11385,11393,11395,11397,11401,11404,11412,11414,11418,11421,11424,11430,11439,11455,11571,11575,11578,11582,11585,11589,11591,11593,11602,11604,11607,11608,11618,11621,11625,11627,11629,11631,11636,11645,11651,11666,11672,11786,11790,11796,11798,11800,11802,11817,11821,11830,11834,11870,11959,11962,11965,11988,11991,11993,12004,12008,12012,12016,12019,12038,12176,12180,12182,12185,12192,12195,12199,12228,12231,12234,12237,12239,12241,12243,12254,12344,12363,12370,12376,12380,12383,12394,12396,12401,12404,12542,12544,12545,12548,12552,12557,12562,12564,12567,12572,12574,12575,12581,12583,12730,12734,12740,12741,12747,12763,12764,12766,12768,12773,12775,12793,12840,12922,12933,12934,12939,12944,12946,12949,13097,13432,13440,13442,13443,13446,13449,13453,13454,13456,13464,13467,13472,13493,13645,13647,13661,13668,13675,13677,13680,13684,13806,13815,13820,13833,13835,13837,13841,13848,13999,14001,14011,14015,14017,14020,14026,14028,14030,14036,14038,14040,14072,14212,14215,14217,14222,14225,14426,14431,14441,14463,14583,14605,14606,14608,14613,14804,14807,14819,14829,14981,14988,14990,15011,15014,15191,15195,15209,15211,15212,15216,15218,15257,15352,15356,15362,15371,15374,15377,15379,15382,15385,15387,15391,15397,15409,15416,15419,15422,15576,15582,15586,15588,15590,15591,15595,15597,15601,15606,15627,15644,15650,15771,15773,15777,15780,15791,15794,15815,15828,15833,15845,15853,15856, +chr19 47496290 47515520 m84008_230107_003043_s1/206769025/ccs 167,370,561,792,965,1372,1562,1752,1953,2160,2416,2606,2780,2984,3185,3375,3527,3726,3956,4119,4332,4507,4707,4911,5070,5290,5456,5636,5848,6034,6212,6409,6595,6766,6939,7092,7339,7518,7701,7868,8054,8238,8439,8609,8781,8983,9161,9350,9572,9755,9996,10143,10310,10535,10727,10907,11110,11310,11461,11661,11857,12064,12225,12523,12720,12889,13066,13258,13461,13628,13820,14016,14206,14382,14541,14769,14986,15158,15400,15605,15792,15979,16079,16344,16559,16730,16932,17117,17336,17489,17680,17828,18027,18324,18540, 161,141,152,131,123,122,111,140,107,118,118,119,147,120,122,104,166,150,98,125,152,179,151,139,142,112,143,186,172,177,190,138,134,158,152,168,165,137,130,127,136,138,150,136,166,142,183,144,124,155,146,141,189,170,156,141,151,150,133,135,155,114,276,136,127,169,147,124,107,165,136,146,175,158,148,167,100,122,108,101,110,82,175,149,138,108,146,131,98,119,139,138,208,118,97, 129,328,511,713,923,1088,1494,1673,1892,2060,2278,2534,2725,2927,3104,3307,3479,3693,3876,4054,4244,4484,4686,4858,5050,5212,5402,5599,5822,6020,6211,6402,6547,6729,6924,7091,7260,7504,7655,7831,7995,8190,8376,8589,8745,8947,9125,9344,9494,9696,9910,10142,10284,10499,10705,10883,11048,11261,11460,11594,11796,12012,12178,12501,12659,12847,13058,13213,13382,13568,13793,13956,14162,14381,14540,14689,14936,15086,15280,15508,15706,15902,16061,16254,16493,16697,16838,17078,17248,17434,17608,17819,17966,18235,18442, 38,42,50,79,42,284,68,79,61,100,138,72,55,57,81,68,48,33,80,65,88,23,21,53,20,78,54,37,26,14,1,7,48,37,15,1,79,14,46,37,59,48,63,20,36,36,36,6,78,59,86,1,26,36,22,24,62,49,1,67,61,52,47,22,61,42,8,45,79,60,27,60,44,1,1,80,50,72,120,97,86,77,18,90,66,33,94,39,88,55,72,9,61,89,98, . . . 129,134,166,328,334,340,342,346,349,355,360,361,363,364,369,446,511,517,522,535,537,539,544,547,560,713,716,719,722,723,728,730,733,738,744,751,757,758,760,762,764,765,766,769,772,777,784,788,791,923,930,931,933,937,940,942,945,946,953,957,959,964,1088,1092,1120,1128,1133,1146,1149,1165,1168,1170,1175,1184,1246,1249,1283,1309,1318,1321,1331,1333,1358,1360,1366,1371,1494,1496,1500,1517,1518,1523,1526,1527,1529,1532,1537,1539,1561,1673,1675,1677,1682,1684,1687,1690,1694,1695,1698,1705,1707,1712,1717,1720,1722,1724,1726,1727,1729,1732,1733,1735,1739,1740,1749,1751,1847,1892,1896,1897,1899,1901,1908,1909,1911,1916,1919,1924,1931,1933,1934,1947,1952,2028,2060,2072,2076,2090,2092,2105,2111,2113,2129,2134,2135,2137,2139,2142,2143,2146,2148,2155,2157,2159,2244,2278,2281,2283,2284,2287,2310,2312,2315,2323,2326,2329,2332,2339,2341,2347,2350,2355,2358,2362,2379,2390,2403,2404,2410,2415,2534,2536,2540,2546,2561,2564,2567,2572,2575,2585,2587,2600,2603,2605,2725,2730,2732,2735,2736,2750,2751,2756,2760,2767,2771,2779,2834,2927,2932,2941,2943,2949,2962,2971,2977,2981,2983,3052,3104,3114,3119,3123,3125,3138,3139,3163,3165,3178,3183,3184,3307,3311,3314,3316,3322,3325,3328,3330,3333,3336,3337,3339,3346,3348,3359,3360,3362,3366,3374,3417,3451,3479,3493,3495,3498,3506,3510,3511,3521,3524,3526,3569,3693,3694,3701,3703,3708,3715,3717,3725,3876,3879,3892,3932,3955,4054,4072,4078,4079,4086,4087,4089,4092,4095,4099,4104,4108,4110,4114,4118,4244,4249,4261,4274,4275,4282,4286,4289,4290,4296,4301,4303,4313,4331,4484,4492,4506,4686,4688,4690,4702,4706,4858,4859,4863,4870,4881,4889,4892,4903,4910,5050,5061,5063,5069,5096,5212,5238,5258,5260,5262,5266,5271,5273,5277,5289,5402,5425,5429,5432,5435,5436,5438,5440,5446,5455,5599,5635,5822,5829,5832,5843,5847,6020,6031,6033,6211,6402,6408,6547,6549,6553,6571,6575,6576,6594,6729,6730,6732,6765,6924,6931,6934,6938,7091,7141,7260,7278,7301,7307,7311,7316,7331,7338,7504,7508,7517,7655,7661,7665,7668,7673,7680,7682,7685,7690,7693,7700,7831,7836,7838,7862,7867,7995,7998,8001,8010,8029,8038,8039,8047,8053,8190,8192,8195,8202,8212,8237,8376,8378,8384,8388,8390,8392,8394,8400,8421,8423,8438,8589,8608,8745,8757,8773,8776,8780,8947,8967,8970,8973,8982,9125,9149,9154,9160,9344,9349,9494,9497,9500,9505,9524,9529,9535,9549,9552,9558,9565,9571,9696,9698,9702,9704,9721,9743,9745,9754,9910,9915,9928,9974,9995,10142,10284,10309,10499,10501,10513,10519,10524,10529,10532,10534,10599,10705,10720,10726,10883,10906,11048,11074,11077,11078,11088,11095,11099,11105,11109,11261,11267,11271,11284,11291,11300,11309,11460,11594,11595,11598,11615,11623,11626,11628,11631,11632,11636,11637,11640,11641,11646,11647,11652,11653,11660,11796,11803,11812,11822,11830,11838,11856,12012,12015,12018,12024,12034,12039,12056,12058,12060,12063,12178,12182,12188,12195,12210,12212,12215,12221,12224,12501,12522,12659,12662,12664,12666,12669,12677,12682,12707,12710,12719,12847,12852,12854,12856,12874,12877,12884,12888,13058,13065,13213,13241,13243,13247,13252,13254,13257,13382,13389,13435,13441,13446,13454,13457,13460,13536,13568,13573,13590,13593,13595,13627,13793,13802,13819,13956,13976,13982,13985,13995,13998,14005,14010,14011,14015,14162,14174,14192,14200,14205,14381,14540,14689,14717,14718,14723,14728,14732,14735,14742,14744,14750,14756,14762,14768,14936,14938,14977,14980,14985,15032,15086,15088,15097,15102,15105,15107,15111,15114,15117,15118,15121,15124,15126,15128,15131,15134,15138,15141,15143,15153,15157,15280,15283,15292,15294,15300,15313,15315,15320,15326,15328,15331,15335,15344,15346,15347,15349,15355,15359,15361,15367,15379,15399,15508,15511,15512,15514,15520,15556,15567,15574,15579,15584,15604,15706,15717,15720,15730,15731,15737,15741,15745,15758,15765,15772,15775,15791,15902,15917,15921,15925,15927,15931,15934,15974,15978,16061,16070,16075,16078,16254,16256,16258,16265,16268,16271,16288,16290,16292,16295,16314,16329,16331,16333,16335,16337,16343,16493,16494,16496,16501,16503,16504,16507,16509,16514,16517,16524,16530,16536,16539,16540,16543,16545,16552,16556,16558,16697,16700,16705,16707,16713,16715,16722,16724,16727,16729,16838,16840,16844,16846,16847,16850,16853,16855,16858,16863,16865,16869,16871,16872,16875,16879,16890,16895,16899,16919,16921,16922,16923,16925,16929,16931,17078,17082,17091,17094,17101,17108,17109,17112,17116,17248,17253,17258,17265,17279,17288,17290,17292,17318,17320,17323,17324,17326,17328,17335,17434,17438,17444,17448,17467,17470,17488,17608,17612,17616,17620,17624,17633,17642,17645,17648,17652,17655,17677,17679,17819,17822,17827,17966,17972,17986,17992,17993,17996,17998,18001,18004,18009,18018,18026,18235,18238,18246,18248,18254,18267,18269,18271,18274,18287,18288,18294,18295,18297,18299,18305,18312,18316,18320,18322,18323,18442,18449,18453,18455,18457,18460,18461,18469,18471,18475,18479,18488,18495,18505,18507,18511,18512,18513,18533,18539,18637,18643,18645,18649,18653,18654,18656,18660,18679,18682,18684,18686,18695,18706,18710,18713,18720,18731,18735,18736,18747,18763,18769,18782,18784,18818,18837,18839,18841,18846,18853,18854,18861,18866,18868,18878,18884,18886,18887,18895,18896,18903,18917,18922,18924,18927,18930,18935,18942,18948,18950,18953,18958,18959,18967,18978,18990,18994,18996,19000,19003,19006,19013,19016,19020,19021,19023,19026,19029,19034,19039,19045,19057,19082,19084,19093,19098,19109,19113,19120,19123,19141,19145,19147,19149,19150,19152,19162, +chr19 47496312 47517829 m64076_221119_202646/144639565/ccs 222,428,646,777,1050,1231,1418,1601,1794,1974,2182,2373,2568,2734,2918,3095,3275,3417,3622,3818,3997,4197,4328,5245,5468,5586,5758,5923,6130,6283,6478,6802,7190,7331,7540,7746,7906,8077,8262,8444,8638,8836,9019,9219,9350,9532,9715,9907,10060,10284,10457,10669,10863,11062,11232,11413,11589,11783,11977,12123,12302,12483,12661,12845,13137,13318,13492,13672,13888,14061,14255,14460,14766,14974,15198,15389,15603,15771,15935,16108,16350,16522,16644,16863,17014,17166,17357,17579,17871,18043,18354,18500,19382,19559,19719,19910,20085,20266,20448,20651,20852,20999,21169, 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+chr19 47496976 47518408 m84039_230401_034725_s4/46793118/ccs 190,350,499,721,893,1071,1266,1686,1848,2105,2268,2667,2827,2985,3389,3554,3988,4137,4313,4527,4868,5095,5256,5443,5913,6082,6239,6413,6595,6790,6966,7197,7414,7577,7723,7926,8157,8560,8731,8928,9100,9346,9462,9629,9837,10008,10197,10394,10539,10759,10881,11063,11144,11260,11431,11626,11785,11995,12182,12395,12553,12764,12944,13125,13336,13540,13677,13879,13958,14079,14262,14451,14694,14878,15091,15258,15433,15635,15792,15988,16145,16341,16529,16707,16905,17077,17190,17354,17468,17609,17886,18638,18811,19002,19271,19601,19791,19940,20089,20267,20447,20652,20864,21064, 112,146,113,152,159,163,144,128,116,109,154,88,144,105,116,142,92,90,107,132,130,151,125,90,110,101,173,145,103,171,177,124,150,117,200,102,135,130,139,118,125,96,158,171,100,143,117,144,138,77,131,80,86,116,146,89,167,121,199,137,180,136,165,124,165,136,188,78,81,136,153,160,132,103,121,113,132,90,169,127,123,155,151,166,171,109,163,113,137,137,103,170,131,107,270,113,125,138,168,143,204,160,145,115, 128,302,496,612,873,1052,1234,1410,1814,1964,2214,2422,2755,2971,3090,3505,3696,4080,4227,4420,4659,4998,5246,5381,5533,6023,6183,6412,6558,6698,6961,7143,7321,7564,7694,7923,8028,8292,8690,8870,9046,9225,9442,9620,9800,9937,10151,10314,10538,10677,10836,11012,11143,11230,11376,11577,11715,11952,12116,12381,12532,12733,12900,13109,13249,13501,13676,13865,13957,14039,14215,14415,14611,14826,14981,15212,15371,15565,15725,15961,16115,16268,16496,16680,16873,17076,17186,17353,17467,17605,17746,17989,18808,18942,19109,19541,19714,19916,20078,20257,20410,20651,20812,21009, 62,48,3,109,20,19,32,276,34,141,54,245,72,14,299,49,292,57,86,107,209,97,10,62,380,59,56,1,37,92,5,54,93,13,29,3,129,268,41,58,54,121,20,9,37,71,46,80,1,82,45,51,1,30,55,49,70,43,66,14,21,31,44,16,87,39,1,14,1,40,47,36,83,52,110,46,62,70,67,27,30,73,33,27,32,1,4,1,1,4,140,649,3,60,162,60,77,24,11,10,37,1,52,55, . . . 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+chr19 47497482 47512745 m64076_210328_012155/85001617/ccs 168,347,523,864,1105,1417,1588,1766,1946,2104,2305,2452,2664,2821,3046,3395,3596,3787,3918,4307,4512,4747,4824,5021,5403,5553,6046,6404,6719,6908,7107,7304,7472,8020,8589,8753,8959,9146,9348,9510,9694,9898,10283,10460,10637,11032,11751,11966,12153,12458,12922,13034,13212,13835,14658,14818,14942, 169,128,127,147,105,127,138,109,133,136,102,104,119,142,143,98,151,130,147,176,147,76,173,164,140,114,133,114,152,154,128,117,149,124,110,153,95,91,118,139,136,128,110,130,149,120,132,106,115,128,85,149,141,137,107,123,131, 337,475,650,1011,1210,1544,1726,1875,2079,2240,2407,2556,2783,2963,3189,3493,3747,3917,4065,4483,4659,4823,4997,5185,5543,5667,6179,6518,6871,7062,7235,7421,7621,8144,8699,8906,9054,9237,9466,9649,9830,10026,10393,10590,10786,11152,11883,12072,12268,12586,13007,13183,13353,13972,14765,14941,15073, 10,48,214,94,207,44,40,71,25,65,45,108,38,83,206,103,40,1,242,29,88,1,24,218,10,379,225,201,37,45,69,51,399,445,54,53,92,111,44,45,68,257,67,47,246,599,83,81,190,336,27,29,482,686,53,1,40, . . . 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+chr19 47497550 47514811 m84039_230404_003541_s3/53019764/ccs 184,374,527,736,976,1206,1417,1610,1802,2005,2222,2363,2612,2797,2983,3155,3348,3585,3735,3942,4123,4294,4494,4680,4843,5077,5267,5417,5742,5936,6193,6409,6569,6949,7110,7361,7520,7686,7871,8503,8677,8875,9067,9262,9482,9635,9812,10013,10164,10365,10536,10758,10964,11124,11319,11503,11712,11903,12073,12272,12427,12653,12859,13076,13229,13394,13583,13806,13980,14164,14326,14569,14704,14855,15045,15318,15431,15603,15763,15938,16081,16242,16431,16622,17006, 145,131,119,129,107,124,135,131,150,137,133,173,114,138,132,138,128,104,157,107,144,143,135,160,146,151,149,155,81,173,93,128,121,160,158,107,121,139,157,144,158,146,156,141,124,136,149,115,141,112,148,128,116,149,96,160,137,150,128,148,166,140,150,112,113,188,88,137,122,95,168,113,117,123,89,107,138,158,112,132,126,135,115,102,100, 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+chr19 47498629 47511783 m54329U_210326_192251/74844661/ccs 206,364,553,721,900,1060,1271,1436,1622,1766,1952,2120,2292,2484,2689,2876,3050,3233,3417,3604,3792,3976,4185,4303,4516,4866,5046,5224,5550,5715,5868,6071,6221,6396,6564,6743,6906,7077,7305,7434,7655,7831,7999,8199,8385,8604,8803,8960,9141,9340,9525,9703,10080,10250,10433,10591,10777,10966,11141,11293,11508,11707,11897,12163,12320,12496,12707,12873, 128,136,124,142,148,177,120,158,143,156,144,161,151,164,137,115,154,138,143,162,142,150,117,142,291,151,148,298,132,150,156,145,139,138,127,122,123,133,80,153,139,127,179,170,133,134,115,149,145,134,130,321,137,170,157,143,102,143,147,138,156,105,148,75,133,135,141,134, 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+chr19 47498655 47517467 m64076_210328_012155/132450463/ccs 112,270,455,648,877,1036,1214,1417,1628,1792,1975,2187,2368,2557,2768,2969,3168,3391,3581,3798,3981,4221,4422,4646,4848,5029,5238,5420,5603,5795,5967,6150,6356,6543,6708,6913,7080,7273,7474,7676,7973,8214,8360,8588,8783,8971,9121,9304,9586,9736,9934,10115,10289,10492,10619,10830,11101,11264,11487,11706,11907,12102,12323,12515,12717,12886,13104,13320,13501,13737,13937,14111,14330,14539,14723,14960,15155,15383,16002,16207,16580,17010,17190,17334,17560,17747,17897,18084,18245,18422,18559, 151,128,110,113,99,177,136,163,144,140,150,117,151,142,134,130,141,96,123,116,139,142,131,146,129,139,136,145,111,171,160,147,132,142,131,139,137,144,143,115,101,87,137,128,121,75,117,117,88,116,127,162,148,126,169,136,107,117,94,139,123,131,117,143,135,132,129,120,113,90,122,122,121,112,138,102,159,579,114,97,110,131,136,174,110,121,138,111,130,114,122, 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+chr19 47499085 47514363 m54329U_210326_192251/105579375/ccs 206,421,608,823,1061,1168,1329,1489,1653,1855,2065,2210,2427,2633,2830,3031,3170,3392,3601,3770,3924,4113,4365,4479,4758,4898,5086,5433,5650,5813,6027,6235,6409,6563,6768,6940,7133,7351,7555,7760,7966,8159,8351,8548,8693,8918,9074,9270,9446,9699,9887,10066,10201,10414,10574,10785,10963,11180,11354,11550,11741,11937,12129,12316,12481,12713,12860,13232,13468,13651,13856,14078,14228,14351,14528,14700,14857,15050,15184, 129,127,132,127,76,160,93,141,123,138,106,103,121,128,131,92,150,153,106,135,162,166,108,107,80,119,122,137,125,135,92,121,148,164,124,143,157,140,167,137,132,152,89,136,156,112,139,158,101,125,127,126,170,126,180,144,159,148,175,102,145,154,156,142,149,140,152,128,131,142,138,101,122,141,127,90,111,107,147, 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+chr19 47499206 47516044 m54329U_210813_020940/137365885/ccs 223,589,747,947,1154,1329,1529,1732,1928,2108,2283,2491,2661,2869,3032,3250,3411,3650,3832,4013,4196,4345,4550,4756,4942,5135,5310,5516,5726,5858,6096,6301,6564,6740,6876,7039,7245,7453,7643,7806,8028,8195,8700,8870,9069,9234,9413,9795,9975,10507,10682,10868,11044,11199,11388,11602,11795,11975,12212,12395,12589,12774,12945,13134,13294,13453,13870,14050,14222,14391,14550,14754,14939,15093,15262,15410,15617,16464, 100,96,150,142,111,142,138,137,151,136,147,144,176,132,183,100,139,121,110,115,148,140,131,145,147,160,136,180,116,200,135,106,112,85,121,159,132,111,128,164,117,475,141,147,99,157,148,96,291,136,129,111,123,154,157,157,137,127,87,157,93,136,149,113,158,155,125,164,147,151,128,124,138,137,127,130,106,138, 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+chr19 47499682 47516253 m54329U_210323_190418/100861377/ccs 142,269,474,678,852,1217,1364,1521,1687,1852,1998,2185,2369,2556,2761,2987,3142,3353,3443,3632,3821,3985,4174,4359,4543,4713,4946,5110,5340,5528,5699,5915,6080,6293,6506,6681,6869,7100,7281,7466,7610,7840,8030,8199,8381,8614,8728,8927,9213,9364,9528,9697,9852,10011,10194,10341,10533,10757,10910,11091,11261,11422,11591,11761,11942,12129,12337,12494,12648,12788,12955,13250,13399,13581,13774,14028,14160,14334,14544,14709,14883,15061,15231,15391,15753,15889,16293, 126,153,145,84,133,146,127,121,86,124,118,123,97,156,130,113,127,84,147,113,134,124,119,128,135,130,116,127,120,117,124,132,151,125,92,107,139,134,115,118,132,95,105,99,97,89,122,198,136,122,168,110,106,91,123,98,127,102,137,127,109,120,122,146,137,108,115,116,119,130,122,98,148,110,123,86,143,101,126,91,105,108,110,159,82,364,102, 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+chr19 47501338 47519083 m84039_230404_003541_s3/198186026/ccs 141,356,526,698,896,1083,1294,1465,1665,1889,2073,2283,2454,2641,2861,3055,3248,3619,3801,4002,4202,4405,4629,4803,4887,4982,5228,5436,5616,5803,6012,6205,6400,6596,6792,7042,7167,7368,7542,7733,7916,8071,8222,8421,8651,8807,8991,9195,9391,9580,9780,9980,10346,10557,10740,10963,11086,11472,11561,11755,11917,12297,12373,12593,12743,12942,13118,13308,13465,14316,14459,14624,14796,15012,15206,15377,15542,15728,15937,16108,16238,16316,16562,17105,17258,17450, 158,125,155,164,124,146,103,164,141,115,200,162,131,124,124,135,309,155,157,119,143,141,149,83,90,142,131,159,161,175,149,154,95,134,126,97,113,87,115,116,135,127,130,146,113,144,141,136,133,150,166,319,137,106,170,122,240,88,185,130,275,75,146,116,99,139,118,99,125,142,126,121,148,174,153,138,145,147,125,105,77,215,273,152,142,140, 94,299,481,681,862,1020,1229,1397,1629,1806,2004,2273,2445,2585,2765,2985,3190,3557,3774,3958,4121,4345,4546,4778,4886,4977,5124,5359,5595,5777,5978,6161,6359,6495,6730,6918,7139,7280,7455,7657,7849,8051,8198,8352,8567,8764,8951,9132,9331,9524,9730,9946,10299,10483,10663,10910,11085,11326,11560,11746,11885,12192,12372,12519,12709,12842,13081,13236,13407,13590,14458,14585,14745,14944,15186,15359,15515,15687,15875,16062,16213,16315,16531,16835,17257,17400,17590, 47,57,45,17,34,63,65,68,36,83,69,10,9,56,96,70,58,62,27,44,81,60,83,25,1,5,104,77,21,26,34,44,41,101,62,124,28,88,87,76,67,20,24,69,84,43,40,63,60,56,50,34,47,74,77,53,1,146,1,9,32,105,1,74,34,100,37,72,58,726,1,39,51,68,20,18,27,41,62,46,25,1,31,270,1,50,34, . . . 0,2,3,5,6,94,107,110,112,117,118,123,127,134,137,140,299,302,306,309,311,314,317,322,324,328,330,333,334,336,338,355,481,497,498,500,503,506,514,525,681,690,695,697,862,867,869,872,876,895,1020,1021,1023,1057,1059,1082,1229,1233,1247,1249,1252,1255,1270,1283,1285,1293,1397,1420,1430,1435,1460,1464,1629,1640,1643,1645,1664,1806,1809,1811,1830,1832,1833,1844,1872,1874,1888,2004,2006,2012,2021,2029,2034,2038,2041,2044,2046,2049,2052,2056,2059,2065,2070,2072,2273,2275,2278,2282,2445,2451,2453,2585,2606,2615,2628,2631,2632,2640,2765,2774,2776,2779,2790,2840,2860,2985,2990,3006,3008,3018,3020,3030,3033,3036,3044,3052,3054,3190,3202,3207,3215,3217,3225,3227,3230,3232,3247,3557,3566,3569,3577,3579,3589,3591,3614,3618,3702,3774,3776,3792,3798,3800,3958,3972,3977,4001,4121,4129,4147,4149,4155,4157,4161,4163,4165,4173,4184,4190,4194,4201,4345,4350,4381,4385,4391,4395,4396,4399,4404,4546,4548,4553,4560,4567,4569,4603,4608,4614,4620,4622,4627,4628,4750,4778,4780,4786,4790,4797,4800,4802,4886,4977,4981,5080,5124,5126,5131,5136,5138,5147,5150,5152,5157,5170,5176,5182,5190,5196,5200,5202,5204,5206,5223,5227,5359,5379,5391,5398,5400,5405,5408,5409,5410,5415,5417,5430,5433,5435,5475,5595,5596,5601,5609,5615,5777,5802,5978,5980,6003,6011,6119,6161,6195,6199,6200,6204,6359,6361,6382,6394,6395,6399,6495,6497,6536,6544,6552,6557,6565,6571,6576,6589,6591,6595,6730,6733,6740,6743,6745,6749,6752,6762,6776,6779,6781,6791,6918,6923,6932,6936,6938,6941,6943,6946,6953,6960,6962,6968,6972,6975,6982,6988,6991,7000,7021,7041,7139,7158,7166,7280,7295,7322,7344,7346,7347,7352,7354,7367,7455,7463,7480,7509,7510,7513,7516,7528,7530,7539,7541,7657,7660,7685,7702,7712,7717,7726,7728,7730,7732,7849,7852,7876,7893,7902,7915,8051,8064,8067,8070,8198,8218,8221,8352,8395,8401,8409,8412,8414,8420,8567,8569,8578,8582,8589,8591,8600,8601,8612,8614,8618,8634,8638,8645,8648,8650,8735,8764,8767,8771,8776,8778,8780,8786,8789,8793,8798,8806,8920,8951,8966,8969,8970,8979,8984,8990,9103,9132,9151,9154,9156,9166,9174,9177,9182,9194,9331,9351,9354,9355,9362,9367,9369,9378,9380,9384,9390,9524,9535,9567,9571,9574,9579,9730,9736,9742,9744,9751,9754,9755,9757,9761,9762,9765,9767,9770,9774,9779,9946,9949,9952,9960,9963,9968,9970,9974,9976,9979,10299,10301,10303,10305,10306,10322,10327,10345,10483,10486,10489,10490,10492,10508,10514,10520,10523,10526,10528,10540,10545,10548,10551,10556,10623,10663,10677,10687,10694,10710,10714,10716,10718,10735,10736,10739,10910,10946,10953,10956,10957,10962,11085,11326,11328,11352,11371,11376,11379,11380,11397,11400,11402,11405,11410,11417,11418,11420,11421,11423,11424,11430,11441,11457,11471,11560,11746,11749,11754,11838,11885,11888,11890,11892,11895,11897,11904,11908,11910,11912,11914,11916,12192,12207,12210,12211,12214,12217,12219,12221,12231,12236,12239,12241,12243,12252,12255,12257,12258,12260,12271,12273,12275,12279,12291,12296,12372,12404,12519,12521,12529,12533,12535,12543,12547,12550,12552,12557,12561,12564,12565,12567,12572,12574,12576,12583,12585,12589,12592,12709,12718,12742,12842,12854,12859,12870,12872,12874,12877,12879,12886,12888,12893,12896,12897,12900,12901,12903,12904,12906,12912,12914,12920,12922,12926,12929,12931,12941,13081,13085,13097,13100,13104,13105,13107,13109,13117,13236,13238,13243,13247,13251,13253,13255,13258,13260,13268,13272,13273,13292,13294,13297,13305,13307,13407,13409,13430,13440,13456,13464,13590,13607,13609,13616,13624,13628,13630,13634,13638,13639,13641,13645,13651,13664,13665,13667,13669,13671,13672,13682,13691,13698,13705,13716,13720,13721,13728,13782,13790,13800,13803,13812,13822,13824,13829,13831,13838,13839,13840,13846,13856,13859,13863,13864,13869,13871,13880,13881,13888,13891,13893,13895,13897,13902,13907,13909,13911,13912,13915,13920,13927,13933,13935,13938,13939,13943,13944,13945,13985,13988,13991,13992,13995,14005,14006,14011,14014,14024,14050,14066,14068,14070,14078,14080,14083,14108,14117,14126,14130,14132,14134,14137,14142,14145,14166,14169,14178,14182,14187,14191,14193,14198,14200,14206,14207,14208,14209,14212,14213,14218,14219,14221,14269,14271,14276,14279,14281,14283,14285,14287,14292,14308,14315,14458,14585,14595,14599,14605,14609,14621,14623,14702,14745,14754,14765,14774,14775,14784,14795,14944,14947,14952,14955,14957,14960,14962,14965,14988,14989,14998,15001,15003,15011,15186,15193,15201,15203,15205,15359,15360,15365,15374,15376,15515,15518,15521,15524,15526,15530,15531,15534,15538,15541,15687,15698,15711,15721,15727,15875,15878,15883,15899,15901,15909,15913,15917,15918,15921,15927,15929,15936,16062,16068,16070,16072,16074,16076,16085,16107,16213,16227,16229,16235,16237,16315,16531,16532,16549,16552,16561,16835,16841,16845,16852,16855,16867,16874,16877,16879,16880,16886,16891,16893,16898,16901,16902,16906,16909,16911,16912,16916,16917,16923,16924,16926,16928,16934,16935,16937,16940,16941,16945,16947,16948,16952,16955,16958,16961,16962,16964,16967,16970,16975,16977,16986,16989,16991,16993,16996,16999,17005,17007,17011,17015,17020,17038,17039,17041,17043,17045,17049,17052,17053,17055,17057,17065,17069,17071,17073,17077,17080,17082,17104,17216,17257,17364,17400,17410,17415,17418,17421,17425,17435,17441,17444,17446,17449,17590,17604,17616,17623,17728,17732, +chr19 47501400 47513749 m54329U_210323_190418/100534861/ccs 205,406,596,784,942,1127,1347,1508,1699,1861,2061,2233,2431,2638,2824,2993,3178,3345,3520,3710,3936,4097,4327,4517,4671,4877,5038,5264,5612,5825,6005,6204,6391,6583,6752,6937,7150,7331,7505,7677,7886,8043,8264,8399,8595,8743,9000,9174,9414,9780,9974,10182,10346,10578,10771,10910,11105,11367,11551,11753,11920, 132,166,150,100,159,139,149,169,137,183,142,178,166,149,137,135,152,152,184,152,152,150,126,120,174,132,163,315,167,136,147,154,149,150,159,166,141,140,159,173,153,162,111,159,135,186,138,162,328,113,146,150,179,122,122,139,121,137,143,117,136, 187,337,572,746,884,1101,1266,1496,1677,1836,2044,2203,2411,2597,2787,2961,3128,3330,3497,3704,3862,4088,4247,4453,4637,4845,5009,5201,5579,5779,5961,6152,6358,6540,6733,6911,7103,7291,7471,7664,7850,8039,8205,8375,8558,8730,8929,9138,9336,9742,9893,10120,10332,10525,10700,10893,11049,11226,11504,11694,11870,12056, 18,69,24,38,58,26,81,12,22,25,17,30,20,41,37,32,50,15,23,6,74,9,80,64,34,32,29,63,33,46,44,52,33,43,19,26,47,40,34,13,36,4,59,24,37,13,71,36,78,38,81,62,14,53,71,17,56,141,47,59,50,38, . . . 7,10,15,17,20,22,187,188,191,193,196,198,203,204,231,337,339,342,345,348,354,359,362,368,371,376,378,384,385,387,392,393,396,397,399,402,405,572,576,578,579,592,595,746,749,752,755,761,768,774,777,783,884,900,905,906,921,923,934,936,941,1101,1107,1113,1114,1116,1126,1266,1268,1272,1273,1275,1297,1304,1306,1307,1309,1311,1313,1317,1318,1320,1324,1326,1329,1330,1336,1346,1496,1497,1499,1504,1507,1677,1691,1698,1836,1839,1843,1860,2044,2045,2047,2058,2060,2203,2210,2222,2225,2232,2411,2424,2426,2430,2597,2600,2602,2605,2613,2619,2630,2631,2637,2787,2790,2792,2799,2823,2961,2968,2982,2990,2992,3128,3131,3134,3140,3143,3145,3149,3153,3155,3163,3168,3170,3171,3177,3330,3332,3344,3497,3500,3506,3513,3519,3704,3707,3709,3862,3875,3884,3885,3888,3893,3894,3898,3903,3905,3911,3913,3935,4088,4090,4092,4096,4247,4251,4254,4258,4263,4264,4273,4309,4322,4325,4326,4453,4463,4465,4468,4470,4474,4481,4487,4489,4492,4493,4501,4508,4516,4637,4644,4646,4651,4663,4670,4845,4851,4859,4862,4876,5009,5010,5013,5016,5019,5021,5026,5028,5031,5033,5037,5201,5203,5218,5219,5221,5224,5226,5235,5263,5579,5580,5582,5587,5591,5594,5608,5611,5779,5796,5798,5824,5961,5967,5973,5978,5980,5982,5986,6001,6004,6152,6155,6156,6160,6162,6166,6168,6179,6180,6183,6186,6188,6190,6192,6195,6203,6309,6358,6363,6366,6367,6370,6375,6380,6383,6390,6470,6540,6544,6547,6549,6552,6553,6567,6578,6581,6582,6677,6733,6736,6739,6751,6911,6913,6916,6917,6922,6923,6927,6933,6936,7103,7109,7116,7119,7123,7131,7133,7136,7147,7149,7291,7298,7312,7316,7319,7321,7330,7471,7477,7483,7485,7492,7504,7664,7666,7670,7672,7674,7676,7850,7854,7859,7865,7871,7873,7882,7885,8009,8039,8042,8072,8151,8205,8215,8217,8228,8231,8232,8237,8241,8259,8263,8375,8380,8396,8398,8558,8571,8573,8578,8582,8585,8594,8730,8733,8737,8742,8929,8943,8947,8965,8969,8971,8984,8992,8999,9138,9141,9167,9171,9173,9336,9339,9341,9350,9354,9357,9360,9361,9364,9366,9368,9372,9377,9379,9383,9384,9390,9392,9413,9742,9744,9752,9761,9779,9893,9899,9921,9923,9926,9933,9937,9941,9943,9945,9946,9949,9954,9970,9973,10120,10123,10125,10129,10131,10133,10136,10139,10146,10148,10149,10152,10153,10160,10165,10178,10181,10306,10332,10339,10345,10525,10528,10533,10536,10537,10543,10547,10553,10556,10577,10700,10712,10715,10719,10723,10725,10727,10730,10735,10737,10738,10740,10742,10743,10745,10746,10749,10756,10760,10768,10770,10893,10895,10900,10906,10909,11049,11054,11055,11069,11080,11085,11086,11092,11101,11104,11226,11242,11258,11260,11262,11264,11266,11268,11272,11274,11276,11278,11281,11285,11289,11309,11314,11319,11322,11324,11327,11328,11330,11338,11350,11353,11359,11360,11366,11504,11506,11508,11510,11512,11513,11517,11523,11529,11532,11544,11545,11547,11550,11694,11697,11701,11704,11707,11709,11711,11712,11716,11719,11726,11728,11731,11752,11870,11884,11889,11891,11896,11919,12056,12071,12091,12094, +chr19 47501413 47515667 m54329U_210810_004956/24643281/ccs 191,388,582,790,947,1175,1351,1550,1754,1906,2083,2282,2477,2691,2872,3167,3366,3580,3795,3980,4159,4344,4550,4793,4979,5169,5357,5560,5770,5932,6156,6378,6551,6768,6979,7156,7356,7558,7766,8111,8333,8496,8691,8874,9090,9291,9494,9679,9916,10063,10259,10467,10654,10846,10980,11146,11423,11642,11758,11966,12161,12357,12607,12777,13273,13431,14203,14349,14622,14769,14973,15146,15360,15571,15827,16123,16323,16503,16700,16908,17229,17379,17552,17695,17873,18234,18472,18859,19020,19233,19336,19557,19717,19920,20069,20308,20456,20679,21086,21488,21608,21783,22081,22318,22483,22643,22824,22986,23377,23498,23680, 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+chr19 47501574 47511800 m84039_230404_003541_s3/123732821/ccs 172,356,573,747,1084,1254,1434,1662,1849,2011,2195,2417,2818,3015,3233,3422,3632,4024,4194,4375,4536,4688,4847,5047,5209,5412,5747,5886,6037,6262,6438,6980,7169,7327,7459,7643,7890,8139,8334,8490,8635,8838,9055,9234,9430,9774,9916, 143,173,150,287,116,153,136,119,144,175,131,400,158,170,159,149,128,133,180,88,108,142,162,149,153,245,138,145,128,120,446,132,136,131,162,246,171,131,97,138,155,121,140,162,291,91,140, 135,315,529,723,1034,1200,1407,1570,1781,1993,2186,2326,2817,2976,3185,3392,3571,3760,4157,4374,4463,4644,4830,5009,5196,5362,5657,5885,6031,6165,6382,6884,7112,7305,7458,7621,7889,8061,8270,8431,8628,8790,8959,9195,9396,9721,9865,10056, 37,41,44,24,50,54,27,92,68,18,9,91,1,39,48,30,61,264,37,1,73,44,17,38,13,50,90,1,6,97,56,96,57,22,1,22,1,78,64,59,7,48,96,39,34,53,51,3, . . . 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+chr19 47501949 47517076 m64076_210328_012155/98043755/ccs 127,287,456,879,1175,1343,1558,1733,1883,2190,2451,2644,2817,2988,3271,3478,3659,3862,4047,4273,4442,4605,4807,5001,5159,5375,5553,5770,5932,6130,6292,6501,6683,6873,7068,7234,7543,7749,7935,8101,8307,8465,8645,8814,8995,9173,9374,9562,9733,9914,10115,10469,10637,10932,11120,11292,11494,11695,11884,12191,12347,12499,12674,12905,13706,13881,14033,14222,14436,14578,14802,14978, 143,162,123,252,167,150,130,147,287,115,104,103,127,110,121,81,130,119,133,104,128,148,118,124,123,116,108,113,124,141,144,116,148,148,120,278,147,100,119,141,124,147,114,115,102,131,120,100,134,119,112,117,268,117,116,126,107,132,306,136,151,123,97,108,116,123,148,136,113,174,110,118, 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+chr19 47501977 47526503 m54329U_210814_130637/126552497/ccs 180,473,653,836,946,1308,1514,1664,1861,2052,2222,2368,2564,2757,2935,3116,3320,3467,3655,3869,4054,4230,4403,4623,4817,5007,5252,5421,5637,5813,6000,6185,6353,6536,6731,6954,7133,7299,7493,7625,7870,8078,8244,8428,8592,8820,8982,9141,9282,9477,9705,10445,10800,11007,11163,11336,11483,11670,11827,11994,12176,12342,12842,13665,13867,14144,14332,14488,14689,14881,15211,15392,15584,15752,15971,16210,16400,16571,16759,17076,17234,17417,17561,17704,17922,18124,18330,18535,18711,18848,19068,19271,19459,19638,19818,20023,20170,20365,20580,20748,20936,21069,21402,21621,21805,21994,22197,22399,22594,22779,22971,23122,23277,23479,23636,23877,24026,24297, 292,133,126,109,361,134,118,120,131,131,145,151,126,177,114,150,121,150,186,139,144,148,159,114,133,146,87,96,112,106,114,112,147,145,142,98,125,94,119,143,134,115,146,125,159,127,114,140,180,183,726,289,154,155,122,144,143,126,140,158,130,443,99,92,235,112,153,128,133,277,142,161,167,187,165,133,141,137,316,141,140,114,129,166,146,152,136,148,136,170,136,136,138,122,158,143,162,150,127,153,123,297,153,120,110,127,146,140,137,115,126,147,158,151,143,144,198,97, 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+chr19 47502070 47519370 m84039_230404_003541_s3/182191703/ccs 166,351,528,744,880,1061,1243,1431,1612,1759,1968,2152,2322,2516,2732,2958,3140,3333,3525,3704,3896,4074,4248,4414,4611,4792,4948,5133,5324,5513,5764,5934,6111,6308,6526,6672,6839,6999,7171,7374,7567,7758,7930,8112,8267,8468,8655,8819,9009,9220,9413,9610,9813,9962,10165,10325,10779,10968,11182,11413,11565,11740,11910,12162,12282,12466,12585,12827,13571,13692,13983,14133,14231,14371,14567,14869,15066,15158,15455,15642,15857,15983,16241,16443,16631,16816,17003, 95,123,142,87,138,134,107,115,123,165,136,121,151,137,148,135,148,127,126,132,139,133,128,137,130,140,150,136,160,135,93,127,137,129,92,133,126,167,126,108,121,133,153,142,163,104,132,108,127,133,141,108,106,123,113,301,108,104,140,109,124,161,132,105,138,118,153,102,120,104,108,87,139,148,114,148,91,169,106,114,109,117,110,134,130,138,114, 261,474,670,831,1018,1195,1350,1546,1735,1924,2104,2273,2473,2653,2880,3093,3288,3460,3651,3836,4035,4207,4376,4551,4741,4932,5098,5269,5484,5648,5857,6061,6248,6437,6618,6805,6965,7166,7297,7482,7688,7891,8083,8254,8430,8572,8787,8927,9136,9353,9554,9718,9919,10085,10278,10626,10887,11072,11322,11522,11689,11901,12042,12267,12420,12584,12738,12929,13691,13796,14091,14220,14370,14519,14681,15017,15157,15327,15561,15756,15966,16100,16351,16577,16761,16954,17117, 90,54,74,49,43,48,81,66,24,44,48,49,43,79,78,47,45,65,53,60,39,41,38,60,51,16,35,55,29,116,77,50,60,89,54,34,34,5,77,85,70,39,29,13,38,83,32,82,84,60,56,95,43,80,47,153,81,110,91,43,51,9,120,15,46,1,89,642,1,187,42,11,1,48,188,49,1,128,81,101,17,141,92,54,55,49,49, . . . 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253,403,756,934,1127,1333,1488,1674,1870,2097,2288,2462,2644,2804,3062,3235,3379,3521,3662,3780,3975,4111,4190,4347,4507,4608,4752,4909,5082,5276,5381,5650,5835,6049,6269,6437,6620,6818,7026,7216,7382,7548,7719,7933,8102,8308,8530,8710,8860,9079,9292,9481,9686,9803,9884,10030,10241,10439,10647,10804,10992,11146,11332,11543,11693,11887,12070,12255,12425,12646,12797,13644,13959,14206,14414,14597,14733,14861,15040,15248,15634,15785, 58,26,14,31,13,10,42,55,19,1,4,1,1,89,1,34,1,1,3,26,9,1,4,58,1,4,1,26,25,24,119,40,116,53,45,20,42,4,4,1,13,38,59,15,45,25,22,12,78,65,57,58,14,1,29,95,6,16,26,50,23,41,50,17,74,35,31,64,98,8,698,1,94,59,26,1,1,1,1,3,20,1, . . . 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+chr19 47502336 47514147 m54329U_210323_190418/43647472/ccs 122,341,523,948,1689,2239,2378,2596,2783,2966,3159,3303,3492,3654,3826,4178,4302,4498,4657,4827,5019,5185,5397,5587,5743,5895,6075,6267,6443,6604,6739,7077,7235,7364,7551,7701,7903,8093,8287,8465,8663,8842,9044,9234,9390,10169,10549,10680,10844,11000,11185,11343, 142,114,93,85,86,100,133,123,136,102,100,120,96,115,115,123,140,119,113,123,84,102,95,87,108,130,118,122,133,128,181,127,123,135,120,138,142,141,148,162,129,109,103,96,88,255,80,131,106,149,121,316, 84,264,455,616,1033,1775,2339,2511,2719,2919,3068,3259,3423,3588,3769,3941,4301,4442,4617,4770,4950,5103,5287,5492,5674,5851,6025,6193,6389,6576,6732,6920,7204,7358,7499,7671,7839,8045,8234,8435,8627,8792,8951,9147,9330,9478,10424,10629,10811,10950,11149,11306,11659, 38,77,68,332,656,464,39,85,64,47,91,44,69,66,57,237,1,56,40,57,69,82,110,95,69,44,50,74,54,28,7,157,31,6,52,30,64,48,53,30,36,50,93,87,60,691,125,51,33,50,36,37,90, . . . 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+chr19 47502433 47514189 m64076_221119_202646/39062020/ccs 158,472,639,829,996,1194,1354,1494,1702,1864,1998,2183,2374,2556,2749,2933,3139,3309,3510,3685,3864,4190,4399,4555,4837,5010,5167,5348,5532,5701,5892,6049,6262,6398,7059,7237,7402,7564,7757,7936,8076,8218,8412,8607,8786,8947,9143,9338,9491,9649,9778,9992,10148,10341,10486,10665,10796,11067,11210,11383, 313,163,145,135,135,125,139,175,115,129,100,145,147,124,154,157,138,140,118,121,288,124,85,235,106,121,130,162,117,126,113,130,135,614,136,134,127,116,124,139,141,149,140,130,137,131,143,152,126,128,111,108,136,108,120,130,139,95,104,91, 141,471,635,784,964,1131,1319,1493,1669,1817,1993,2098,2328,2521,2680,2903,3090,3277,3449,3628,3806,4152,4314,4484,4790,4943,5131,5297,5510,5649,5827,6005,6179,6397,7012,7195,7371,7529,7680,7881,8075,8217,8367,8552,8737,8923,9078,9286,9490,9617,9777,9889,10100,10284,10449,10606,10795,10935,11162,11314,11474, 17,1,4,45,32,63,35,1,33,47,5,85,46,35,69,30,49,32,61,57,58,38,85,71,47,67,36,51,22,52,65,44,83,1,47,42,31,35,77,55,1,1,45,55,49,24,65,52,1,32,1,103,48,57,37,59,1,132,48,69,186, . . . 141,147,150,151,155,157,471,635,638,784,786,804,805,807,811,813,815,828,964,967,970,972,973,978,980,983,985,990,995,1131,1140,1150,1152,1154,1157,1163,1164,1169,1171,1175,1181,1186,1193,1319,1334,1337,1345,1349,1351,1353,1493,1669,1673,1682,1684,1693,1698,1701,1817,1825,1826,1829,1832,1837,1840,1842,1849,1855,1857,1861,1863,1993,1995,1997,2098,2104,2110,2115,2119,2123,2125,2127,2135,2138,2140,2141,2152,2155,2157,2181,2182,2328,2334,2349,2351,2354,2357,2373,2521,2526,2535,2541,2543,2545,2549,2555,2680,2699,2701,2714,2715,2718,2722,2725,2735,2737,2741,2743,2748,2873,2903,2910,2913,2916,2918,2922,2927,2930,2932,3090,3092,3093,3097,3099,3102,3103,3110,3113,3115,3118,3130,3137,3138,3277,3281,3290,3293,3305,3308,3449,3455,3457,3461,3476,3484,3487,3490,3492,3496,3498,3505,3509,3628,3632,3639,3643,3646,3650,3652,3659,3671,3674,3678,3684,3806,3808,3813,3819,3827,3830,3834,3839,3843,3844,3846,3850,3859,3863,4152,4157,4161,4163,4169,4179,4189,4314,4324,4326,4330,4339,4342,4344,4351,4355,4360,4363,4375,4384,4386,4387,4398,4484,4496,4498,4501,4502,4504,4505,4508,4510,4518,4519,4520,4524,4525,4531,4535,4536,4541,4547,4554,4790,4800,4802,4804,4810,4814,4820,4827,4829,4831,4836,4943,4945,4947,4958,4965,4966,4969,4973,4976,4979,4983,4985,4989,4993,5009,5131,5148,5151,5155,5160,5166,5297,5316,5320,5322,5327,5330,5339,5344,5347,5510,5511,5516,5521,5531,5649,5658,5661,5663,5668,5671,5674,5678,5681,5684,5685,5688,5700,5827,5850,5856,5858,5862,5865,5869,5871,5875,5881,5884,5891,6005,6013,6019,6027,6030,6036,6038,6041,6048,6179,6204,6206,6220,6222,6225,6229,6231,6256,6261,6364,6397,7012,7018,7024,7027,7029,7036,7050,7053,7058,7195,7196,7205,7207,7210,7211,7217,7225,7233,7236,7371,7401,7529,7536,7543,7547,7550,7554,7559,7563,7680,7685,7698,7702,7707,7709,7714,7715,7728,7730,7733,7737,7739,7742,7744,7747,7754,7756,7881,7891,7893,7898,7907,7908,7911,7913,7915,7924,7933,7935,8075,8146,8217,8367,8374,8384,8389,8393,8411,8552,8569,8572,8580,8585,8590,8594,8600,8601,8606,8737,8741,8742,8747,8749,8756,8760,8763,8767,8781,8785,8923,8931,8932,8935,8939,8944,8946,9078,9091,9093,9095,9101,9108,9111,9114,9115,9118,9127,9132,9134,9142,9286,9292,9294,9295,9298,9301,9307,9318,9323,9333,9337,9490,9617,9619,9625,9627,9631,9635,9645,9648,9777,9889,9901,9904,9905,9907,9911,9917,9920,9923,9927,9930,9931,9934,9936,9938,9941,9945,9949,9951,9958,9963,9966,9969,9975,9991,10100,10110,10111,10116,10119,10121,10123,10127,10129,10133,10137,10147,10284,10286,10289,10290,10292,10300,10310,10312,10315,10319,10320,10321,10327,10328,10340,10449,10451,10459,10463,10466,10470,10472,10485,10606,10612,10617,10620,10622,10631,10634,10637,10642,10656,10659,10664,10795,10935,10940,10944,10946,10948,10950,10952,10956,10957,10962,10967,10971,10975,10980,10982,10984,10986,10987,10993,10994,10998,11001,11002,11005,11009,11014,11016,11017,11019,11022,11023,11028,11032,11034,11036,11054,11057,11066,11162,11183,11185,11189,11201,11206,11209,11314,11327,11331,11334,11337,11349,11353,11356,11358,11360,11382,11474,11477,11482,11484,11489,11490,11496,11499,11502,11506,11507,11512,11516,11518,11521,11527,11531,11536,11546,11562,11571,11642,11644,11652,11660, +chr19 47502578 47527331 m84008_230107_003043_s1/93585759/ccs 207,355,578,779,1020,1185,1381,1557,1750,1895,2091,2281,2715,2860,3036,3241,3384,3590,3754,3985,4196,4396,4583,4762,4952,5146,5351,5520,5702,5889,6111,6316,6479,6606,6938,7099,7258,7475,7688,7869,8061,8231,8470,8629,8849,9072,9243,9456,9705,9896,10065,10377,10630,10831,10994,11172,11324,11470,11661,11824,11967,12114,12255,12469,13025,13258,13401,13601,13760,13906,14115,14296,14454,14629,14777,14988,15307,15557,15707,16160,16299,16489,16687,16942,17100,17248,17418,17736,17963,18110,18288,18463,18645,18835,19098,19261,19433,19619,19841,20029,20216,20358,20526,20871,21079,21278,21439,21627,21944,22111,22521,22694,22877,23071,23262,23492,23805,23906,24089,24338, 115,147,127,121,98,157,110,166,142,195,187,355,127,153,178,139,158,163,178,175,166,164,148,137,126,153,152,131,186,207,160,111,126,273,150,155,172,148,110,127,124,122,136,157,181,135,158,248,128,99,158,190,140,106,155,135,126,130,125,131,114,133,131,116,232,131,199,81,124,155,128,157,141,139,116,318,107,146,335,124,145,135,154,122,118,169,315,165,146,155,106,143,123,126,81,135,154,161,187,147,141,140,284,167,198,127,162,304,144,329,156,165,173,137,131,312,100,119,111,124, 179,322,502,705,900,1118,1342,1491,1723,1892,2090,2278,2636,2842,3013,3214,3380,3542,3753,3932,4160,4362,4560,4731,4899,5078,5299,5503,5651,5888,6096,6271,6427,6605,6879,7088,7254,7430,7623,7798,7996,8185,8353,8606,8786,9030,9207,9401,9704,9833,9995,10223,10567,10770,10937,11149,11307,11450,11600,11786,11955,12081,12247,12386,12585,13257,13389,13600,13682,13884,14061,14243,14453,14595,14768,14893,15306,15414,15703,16042,16284,16444,16624,16841,17064,17218,17417,17733,17901,18109,18265,18394,18606,18768,18961,19179,19396,19587,19780,20028,20176,20357,20498,20810,21038,21277,21405,21601,21931,22088,22440,22677,22859,23050,23208,23393,23804,23905,24025,24200,24462, 28,33,76,74,120,67,39,66,27,3,1,3,79,18,23,27,4,48,1,53,36,34,23,31,53,68,52,17,51,1,15,45,52,1,59,11,4,45,65,71,65,46,117,23,63,42,36,55,1,63,70,154,63,61,57,23,17,20,61,38,12,33,8,83,440,1,12,1,78,22,54,53,1,34,9,95,1,143,4,118,15,45,63,101,36,30,1,3,62,1,23,69,39,67,137,82,37,32,61,1,40,1,28,61,41,1,34,26,13,23,81,17,18,21,54,99,1,1,64,138,73, . . . 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+chr19 47502663 47516933 m84039_230404_003541_s3/96539427/ccs 158,289,486,669,838,1045,1218,1413,1619,1828,1985,2122,2331,2555,2707,2958,3128,3320,3472,3663,3874,4083,4256,4434,4625,4787,4993,5176,5352,5524,5722,5893,6042,6231,6405,6576,6749,6963,7137,7343,7543,7738,7886,8053,8218,8422,8595,8761,8949,9114,9279,9437,9649,9948,10148,10328,10574,10709,10921,11117,11305,11532,11706,11846,12036,12171,12950,13154,13275,13448,13627,13801,14012, 130,136,117,122,128,98,119,140,138,126,136,178,155,114,147,95,110,103,83,136,127,139,142,190,137,139,151,144,128,132,134,129,139,117,117,128,145,106,126,128,155,110,140,143,161,153,112,150,149,101,121,128,199,139,137,135,128,168,143,123,149,140,139,152,134,126,148,110,126,138,136,169,130, 98,288,425,603,791,966,1143,1337,1553,1757,1954,2121,2300,2486,2669,2854,3053,3238,3423,3555,3799,4001,4222,4398,4624,4762,4926,5144,5320,5480,5656,5856,6022,6181,6348,6522,6704,6894,7069,7263,7471,7698,7848,8026,8196,8379,8575,8707,8911,9098,9215,9400,9565,9848,10087,10285,10463,10702,10877,11064,11240,11454,11672,11845,11998,12170,12297,13098,13264,13401,13586,13763,13970, 60,1,61,66,47,79,75,76,66,71,31,1,31,69,38,104,75,82,49,108,75,82,34,36,1,25,67,32,32,44,66,37,20,50,57,54,45,69,68,80,72,40,38,27,22,43,20,54,38,16,64,37,84,100,61,43,111,7,44,53,65,78,34,1,38,1,653,56,11,47,41,38,42, . . . 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+chr19 47502899 47513582 m84039_230401_034725_s4/93523871/ccs 217,434,604,780,1188,1418,1577,1775,2228,2412,2593,2787,3056,3260,3455,3729,3970,4126,4347,4966,5216,5435,5651,5882,6100,6378,6555,6787,6910,7133,7335,7605,7761,7963,8157,8409,8607,8826,9017,9204,9383,9523,9713,9914,10198,10377, 145,125,119,134,139,108,111,112,129,129,119,109,119,115,110,80,103,130,119,110,106,100,110,98,96,119,77,122,141,103,87,111,106,135,96,118,113,78,126,112,111,130,121,119,123,92, 118,362,559,723,914,1327,1526,1688,1887,2357,2541,2712,2896,3175,3375,3565,3809,4073,4256,4466,5076,5322,5535,5761,5980,6196,6497,6632,6909,7051,7236,7422,7716,7867,8098,8253,8527,8720,8904,9143,9316,9494,9653,9834,10033,10321,10469, 99,72,45,57,274,91,51,87,341,55,52,75,160,85,80,164,161,53,91,500,140,113,116,121,120,182,58,155,1,82,99,183,45,96,59,156,80,106,113,61,67,29,60,80,165,56,49, . . . 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+chr19 47503064 47526556 m54329U_210810_004956/74187500/ccs 101,297,510,697,863,953,1062,1267,1448,1639,1809,2043,2247,2442,2622,2817,2996,3181,3309,3537,3752,3948,4143,4326,4519,4715,4914,5056,5249,5443,5630,5796,6004,6195,6351,6536,6715,6921,7106,7335,7496,7672,7871,8281,8460,8621,8857,9048,9211,9392,9571,9734,9917,10115,10611,10819,11408,11584,11741,12500,12734,12975,13146,13290,13653,13836,14072,14253,14412,14920,15385,15523,15653,15831,16183,16375,16552,16781,16938,17095,17332,17514,17734,17877,18075,18286,18443,18654,18853,19025,19172,19385,19553,19666,19833,20012,20219,20393,20627,20806,21017,21230,21421,21631,21803,22000,22232,22405,22620,22799,23161, 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+chr19 47503211 47517758 m84039_230401_034725_s4/253104323/ccs 78,293,474,633,821,998,1184,1376,1713,1908,2076,2252,2454,2619,2771,2970,3145,3351,3482,3703,3895,4093,4274,4477,4625,4814,5008,5182,5341,5509,5648,5860,6069,6242,6436,6625,6850,7001,7248,7435,7607,7778,7967,8157,8329,8519,8736,8936,9107,9599,9807,10025,10185,10322,10520,10834,10934,11138,11328,11689,12432,12515,12858,13091,13259,13418,13549,13724,13878,14044,14259, 156,119,132,139,130,151,140,311,168,136,131,147,143,137,137,139,158,130,161,126,113,133,121,131,156,159,151,109,108,131,139,156,136,136,142,155,126,161,126,128,138,144,155,138,164,147,126,118,391,150,141,136,123,144,233,99,147,106,226,79,82,164,211,165,151,113,174,118,148,122,142, 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2,4,6,26,57,65,77,234,237,258,265,270,273,276,283,286,290,292,354,412,422,429,432,438,451,466,473,606,614,616,620,624,632,772,776,778,782,789,794,796,801,819,820,951,958,963,966,969,974,977,980,982,985,989,995,997,1149,1152,1159,1165,1169,1173,1175,1181,1183,1324,1330,1339,1343,1345,1353,1358,1360,1372,1375,1687,1693,1696,1700,1701,1702,1704,1706,1712,1881,1891,1894,1899,1903,1907,2044,2047,2075,2207,2214,2222,2224,2228,2231,2243,2249,2251,2399,2414,2416,2420,2422,2426,2438,2441,2446,2453,2500,2597,2612,2614,2618,2756,2770,2908,2911,2918,2925,2926,2928,2930,2934,2937,2939,2944,2956,2964,2965,2969,3109,3133,3142,3144,3235,3303,3309,3314,3320,3323,3329,3331,3342,3350,3381,3481,3562,3602,3643,3651,3668,3673,3675,3680,3702,3829,3835,3838,3840,3845,3851,3855,3859,3864,3869,3871,3876,3880,3894,4008,4010,4018,4020,4022,4038,4041,4042,4045,4047,4049,4051,4054,4056,4064,4070,4074,4077,4083,4085,4090,4092,4226,4232,4234,4236,4240,4243,4246,4249,4252,4257,4261,4264,4273,4395,4397,4400,4404,4407,4411,4415,4424,4426,4429,4476,4608,4609,4612,4618,4624,4781,4784,4786,4787,4790,4794,4798,4805,4810,4813,4973,4981,4983,4998,5002,5004,5007,5159,5166,5181,5291,5298,5308,5313,5315,5318,5322,5331,5338,5340,5449,5466,5471,5473,5474,5479,5481,5485,5487,5502,5504,5508,5640,5647,5761,5787,5795,5801,5804,5807,5809,5811,5812,5819,5826,5829,5833,5838,5839,5841,5843,5844,5847,5849,5853,5855,5857,5859,6016,6029,6040,6041,6052,6054,6056,6065,6068,6205,6215,6220,6221,6223,6227,6235,6239,6241,6378,6379,6405,6409,6412,6413,6422,6424,6427,6428,6435,6578,6588,6596,6618,6624,6780,6799,6810,6822,6849,6976,6992,6995,7000,7162,7165,7168,7171,7174,7180,7183,7185,7190,7191,7193,7197,7201,7204,7213,7215,7217,7219,7221,7226,7236,7247,7374,7404,7406,7411,7414,7418,7434,7563,7584,7586,7588,7591,7593,7601,7604,7606,7745,7769,7777,7818,7922,7924,7932,7935,7937,7938,7941,7943,7950,7954,7958,7959,7961,7966,8122,8128,8133,8135,8140,8148,8149,8152,8156,8295,8308,8310,8312,8318,8324,8325,8328,8493,8503,8518,8666,8668,8671,8674,8677,8680,8689,8707,8712,8715,8716,8722,8726,8732,8735,8862,8868,8879,8883,8886,8888,8891,8894,8898,8902,8904,8906,8909,8914,8917,8919,8922,8924,8928,8935,9054,9057,9061,9072,9074,9079,9082,9085,9088,9093,9094,9098,9106,9498,9501,9503,9506,9507,9509,9517,9520,9521,9522,9524,9527,9529,9532,9537,9538,9539,9544,9545,9547,9548,9551,9553,9554,9556,9557,9574,9577,9581,9598,9749,9755,9758,9762,9767,9771,9773,9776,9783,9788,9791,9793,9795,9797,9799,9802,9804,9806,9948,9950,9954,9956,9957,9960,9965,9972,9973,9975,9979,9981,9982,9985,9988,9989,10000,10009,10012,10015,10022,10024,10075,10161,10163,10176,10184,10308,10321,10466,10468,10471,10481,10488,10494,10501,10503,10519,10753,10763,10771,10782,10788,10809,10833,10933,11081,11083,11107,11109,11112,11115,11137,11244,11252,11266,11271,11285,11291,11295,11302,11308,11320,11327,11554,11567,11572,11579,11581,11583,11588,11591,11600,11605,11607,11614,11615,11617,11619,11623,11624,11625,11627,11632,11634,11637,11639,11640,11643,11645,11649,11651,11666,11688,11768,11778,11791,11792,11794,11796,11798,11799,11807,11818,11822,11825,11828,11832,11843,11847,11881,11884,11891,11894,11896,11909,11917,11919,11927,11930,11939,11949,11951,11953,11956,11958,11965,11966,11967,11976,11983,12007,12008,12015,12018,12020,12022,12024,12028,12033,12035,12037,12038,12041,12043,12046,12050,12053,12055,12059,12061,12064,12065,12069,12070,12071,12075,12077,12078,12089,12101,12105,12107,12111,12114,12117,12118,12121,12124,12127,12130,12131,12132,12134,12137,12140,12145,12150,12156,12168,12174,12176,12182,12191,12192,12194,12196,12200,12202,12204,12206,12209,12211,12216,12218,12220,12222,12224,12227,12229,12231,12234,12243,12252,12256,12258,12260,12263,12268,12271,12277,12292,12295,12297,12304,12311,12313,12317,12318,12319,12325,12326,12328,12332,12335,12338,12340,12344,12345,12347,12350,12356,12360,12364,12366,12368,12374,12376,12377,12379,12382,12383,12385,12388,12389,12390,12397,12402,12404,12405,12407,12409,12411,12413,12418,12431,12514,12679,12685,12688,12693,12701,12703,12704,12707,12711,12713,12716,12718,12721,12725,12731,12733,12735,12737,12739,12741,12743,12747,12749,12766,12769,12771,12772,12774,12776,12780,12806,12807,12816,12818,12857,13069,13080,13085,13087,13090,13256,13258,13410,13412,13414,13417,13531,13537,13548,13723,13842,13852,13855,13857,13860,13861,13865,13868,13874,13877,14026,14034,14038,14043,14166,14168,14171,14175,14184,14187,14197,14199,14201,14202,14211,14215,14223,14235,14246,14248,14258,14401,14405,14407,14412,14424,14428,14429,14430,14432,14435,14436,14439,14443,14446,14452,14460,14472,14479,14527,14529,14530,14531,14532,14533, +chr19 47503318 47514068 m54329U_210326_192251/32048678/ccs 160,367,510,757,947,1077,1265,1488,1666,1865,2058,2247,2446,2665,2869,3104,3298,3565,3736,3855,4119,4332,4498,4710,4885,5107,5294,5505,5672,5906,6083,6271,6463,6626,6802,7032,7206,7382,7589,7759,8022,8212,8389,8674,8809,9004,9204,9419,9603,9756,9966,10128,10362,10516, 141,85,142,125,98,119,145,151,127,154,118,145,147,133,148,112,120,75,118,134,86,101,135,144,173,108,127,111,132,173,140,134,146,126,136,139,136,157,134,123,112,120,108,134,159,123,150,142,106,114,115,146,141,117, 105,301,452,652,882,1045,1196,1410,1639,1793,2019,2176,2392,2593,2798,3017,3216,3418,3640,3854,3989,4205,4433,4633,4854,5058,5215,5421,5616,5804,6079,6223,6405,6609,6752,6938,7171,7342,7539,7723,7882,8134,8332,8497,8808,8968,9127,9354,9561,9709,9870,10081,10274,10503,10633, 55,66,58,105,65,32,69,78,27,72,39,71,54,72,71,87,82,147,96,1,130,127,65,77,31,49,79,84,56,102,4,48,58,17,50,94,35,40,50,36,140,78,57,177,1,36,77,65,42,47,96,47,88,13,57, . . . 79,105,110,121,127,128,130,131,134,135,138,141,143,148,151,158,159,301,305,315,320,322,323,325,327,329,331,344,347,348,351,352,353,357,359,365,366,452,454,494,509,536,652,655,656,659,664,673,675,676,681,684,686,689,691,696,705,707,709,713,714,717,718,723,728,729,736,741,743,746,748,750,753,755,756,882,905,910,935,937,940,946,1045,1049,1052,1055,1062,1068,1071,1072,1074,1076,1196,1198,1231,1235,1239,1241,1245,1249,1251,1254,1256,1257,1262,1263,1264,1410,1417,1421,1423,1425,1427,1429,1431,1464,1466,1469,1471,1475,1487,1639,1648,1654,1662,1663,1665,1750,1793,1828,1829,1831,1832,1846,1857,1859,1864,2019,2024,2026,2029,2046,2048,2051,2057,2113,2176,2186,2188,2190,2192,2194,2198,2204,2206,2209,2213,2215,2218,2219,2226,2230,2231,2236,2245,2246,2392,2396,2415,2419,2420,2423,2429,2432,2434,2435,2436,2439,2441,2442,2443,2445,2593,2607,2616,2621,2623,2627,2632,2635,2637,2641,2646,2647,2651,2654,2661,2662,2664,2798,2802,2810,2817,2824,2825,2827,2829,2833,2836,2838,2843,2854,2861,2863,2864,2866,2868,2905,3017,3019,3024,3041,3043,3047,3049,3053,3056,3063,3066,3067,3068,3075,3079,3091,3093,3095,3096,3099,3103,3216,3222,3223,3228,3241,3243,3245,3249,3252,3253,3258,3260,3261,3262,3265,3269,3272,3276,3278,3297,3418,3423,3425,3427,3432,3442,3444,3448,3452,3454,3457,3460,3462,3469,3473,3474,3478,3481,3482,3483,3485,3486,3491,3503,3519,3525,3531,3533,3538,3541,3543,3554,3555,3558,3560,3561,3563,3564,3640,3643,3645,3646,3649,3662,3667,3668,3670,3679,3699,3702,3704,3707,3709,3710,3712,3714,3735,3854,3989,3995,3998,4006,4017,4020,4021,4023,4025,4027,4029,4030,4034,4036,4037,4041,4045,4051,4057,4060,4063,4068,4070,4072,4074,4083,4086,4087,4090,4091,4094,4098,4101,4108,4118,4205,4215,4218,4220,4222,4227,4228,4230,4232,4234,4235,4239,4241,4243,4246,4247,4251,4253,4257,4259,4264,4265,4269,4271,4281,4283,4287,4288,4294,4296,4302,4303,4305,4307,4310,4312,4314,4317,4321,4325,4331,4433,4437,4441,4445,4449,4451,4456,4459,4460,4463,4468,4470,4473,4476,4481,4483,4488,4494,4497,4633,4637,4651,4654,4661,4666,4667,4671,4674,4675,4683,4688,4692,4695,4697,4698,4705,4709,4854,4858,4862,4866,4868,4873,4878,4880,4884,5058,5061,5066,5073,5077,5080,5082,5088,5106,5215,5229,5232,5252,5254,5263,5266,5274,5275,5276,5278,5281,5284,5286,5288,5293,5421,5440,5443,5446,5450,5452,5463,5466,5468,5475,5496,5504,5616,5630,5634,5635,5638,5642,5644,5650,5652,5659,5665,5671,5804,5812,5814,5819,5823,5826,5828,5830,5831,5834,5836,5839,5842,5846,5849,5851,5853,5854,5855,5857,5861,5869,5871,5873,5878,5882,5891,5894,5897,5905,6079,6082,6223,6235,6237,6240,6247,6248,6258,6260,6263,6264,6268,6270,6405,6414,6417,6421,6450,6451,6454,6456,6462,6609,6611,6612,6614,6625,6752,6759,6767,6772,6773,6775,6777,6801,6938,6943,6951,6962,6968,6972,6976,7014,7031,7171,7174,7178,7205,7342,7345,7350,7369,7373,7381,7539,7541,7544,7546,7547,7549,7556,7565,7588,7723,7725,7727,7729,7733,7734,7739,7740,7744,7748,7751,7758,7882,7893,7896,7897,7900,7903,7906,7907,7909,7911,7914,7918,7920,7921,7928,7932,7934,7936,7937,7942,7946,7948,7949,7951,7953,7955,7958,7961,7964,7968,7972,7994,7997,8005,8010,8012,8021,8134,8139,8143,8145,8148,8149,8151,8153,8156,8159,8161,8169,8190,8191,8195,8198,8211,8332,8339,8343,8345,8348,8350,8354,8359,8360,8364,8366,8367,8369,8374,8382,8388,8497,8505,8509,8511,8515,8526,8529,8532,8533,8535,8538,8539,8541,8545,8551,8557,8559,8563,8566,8569,8571,8573,8577,8583,8585,8588,8591,8594,8597,8599,8602,8603,8604,8606,8607,8609,8610,8616,8618,8621,8624,8629,8632,8633,8639,8643,8649,8652,8656,8658,8659,8666,8670,8673,8808,8968,8970,8973,8987,8994,8998,9000,9003,9127,9149,9175,9180,9181,9189,9196,9199,9203,9328,9354,9358,9360,9362,9368,9370,9372,9375,9379,9386,9418,9561,9565,9568,9577,9581,9583,9591,9602,9709,9711,9725,9726,9731,9736,9739,9741,9748,9750,9753,9755,9870,9873,9888,9891,9895,9897,9898,9901,9914,9916,9921,9925,9928,9931,9933,9934,9938,9955,9959,9963,9965,10081,10100,10113,10115,10117,10119,10120,10127,10274,10290,10291,10295,10298,10300,10302,10311,10316,10318,10334,10335,10339,10341,10344,10346,10349,10350,10352,10354,10361,10447,10503,10507,10512,10515,10633,10636,10643,10644,10648,10650,10652,10656,10662,10671,10674,10677,10681,10684,10690, +chr19 47503416 47522747 m84008_230107_003043_s1/199754789/ccs 182,371,590,765,977,1157,1348,1568,1762,1946,2134,2369,2632,2772,2957,3196,3396,3534,3754,3953,4174,4508,4758,4973,5128,5308,5491,5635,5979,6161,6337,6546,6760,6956,7148,7862,8051,8245,8394,8608,8828,9586,9724,9981,10181,10338,10523,10717,10900,11039,11203,11589,12167,12394,12721,12914,13082,13254,13470,13682,13796,14033,14253,14478,14742,14979,15143,15305,15772,16015,16145,16456,16634,16807,16968,17176,17366,17583,17781,17969,18142,18359,18552,18797,18984, 184,162,137,182,173,166,152,159,167,163,155,130,94,179,208,143,134,166,157,152,273,113,137,127,153,146,141,324,160,129,161,117,174,140,705,153,126,116,142,148,377,111,144,170,134,140,176,144,138,151,310,76,139,276,160,167,154,147,131,113,178,146,127,144,138,149,141,466,136,120,269,136,147,130,155,158,170,131,146,159,169,128,125,123,147, 154,366,533,727,947,1150,1323,1500,1727,1929,2109,2289,2499,2726,2951,3165,3339,3530,3700,3911,4105,4447,4621,4895,5100,5281,5454,5632,5959,6139,6290,6498,6663,6934,7096,7853,8015,8177,8361,8536,8756,9205,9697,9868,10151,10315,10478,10699,10861,11038,11190,11513,11665,12306,12670,12881,13081,13236,13401,13601,13795,13974,14179,14380,14622,14880,15128,15284,15771,15908,16135,16414,16592,16781,16937,17123,17334,17536,17714,17927,18128,18311,18487,18677,18920,19131, 28,5,57,38,30,7,25,68,35,17,25,80,133,46,6,31,57,4,54,42,69,61,137,78,28,27,37,3,20,22,47,48,97,22,52,9,36,68,33,72,72,381,27,113,30,23,45,18,39,1,13,76,502,88,51,33,1,18,69,81,1,59,74,98,120,99,15,21,1,107,10,42,42,26,31,53,32,47,67,42,14,48,65,120,64,16, . . . 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+chr19 47504647 47518528 m54329U_210323_190418/144705180/ccs 707,1089,1804,2137,3069,3457,3659,4010,4169,4471,4647,5020,5390,5575,5938,7670,7998,8235,8539,8856,9020,9652,10031,11258,12358,12551,13227, 116,126,109,130,110,120,99,106,193,132,86,113,143,133,158,123,99,159,105,125,105,112,84,152,99,135,95, 258,823,1215,1913,2267,3179,3577,3758,4116,4362,4603,4733,5133,5533,5708,6096,7793,8097,8394,8644,8981,9125,9764,10115,11410,12457,12686,13322, 449,266,589,224,802,278,82,252,53,109,44,287,257,42,230,1574,205,138,145,212,39,527,267,1143,948,94,541,416, . . . 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75,271,500,622,860,1055,1228,1398,1593,1749,1919,2095,2287,2465,2629,2803,2989,3157,3311,3511,3832,4001,4169,4343,4545,4708,4890,5057,5259,5415,5624,5798,5981,6188,6397,6580,6803,6983,7201,7385,7509,7726,7935,8088,8287,8444,8923,9410,9639,9754,10595,10827,11035,11209,11378,11831,11979,12169,12314,12516,12699,12844,12990,13437,13639,13949,14118,14365,14540,14734,15111,15315,15499,15704,15870,16040,16235,16433,16617,16794,16940,17181,17377,17710,17892,18098,18238,18458,18668,18816,18994,19233,19394, 66,47,1,104,49,25,43,33,26,1,35,49,15,22,54,39,27,34,26,1,23,23,36,51,12,32,27,30,1,21,6,32,69,57,22,81,43,74,1,1,60,19,24,32,7,6,1,94,10,713,87,65,48,39,69,4,37,12,72,8,18,18,294,67,31,33,113,51,67,48,57,19,40,31,1,48,86,38,27,22,98,37,27,13,35,26,117,63,31,39,100,27,63, . . . 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+chr19 47505293 47522617 m54329U_210323_190418/102761996/ccs 55,245,435,853,1090,1255,1457,1635,1841,2025,2212,2420,2618,2796,2982,3166,3349,3579,3718,3904,4106,4286,4475,4656,4861,5030,5237,5424,5596,5779,5977,6144,6336,6519,6705,6857,7057,7250,7393,7640,7820,8037,8203,8367,8528,8719,8854,9369,9561,10374,10566,10737,10902,11074,11442,11605,11805,11963,12185,12299,12488,12706,12872,13124,13510,13770,14026,14310,14456,14635,14835,15028,15220,15335,15556,15750,15943,16157,16317,16528,16705,16877,17132, 146,122,133,131,91,150,105,140,124,118,91,117,117,139,109,129,139,86,117,178,121,124,146,169,165,117,95,108,118,147,134,143,142,116,127,125,131,125,175,117,132,124,143,131,137,134,500,125,121,92,95,148,137,340,110,133,122,144,79,159,130,107,148,249,209,121,194,133,150,138,123,125,114,153,141,139,146,92,130,137,139,119,130, 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+chr19 47505522 47515592 m54329U_210323_190418/71500016/ccs 167,368,552,720,932,1103,1303,1413,1676,1865,2053,2265,2463,2607,2853,3110,3244,3405,3772,3952,4105,4303,4529,4706,4902,5080,5446,5617,5809,5950,6177,6340,6505,6654,6812,6966,7155,7349,7561,7761,8130,8279,8467,8642,8855,9012,9180, 134,128,78,148,104,136,109,176,145,133,116,122,94,104,204,133,147,303,89,97,135,141,131,96,112,125,114,126,120,136,81,97,103,123,136,188,151,101,118,358,129,142,110,102,90,115,259, 103,301,496,630,868,1036,1239,1412,1589,1821,1998,2169,2387,2557,2711,3057,3243,3391,3708,3861,4049,4240,4444,4660,4802,5014,5205,5560,5743,5929,6086,6258,6437,6608,6777,6948,7154,7306,7450,7679,8119,8259,8421,8577,8744,8945,9127, 64,67,56,90,64,67,64,1,87,44,55,96,76,50,142,53,1,14,64,91,56,63,85,46,100,66,241,57,66,21,91,82,68,46,35,18,1,43,111,82,11,20,46,65,111,67,53, . . . 61,103,107,109,113,116,122,123,124,127,131,134,138,139,141,144,146,166,301,306,312,315,320,322,325,328,339,343,345,348,350,354,367,421,496,500,518,525,530,532,544,547,548,551,630,637,672,675,683,687,690,692,695,698,706,711,714,719,786,868,872,886,888,889,892,895,896,898,900,905,907,911,913,931,1036,1038,1040,1044,1047,1048,1096,1102,1239,1245,1254,1257,1266,1271,1275,1278,1299,1302,1412,1589,1620,1623,1627,1632,1637,1639,1641,1653,1656,1658,1662,1663,1675,1821,1823,1830,1831,1835,1838,1857,1862,1864,1998,2017,2022,2025,2027,2029,2030,2034,2036,2038,2046,2048,2052,2169,2172,2175,2183,2185,2190,2193,2194,2196,2200,2203,2206,2211,2217,2218,2223,2236,2240,2242,2247,2264,2387,2400,2401,2404,2406,2418,2420,2424,2428,2431,2441,2442,2445,2446,2451,2452,2457,2458,2462,2557,2560,2562,2567,2570,2576,2579,2581,2583,2588,2591,2595,2598,2601,2602,2606,2711,2718,2722,2726,2728,2732,2746,2751,2755,2757,2760,2762,2764,2766,2769,2771,2774,2777,2781,2784,2788,2790,2794,2796,2799,2800,2803,2810,2816,2848,2852,3057,3064,3066,3067,3070,3086,3088,3109,3212,3243,3391,3398,3399,3404,3708,3710,3728,3736,3740,3743,3744,3750,3757,3759,3765,3766,3768,3771,3861,3865,3867,3868,3870,3872,3874,3876,3888,3894,3897,3899,3900,3903,3905,3909,3928,3951,4049,4052,4057,4059,4073,4079,4085,4090,4094,4104,4240,4241,4244,4246,4247,4249,4252,4254,4256,4260,4263,4266,4268,4271,4277,4282,4284,4286,4290,4302,4444,4446,4452,4459,4460,4461,4466,4470,4473,4475,4477,4480,4481,4482,4485,4486,4500,4503,4505,4516,4519,4526,4528,4660,4662,4665,4667,4670,4677,4679,4682,4684,4691,4697,4699,4700,4705,4802,4814,4815,4820,4828,4829,4833,4841,4849,4851,4855,4857,4861,4873,4876,4881,4885,4887,4889,4894,4897,4901,5014,5016,5020,5023,5026,5042,5049,5058,5072,5073,5075,5078,5079,5145,5205,5214,5220,5223,5225,5227,5231,5234,5241,5244,5245,5250,5252,5256,5261,5263,5267,5268,5273,5274,5276,5279,5282,5286,5290,5292,5295,5297,5316,5323,5390,5397,5401,5404,5407,5409,5415,5419,5423,5426,5429,5433,5437,5445,5560,5572,5581,5587,5591,5592,5597,5599,5600,5604,5609,5610,5614,5616,5743,5746,5749,5752,5778,5789,5797,5799,5805,5808,5929,5935,5937,5939,5942,5945,5949,5978,6086,6090,6093,6095,6099,6100,6107,6109,6113,6115,6116,6120,6122,6125,6129,6131,6133,6136,6138,6142,6143,6147,6148,6149,6153,6155,6158,6170,6176,6258,6261,6280,6285,6289,6291,6293,6299,6303,6306,6317,6320,6321,6323,6326,6327,6339,6437,6440,6444,6452,6454,6458,6461,6464,6470,6481,6485,6487,6490,6491,6495,6497,6499,6504,6608,6610,6620,6628,6630,6631,6634,6641,6653,6777,6784,6811,6948,6953,6954,6959,6965,7154,7306,7308,7326,7329,7331,7342,7348,7450,7456,7459,7463,7468,7474,7477,7478,7480,7484,7489,7492,7494,7496,7498,7500,7501,7503,7505,7510,7511,7516,7518,7519,7521,7524,7530,7535,7538,7540,7555,7560,7679,7681,7682,7744,7750,7755,7760,8119,8120,8126,8129,8259,8267,8271,8274,8276,8278,8421,8425,8426,8431,8434,8435,8437,8440,8446,8450,8455,8458,8461,8465,8466,8577,8594,8597,8599,8601,8604,8607,8609,8611,8613,8616,8618,8621,8622,8625,8632,8633,8636,8641,8689,8744,8750,8752,8756,8761,8763,8771,8773,8780,8784,8786,8804,8807,8810,8812,8815,8818,8832,8854,8945,8947,8962,8969,8974,8978,8982,8985,8988,8991,8992,8994,8998,9002,9008,9011,9127,9149,9162,9177,9179,9439,9468,9490,9491,9493,9495,9497,9498,9502,9506,9508,9517,9521,9524,9527,9531,9542,9546,9547,9574,9580,9583,9593,9595,9608,9616,9618,9638,9648,9650,9652,9655,9657,9664,9665,9673,9680,9686,9690,9696,9707,9715,9718,9720,9722,9724,9734,9736,9738,9739,9742,9744,9747,9751,9754,9756,9760,9762,9765,9766,9770,9771,9772,9776,9778,9779,9802,9806,9808,9809,9812,9815,9819,9822,9825,9828,9831,9832,9833,9835,9838,9841,9851,9857,9876,9884,9893,9894,9896,9898,9902,9904,9906,9908,9911,9913,9920,9922,9926,9929,9933,9936,9945,9958,9960,9962,9963,9965,9970,9973,9977,9994,9997,9999,10009,10011,10012,10014,10016,10021,10026,10028,10030,10034,10036,10037,10040,10046,10047,10049,10052,10053,10054,10055,10056,10058,10062,10066, +chr19 47506015 47516286 m54329U_210323_190418/26544028/ccs 140,345,516,681,904,1113,1291,1479,1679,1855,2033,2234,2377,2567,2744,2927,3122,3271,3465,3628,3835,4005,4198,4399,4633,4801,5040,5220,5423,5646,5857,6031,6209,6422,6608,6755,7008,7195,7376,7558,7738,7919,8092,8244,8482,8681,8863,9766,10071, 138,130,158,171,132,120,131,133,135,128,142,134,138,139,124,128,132,155,120,132,160,159,157,135,88,146,131,162,135,136,143,156,145,139,136,135,125,147,138,145,124,133,114,135,115,130,113,260,108, 109,278,475,674,852,1036,1233,1422,1612,1814,1983,2175,2368,2515,2706,2868,3055,3254,3426,3585,3760,3995,4164,4355,4534,4721,4947,5171,5382,5558,5782,6000,6187,6354,6561,6744,6890,7133,7342,7514,7703,7862,8052,8206,8379,8597,8811,8976,10026,10179, 31,67,41,7,52,77,58,57,67,41,50,59,9,52,38,59,67,17,39,43,75,10,34,44,99,80,93,49,41,88,75,31,22,68,47,11,118,62,34,44,35,57,40,38,103,84,52,790,45,56, . . . 108,111,114,118,125,128,130,135,139,278,285,286,289,305,309,318,320,333,342,344,475,498,504,513,515,674,680,852,867,874,876,881,903,1036,1041,1052,1056,1060,1065,1068,1070,1072,1075,1077,1079,1081,1085,1098,1112,1233,1239,1242,1243,1246,1248,1250,1252,1255,1257,1265,1271,1275,1278,1284,1286,1290,1422,1424,1427,1435,1437,1441,1444,1447,1453,1458,1462,1465,1478,1612,1616,1631,1632,1640,1644,1645,1649,1651,1653,1669,1672,1675,1678,1814,1820,1824,1826,1833,1838,1841,1854,1983,1986,1988,1989,2007,2012,2015,2032,2059,2175,2185,2191,2204,2206,2209,2212,2216,2219,2223,2227,2229,2233,2368,2370,2376,2515,2517,2520,2526,2529,2531,2533,2534,2540,2542,2549,2551,2554,2559,2566,2706,2715,2723,2726,2727,2728,2731,2734,2743,2868,2870,2877,2883,2885,2887,2889,2893,2899,2901,2903,2904,2906,2926,3055,3057,3059,3061,3085,3086,3089,3091,3093,3094,3099,3101,3106,3110,3113,3115,3121,3254,3256,3258,3260,3267,3270,3426,3432,3438,3440,3442,3444,3447,3449,3452,3456,3464,3585,3598,3601,3602,3608,3612,3616,3621,3622,3625,3627,3760,3768,3779,3787,3823,3828,3831,3834,3995,4004,4164,4176,4178,4188,4190,4197,4355,4361,4370,4373,4376,4385,4388,4390,4395,4398,4534,4552,4556,4558,4559,4568,4570,4576,4579,4580,4584,4609,4611,4616,4632,4721,4724,4735,4739,4742,4746,4747,4752,4754,4758,4761,4764,4766,4770,4771,4776,4777,4779,4782,4785,4789,4791,4793,4795,4798,4800,4947,4954,4958,4963,4976,4980,4984,4989,4991,4993,4996,4999,5000,5004,5009,5018,5024,5025,5039,5171,5180,5187,5188,5191,5205,5209,5210,5212,5219,5382,5387,5388,5390,5394,5396,5399,5402,5407,5410,5413,5415,5419,5422,5558,5561,5564,5566,5567,5576,5579,5581,5590,5593,5597,5599,5602,5603,5604,5614,5616,5618,5619,5623,5625,5630,5636,5638,5639,5641,5645,5782,5787,5795,5801,5805,5808,5815,5816,5819,5822,5823,5825,5828,5843,5853,5856,6000,6005,6010,6016,6020,6027,6030,6187,6188,6190,6192,6194,6195,6199,6201,6203,6204,6205,6208,6354,6355,6358,6360,6362,6365,6373,6387,6390,6393,6408,6412,6415,6416,6421,6561,6584,6587,6590,6607,6744,6751,6754,6890,6892,6901,6907,6913,6916,6920,6922,6928,6929,6931,6934,6938,6941,6944,6946,6949,6954,6960,6963,6967,6972,6976,6978,6981,6982,6984,6986,6988,6993,6996,7002,7007,7133,7137,7138,7143,7144,7149,7154,7156,7160,7162,7163,7166,7169,7171,7173,7174,7178,7179,7181,7185,7187,7188,7191,7194,7342,7343,7349,7361,7365,7367,7369,7371,7375,7514,7525,7528,7536,7538,7540,7543,7547,7550,7552,7557,7703,7705,7707,7709,7715,7717,7719,7721,7725,7727,7728,7737,7862,7876,7883,7888,7890,7894,7897,7898,7900,7905,7909,7916,7918,8052,8058,8066,8068,8076,8081,8091,8206,8224,8229,8232,8236,8237,8239,8240,8242,8243,8379,8390,8400,8401,8403,8405,8407,8412,8413,8415,8418,8422,8425,8429,8431,8434,8437,8441,8442,8444,8446,8452,8454,8458,8469,8476,8481,8597,8602,8603,8605,8610,8616,8621,8623,8627,8629,8631,8634,8636,8638,8642,8644,8645,8657,8661,8663,8664,8670,8672,8676,8680,8811,8816,8818,8825,8828,8830,8836,8838,8843,8845,8847,8848,8850,8856,8862,8976,8979,9002,9003,9005,9007,9009,9010,9014,9015,9019,9021,9030,9034,9037,9040,9044,9055,9059,9060,9092,9093,9096,9103,9106,9108,9121,9129,9131,9139,9142,9161,9163,9165,9168,9170,9179,9180,9186,9188,9189,9191,9193,9220,9221,9228,9231,9233,9235,9237,9243,9248,9250,9252,9253,9257,9259,9262,9266,9269,9271,9275,9277,9280,9281,9285,9286,9287,9291,9293,9294,9318,9322,9324,9325,9328,9331,9334,9335,9338,9341,9344,9347,9348,9351,9354,9357,9363,9368,9374,9386,9409,9410,9412,9414,9418,9420,9422,9424,9429,9434,9436,9438,9440,9442,9445,9447,9449,9452,9461,9470,9471,9474,9476,9478,9479,9481,9486,9489,9511,9514,9516,9525,9527,9528,9531,9532,9534,9540,9541,9542,9551,9555,9556,9557,9558,9561,9563,9567,9568,9570,9573,9574,9575,9605,9606,9618,9620,9625,9627,9628,9630,9632,9634,9639,9640,9641,9643,9644,9645,9646,9647,9651,9652,9654,9657,9658,9660,9662,9664,9666,9668,9671,9672,9673,9684,9688,9690,9691,9693,9703,9707,9711,9712,9713,9718,9720,9723,9727,9730,9732,9734,9738,9744,9754,9757,9759,9765,10026,10028,10031,10032,10034,10035,10046,10048,10051,10070,10179,10196,10222,10228,10230,10234, +chr19 47506215 47513023 m64076_221119_202646/55771763/ccs 170,333,562,725,915,1132,1341,1496,1641,1820,2029,2228,2401,2588,2742,2940,3067,3256,3460,3633,3841,4030,4168,4356,4524,4835,4991,5166,5328,5680,5852,5997,6156,6393, 134,141,112,99,124,92,98,117,123,162,117,137,141,109,108,126,140,128,130,148,120,100,134,103,103,89,86,111,96,87,85,111,100,95, 106,304,474,674,824,1039,1224,1439,1613,1764,1982,2146,2365,2542,2697,2850,3066,3207,3384,3590,3781,3961,4130,4302,4459,4627,4924,5077,5277,5424,5767,5937,6108,6256, 64,29,88,51,91,93,117,57,28,56,47,82,36,46,45,90,1,49,76,43,60,69,38,54,65,208,67,89,51,256,85,60,48,137, . . . 105,109,118,120,125,141,142,144,148,150,154,157,159,160,164,167,169,304,310,313,315,321,325,330,332,474,480,482,483,487,496,498,502,503,507,510,516,520,526,528,533,543,549,558,561,674,676,681,688,696,698,703,707,711,712,717,724,824,830,836,839,841,844,846,852,856,860,865,866,868,870,872,875,877,879,881,885,891,893,895,898,904,908,912,914,1039,1042,1046,1048,1050,1052,1055,1057,1063,1065,1067,1071,1074,1075,1078,1080,1084,1086,1090,1091,1093,1097,1101,1106,1108,1112,1125,1131,1224,1227,1228,1235,1237,1241,1244,1247,1250,1253,1258,1259,1262,1267,1270,1274,1278,1281,1284,1287,1289,1297,1298,1300,1305,1308,1311,1313,1317,1320,1323,1327,1336,1339,1340,1439,1444,1448,1450,1452,1454,1455,1459,1468,1471,1474,1482,1484,1487,1493,1495,1613,1623,1625,1632,1637,1640,1764,1782,1785,1787,1788,1791,1795,1799,1806,1811,1814,1819,1982,1999,2003,2005,2008,2015,2022,2026,2028,2146,2153,2160,2162,2164,2167,2169,2182,2185,2186,2189,2191,2197,2200,2203,2217,2219,2227,2365,2367,2368,2371,2373,2380,2385,2387,2390,2397,2398,2400,2542,2546,2555,2557,2570,2583,2587,2697,2698,2703,2717,2721,2722,2725,2729,2730,2731,2732,2736,2737,2741,2850,2854,2856,2858,2860,2883,2884,2885,2888,2890,2892,2893,2894,2898,2900,2905,2909,2912,2914,2916,2917,2920,2922,2925,2932,2939,3066,3207,3227,3229,3231,3236,3237,3241,3243,3246,3248,3255,3384,3388,3392,3408,3411,3414,3415,3420,3421,3423,3424,3426,3429,3430,3434,3436,3437,3446,3449,3452,3455,3459,3590,3598,3620,3621,3626,3629,3632,3781,3782,3793,3797,3799,3801,3805,3806,3812,3822,3824,3829,3840,3961,3963,3966,3973,3978,3980,3985,3987,3990,3994,3996,3997,4002,4011,4029,4130,4146,4148,4152,4154,4158,4167,4235,4302,4305,4307,4310,4312,4314,4316,4317,4318,4321,4322,4325,4331,4339,4349,4353,4355,4459,4473,4476,4479,4482,4483,4488,4489,4490,4495,4497,4500,4504,4506,4508,4511,4521,4523,4627,4630,4639,4642,4651,4652,4654,4657,4658,4663,4666,4667,4669,4673,4674,4678,4680,4682,4685,4688,4693,4695,4699,4702,4705,4707,4712,4713,4715,4717,4721,4724,4727,4730,4731,4733,4735,4742,4743,4747,4749,4753,4758,4760,4761,4762,4766,4768,4769,4771,4774,4775,4779,4783,4784,4786,4788,4791,4794,4795,4799,4804,4806,4809,4811,4813,4815,4819,4820,4825,4826,4834,4924,4926,4930,4933,4934,4937,4939,4940,4943,4945,4952,4956,4960,4961,4963,4966,4968,4975,4979,4983,4990,5077,5088,5091,5096,5098,5104,5111,5114,5118,5122,5124,5126,5127,5130,5135,5137,5142,5146,5150,5151,5154,5158,5163,5165,5277,5281,5284,5286,5288,5293,5297,5301,5304,5306,5310,5312,5314,5320,5327,5424,5429,5431,5434,5436,5440,5445,5450,5452,5455,5459,5461,5465,5467,5473,5478,5479,5480,5482,5483,5485,5487,5488,5490,5491,5493,5495,5497,5504,5505,5507,5508,5509,5511,5513,5520,5526,5543,5546,5567,5636,5638,5642,5648,5651,5656,5662,5668,5679,5767,5776,5778,5781,5783,5786,5790,5793,5795,5800,5802,5805,5811,5812,5815,5818,5819,5822,5825,5827,5832,5835,5836,5838,5842,5844,5846,5847,5851,5937,5942,5951,5973,5977,5983,5985,5987,5994,5996,6108,6126,6130,6136,6139,6142,6146,6149,6150,6155,6256,6263,6267,6268,6278,6283,6286,6290,6293,6294,6297,6299,6301,6303,6306,6307,6309,6314,6319,6323,6329,6330,6331,6335,6338,6340,6342,6346,6348,6352,6356,6366,6379,6382,6385,6392,6488,6495,6498,6499,6500,6503,6505,6508,6509,6511,6519,6520,6522,6524,6526,6529,6531,6534,6539,6540,6541,6546,6547,6549,6550,6552,6553,6555,6556,6559,6566,6570,6576,6579,6583,6586,6588,6589,6590,6592,6593,6600,6605,6606,6608,6613,6616,6619,6621,6622,6625,6626,6629,6631,6633,6634,6636,6639,6641,6642,6646,6648,6651,6652,6655,6657,6659,6660,6661,6664,6668,6670,6674,6678,6685,6689,6691,6693,6694,6699,6769,6790,6793, +chr19 47506222 47514314 m84008_230107_003043_s1/177932302/ccs 80,246,416,577,767,977,1182,1410,1581,1759,1976,2169,2333,2533,2735,2884,3063,3257,3478,3669,3898,4081,4254,4430,4646,4866,5044,5214,5449,5644,5811,5974,6180,6374,6719,6876,7056,7244,7426,7573,7741, 105,118,120,124,117,138,150,118,147,153,123,115,132,97,106,135,193,151,144,125,143,133,147,190,151,150,169,164,139,131,117,159,146,274,107,131,146,148,141,146,145, 185,364,536,701,884,1115,1332,1528,1728,1912,2099,2284,2465,2630,2841,3019,3256,3408,3622,3794,4041,4214,4401,4620,4797,5016,5213,5378,5588,5775,5928,6133,6326,6648,6826,7007,7202,7392,7567,7719,7886, 61,52,41,66,93,67,78,53,31,64,70,49,68,105,43,44,1,70,47,104,40,40,29,26,69,28,1,71,56,36,46,47,48,71,50,49,42,34,6,22,40, . . . 10,12,15,20,25,39,42,56,79,185,187,189,193,196,199,201,205,206,208,211,217,221,245,364,369,373,375,381,383,398,401,404,406,408,415,536,538,542,551,554,563,567,576,701,708,710,713,716,722,725,730,734,736,737,740,753,758,766,884,886,888,891,898,901,905,907,915,918,922,927,932,934,936,940,948,953,958,960,964,965,976,1115,1117,1122,1124,1125,1129,1132,1138,1144,1147,1150,1155,1157,1170,1174,1177,1178,1181,1220,1332,1337,1343,1345,1351,1367,1387,1394,1401,1409,1528,1532,1542,1546,1551,1556,1559,1564,1566,1577,1580,1728,1743,1750,1754,1757,1758,1912,1927,1935,1939,1943,1947,1959,1965,1975,2021,2099,2103,2109,2112,2118,2131,2133,2136,2139,2142,2153,2157,2160,2162,2168,2284,2295,2307,2309,2312,2332,2465,2467,2468,2473,2475,2489,2493,2496,2498,2504,2507,2512,2520,2523,2526,2530,2532,2630,2634,2648,2654,2656,2660,2662,2665,2669,2675,2677,2679,2681,2683,2685,2690,2691,2693,2696,2698,2710,2714,2715,2718,2722,2729,2734,2841,2843,2847,2849,2878,2883,3019,3023,3027,3031,3034,3035,3046,3048,3050,3059,3062,3256,3408,3417,3422,3427,3429,3442,3445,3461,3465,3468,3477,3575,3622,3631,3636,3664,3665,3668,3794,3805,3815,3827,3828,3831,3836,3838,3842,3844,3851,3852,3854,3856,3877,3878,3880,3881,3885,3888,3892,3897,4041,4051,4080,4214,4231,4250,4253,4295,4369,4401,4421,4422,4428,4429,4504,4593,4620,4623,4632,4635,4644,4645,4797,4804,4806,4812,4813,4827,4830,4837,4839,4843,4845,4851,4855,4857,4863,4865,5016,5019,5020,5021,5025,5027,5032,5034,5037,5043,5213,5378,5398,5404,5407,5411,5413,5416,5422,5424,5427,5429,5438,5443,5445,5448,5588,5609,5610,5612,5615,5616,5643,5775,5778,5794,5797,5803,5810,5928,5940,5942,5948,5951,5952,5956,5973,6133,6137,6140,6141,6144,6146,6148,6151,6155,6157,6159,6161,6163,6167,6168,6170,6173,6175,6176,6179,6326,6331,6333,6337,6339,6343,6347,6350,6373,6648,6659,6661,6680,6682,6684,6689,6690,6695,6700,6703,6715,6718,6826,6851,6868,6873,6875,7007,7009,7016,7020,7029,7039,7041,7046,7055,7202,7203,7207,7211,7218,7219,7225,7226,7237,7243,7392,7394,7398,7410,7422,7425,7567,7569,7572,7719,7727,7730,7736,7740,7886,7888,7890,7893,7896,7898,7900,7902,7903,7905,7907,7910,7913,7914,7922,7925,8050,8060,8062,8069, +chr19 47506398 47523529 m54329U_210326_192251/95750173/ccs 139,321,518,732,919,1096,1311,1485,1662,1829,2011,2158,2357,2518,2676,2829,3169,3329,3536,3722,3925,4102,4300,4484,4652,4831,5048,5267,5420,5619,5798,5929,6156,6300,6646,6802,6993,7136,7288,7575,7726,7897,8090,8299,8448,9255,9615,9759,9901,10077,10261,10479,10832,10995,11201,11340,11520,11693,11994,12214,12367,12637,12801,13035,13201,13368,13539,13749,13910,14242,14415,14613,14797,14995,15136,15334,15507,16027,16199,16334,16668, 136,140,123,104,122,129,116,138,139,134,119,126,97,119,100,237,117,127,134,140,104,121,144,146,146,139,139,126,139,133,130,123,102,271,126,133,142,124,254,114,128,113,112,121,116,234,118,130,107,124,151,145,134,113,110,152,117,103,109,128,253,135,147,106,139,141,140,139,270,117,124,122,124,120,143,116,430,130,132,291,347, 82,275,461,641,836,1041,1225,1427,1623,1801,1963,2130,2284,2454,2637,2776,3066,3286,3456,3670,3862,4029,4223,4444,4630,4798,4970,5187,5393,5559,5752,5928,6052,6258,6571,6772,6935,7135,7260,7542,7689,7854,8010,8202,8420,8564,9489,9733,9889,10008,10201,10412,10624,10966,11108,11311,11492,11637,11796,12103,12342,12620,12772,12948,13141,13340,13509,13679,13888,14180,14359,14539,14735,14921,15115,15279,15450,15937,16157,16331,16625,17015, 57,46,57,91,83,55,86,58,39,28,48,28,73,64,39,53,103,43,80,52,63,73,77,40,22,33,78,80,27,60,46,1,104,42,75,30,58,1,28,33,37,43,80,97,28,691,126,26,12,69,60,67,208,29,93,29,28,56,198,111,25,17,29,87,60,28,30,70,22,62,56,74,62,74,21,55,57,90,42,3,43,1, . . . 81,83,86,92,97,117,121,132,138,275,278,291,293,295,297,299,300,304,310,313,315,319,320,428,461,465,469,470,473,475,476,478,480,487,491,493,517,598,641,647,653,656,658,661,669,673,677,682,683,685,687,689,692,696,698,702,708,710,712,731,809,836,838,840,846,859,860,863,865,867,869,872,874,880,882,884,888,892,901,903,918,1041,1044,1045,1050,1052,1054,1058,1064,1067,1070,1079,1082,1084,1087,1091,1095,1225,1231,1242,1244,1247,1248,1256,1258,1260,1261,1265,1267,1269,1272,1276,1278,1279,1280,1285,1288,1291,1310,1427,1430,1438,1440,1442,1449,1454,1457,1461,1470,1474,1477,1478,1484,1623,1628,1631,1637,1643,1648,1652,1656,1658,1661,1801,1820,1825,1828,1963,1966,1970,1977,1981,1984,1986,1992,2003,2010,2130,2132,2135,2155,2157,2284,2289,2291,2299,2303,2313,2315,2317,2320,2322,2326,2328,2331,2336,2339,2347,2354,2356,2454,2455,2458,2461,2473,2475,2480,2484,2486,2489,2493,2505,2507,2509,2517,2637,2647,2667,2673,2675,2776,2785,2794,2797,2808,2822,2826,2828,3066,3073,3094,3095,3097,3101,3105,3108,3113,3119,3124,3127,3129,3131,3134,3139,3141,3144,3151,3168,3286,3290,3293,3298,3302,3303,3309,3316,3318,3325,3328,3456,3474,3476,3482,3488,3489,3490,3493,3510,3513,3515,3516,3518,3524,3528,3529,3533,3535,3670,3688,3695,3696,3698,3701,3702,3712,3716,3721,3862,3865,3871,3875,3896,3905,3924,4029,4031,4038,4055,4060,4062,4066,4074,4077,4081,4084,4096,4099,4101,4223,4225,4233,4245,4252,4253,4255,4267,4271,4272,4274,4276,4284,4293,4296,4299,4444,4459,4469,4483,4630,4632,4636,4637,4642,4643,4647,4651,4798,4799,4802,4809,4822,4828,4830,4970,4974,4979,4981,4988,4991,4993,4995,4998,5001,5005,5007,5010,5013,5016,5018,5021,5024,5026,5030,5033,5036,5040,5041,5043,5045,5047,5187,5190,5192,5193,5194,5201,5204,5208,5210,5213,5223,5227,5230,5234,5236,5252,5266,5393,5398,5402,5406,5408,5410,5412,5416,5419,5559,5565,5571,5574,5577,5583,5588,5589,5592,5594,5618,5752,5764,5766,5775,5781,5785,5788,5794,5797,5928,6052,6055,6064,6068,6072,6075,6076,6077,6078,6082,6083,6089,6091,6093,6098,6101,6105,6108,6109,6112,6118,6122,6124,6129,6131,6150,6153,6155,6258,6260,6262,6264,6268,6272,6274,6277,6281,6285,6299,6571,6583,6587,6589,6592,6593,6595,6597,6599,6604,6607,6609,6611,6613,6615,6616,6618,6620,6622,6631,6633,6636,6639,6641,6645,6772,6776,6779,6784,6788,6789,6791,6795,6797,6798,6801,6935,6939,6952,6953,6957,6959,6962,6963,6966,6968,6971,6972,6973,6975,6977,6979,6981,6983,6985,6986,6988,6992,7135,7260,7271,7287,7542,7546,7550,7553,7559,7563,7568,7570,7571,7574,7689,7709,7711,7725,7854,7856,7862,7864,7868,7871,7873,7875,7883,7896,8010,8017,8023,8027,8028,8030,8034,8036,8042,8046,8047,8049,8051,8059,8063,8067,8081,8086,8089,8202,8210,8214,8215,8221,8222,8224,8226,8228,8232,8234,8236,8239,8241,8242,8243,8247,8249,8250,8261,8265,8267,8268,8274,8276,8280,8284,8289,8291,8298,8420,8422,8429,8432,8438,8439,8440,8442,8447,8564,8566,8570,8572,8576,8580,8581,8583,8585,8587,8606,8607,8609,8611,8613,8614,8618,8622,8624,8633,8637,8638,8640,8643,8647,8658,8662,8663,8690,8695,8696,8699,8706,8709,8711,8742,8745,8764,8766,8768,8771,8773,8781,8782,8783,8789,8792,8802,8806,8812,8823,8824,8831,8834,8836,8838,8840,8845,8850,8852,8854,8855,8858,8860,8863,8867,8870,8872,8876,8878,8881,8882,8886,8887,8888,8892,8895,8906,8924,8925,8928,8931,8934,8935,8938,8941,8944,8947,8948,8951,8954,8957,8962,8967,8973,8993,8999,9008,9009,9011,9013,9017,9019,9021,9023,9026,9028,9033,9035,9037,9039,9041,9044,9046,9048,9051,9060,9069,9073,9075,9077,9080,9085,9087,9088,9090,9091,9094,9109,9112,9114,9121,9122,9123,9125,9126,9128,9134,9135,9136,9141,9143,9145,9152,9155,9156,9157,9161,9162,9164,9167,9168,9169,9171,9174,9199,9200,9212,9214,9221,9222,9224,9226,9228,9230,9243,9254,9489,9496,9499,9502,9505,9509,9518,9520,9521,9524,9528,9530,9533,9535,9538,9542,9548,9550,9552,9554,9560,9561,9564,9566,9592,9594,9596,9600,9614,9733,9734,9736,9738,9740,9742,9744,9758,9889,9891,9892,9895,9896,9900,10008,10031,10034,10037,10046,10049,10051,10062,10076,10201,10202,10205,10207,10210,10216,10225,10226,10227,10230,10232,10234,10237,10238,10239,10241,10243,10245,10249,10255,10257,10258,10260,10412,10415,10421,10423,10426,10428,10431,10435,10437,10438,10441,10444,10445,10446,10448,10449,10452,10457,10460,10468,10470,10475,10478,10624,10627,10630,10631,10635,10637,10642,10644,10647,10650,10655,10661,10668,10684,10752,10754,10756,10773,10775,10780,10795,10800,10802,10804,10805,10806,10809,10810,10812,10819,10822,10824,10827,10829,10831,10966,10971,10974,10979,10985,10987,10990,10994,11108,11111,11114,11120,11121,11123,11126,11136,11139,11145,11147,11150,11151,11153,11157,11161,11163,11167,11169,11171,11173,11175,11178,11179,11181,11200,11311,11316,11318,11320,11339,11492,11496,11500,11502,11505,11511,11514,11515,11519,11637,11640,11641,11645,11649,11651,11654,11661,11662,11663,11665,11666,11667,11674,11677,11687,11692,11796,11799,11811,11817,11818,11821,11823,11824,11830,11831,11835,11837,11842,11845,11846,11850,11852,11853,11855,11856,11860,11861,11867,11868,11870,11872,11874,11875,11877,11878,11879,11881,11882,11884,11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+chr19 47506533 47518567 m54329U_210326_192251/68487112/ccs 211,400,578,784,953,1127,1308,1497,1691,1865,2033,2199,2545,2728,2857,3060,3222,3413,3619,3819,3992,4152,4327,4522,4699,4917,5105,5323,5487,5667,5855,6033,6244,6585,6752,6897,7166,7342,7513,7683,8099,8267,9139,9284,9438,9614,9769,9920,10133,10332,10517,10735,10912,11096,11586, 123,118,133,122,141,168,156,131,129,131,122,122,130,128,171,160,154,147,123,122,151,120,128,141,135,110,156,128,157,159,152,170,118,136,144,259,165,167,129,394,140,144,144,115,135,125,150,133,157,129,154,128,132,471,128, 169,334,518,711,906,1094,1295,1464,1628,1820,1996,2155,2321,2675,2856,3028,3220,3376,3560,3742,3941,4143,4272,4455,4663,4834,5027,5261,5451,5644,5826,6007,6203,6362,6721,6896,7156,7331,7509,7642,8077,8239,8411,9283,9399,9573,9739,9919,10053,10290,10461,10671,10863,11044,11567,11714, 42,66,60,73,47,33,13,33,63,45,37,44,224,53,1,32,2,37,59,77,51,9,55,67,36,83,78,62,36,23,29,26,41,223,31,1,10,11,4,41,22,28,728,1,39,41,30,1,80,42,56,64,49,52,19,180, . . . 10,14,22,25,27,29,33,37,169,175,178,180,184,185,189,192,201,208,210,334,338,358,363,370,385,393,394,399,518,521,523,526,534,538,542,547,548,550,552,554,559,561,563,567,573,577,711,715,721,724,725,728,730,732,734,737,739,747,749,753,757,766,768,783,906,909,917,919,923,926,929,932,935,940,944,952,1094,1112,1121,1123,1125,1126,1295,1305,1307,1464,1467,1469,1473,1477,1481,1488,1493,1496,1628,1664,1677,1687,1690,1820,1825,1828,1831,1835,1842,1844,1849,1864,1996,1998,2001,2012,2014,2015,2019,2021,2023,2029,2032,2155,2157,2179,2181,2187,2189,2198,2321,2322,2325,2328,2339,2345,2351,2353,2356,2360,2372,2384,2453,2469,2472,2478,2480,2486,2489,2494,2497,2506,2511,2514,2518,2538,2540,2542,2544,2675,2685,2688,2689,2691,2701,2710,2714,2722,2727,2856,3028,3030,3033,3038,3040,3042,3043,3054,3056,3059,3220,3221,3376,3381,3382,3384,3386,3387,3388,3390,3394,3395,3399,3401,3405,3412,3560,3568,3576,3579,3583,3588,3590,3592,3595,3596,3601,3605,3618,3742,3746,3763,3765,3771,3774,3775,3776,3778,3781,3782,3784,3797,3802,3818,3941,3944,3948,3951,3958,3960,3962,3963,3966,3968,3970,3971,3972,3975,3978,3989,3991,4143,4151,4272,4287,4288,4290,4292,4326,4455,4463,4472,4475,4478,4479,4483,4488,4490,4493,4495,4497,4499,4503,4504,4518,4521,4663,4666,4667,4670,4673,4676,4684,4688,4689,4691,4698,4834,4842,4847,4849,4854,4859,4861,4863,4866,4867,4869,4873,4875,4878,4881,4884,4886,4889,4892,4894,4898,4901,4911,4916,5027,5030,5035,5037,5039,5045,5055,5058,5060,5061,5062,5069,5072,5076,5078,5081,5082,5083,5089,5090,5093,5095,5097,5098,5102,5104,5261,5266,5270,5272,5276,5278,5280,5284,5287,5301,5302,5304,5322,5451,5460,5462,5465,5467,5470,5471,5486,5644,5645,5656,5666,5826,5834,5837,5844,5848,5854,6007,6019,6022,6024,6030,6032,6203,6208,6210,6215,6218,6230,6233,6242,6243,6362,6382,6388,6394,6397,6403,6409,6410,6412,6415,6419,6420,6422,6425,6427,6430,6431,6435,6437,6441,6444,6448,6453,6457,6462,6469,6474,6548,6566,6572,6577,6581,6584,6611,6721,6733,6735,6738,6740,6751,6869,6896,7156,7159,7160,7165,7331,7333,7341,7509,7512,7642,7654,7661,7664,7672,7682,8077,8098,8239,8242,8246,8250,8252,8254,8257,8258,8261,8264,8266,8411,8414,8419,8421,8423,8426,8428,8434,8436,8440,8442,8446,8450,8451,8453,8457,8463,8476,8477,8479,8481,8483,8484,8488,8492,8494,8503,8507,8508,8510,8513,8517,8528,8532,8533,8594,8602,8604,8612,8615,8624,8634,8636,8638,8641,8643,8650,8651,8652,8658,8660,8661,8663,8681,8692,8693,8700,8703,8705,8707,8709,8714,8719,8721,8723,8724,8728,8730,8740,8742,8746,8748,8751,8752,8756,8757,8758,8762,8764,8765,8776,8788,8793,8795,8796,8799,8802,8805,8806,8809,8812,8815,8818,8819,8820,8822,8825,8828,8833,8838,8844,8857,8863,8865,8880,8881,8883,8885,8889,8891,8893,8895,8898,8900,8905,8907,8909,8911,8913,8916,8918,8920,8932,8941,8947,8949,8952,8957,8959,8960,8962,8981,8984,8986,8993,8994,8995,8997,8998,9000,9002,9003,9006,9007,9008,9013,9014,9015,9017,9021,9022,9024,9027,9029,9033,9034,9036,9039,9040,9070,9076,9077,9078,9083,9085,9092,9093,9095,9097,9099,9101,9106,9112,9119,9122,9125,9127,9131,9133,9136,9137,9138,9283,9399,9404,9409,9413,9419,9423,9427,9429,9431,9433,9435,9437,9573,9578,9579,9581,9588,9595,9597,9598,9599,9602,9603,9605,9607,9611,9613,9739,9746,9748,9751,9754,9757,9759,9760,9768,9890,9919,10053,10056,10083,10084,10095,10098,10100,10102,10105,10106,10109,10111,10113,10125,10132,10290,10292,10297,10300,10304,10307,10310,10317,10320,10321,10331,10461,10493,10496,10499,10500,10511,10513,10516,10671,10673,10674,10675,10678,10679,10681,10683,10688,10691,10693,10696,10698,10700,10712,10714,10716,10717,10722,10731,10734,10863,10867,10872,10875,10877,10878,10881,10885,10887,10889,10890,10911,11044,11069,11077,11095,11567,11570,11574,11578,11580,11585,11714,11724,11729,11730,11736,11737,11739,11741,11743,11744,11746,11747,11748,11750,11751,11753,11754,11755,11756,11758,11760,11761,11765,11768,11771,11774,11775,11777,11778,11780,11783,11784,11788,11790,11792,11794,11797,11799,11802,11804,11806,11809,11812,11818,11820,11824,11827,11828,11830,11833,11835,11836,11841,11842,11843,11844,11847,11848,11852,11854,11856,11858,11862,11866,11868,11870,11871,11872,11874,11881,11882,11884,11886,11887,11888,11893, +chr19 47506600 47515470 m84008_230107_003043_s1/59839140/ccs 77,354,530,709,1111,1277,1460,1627,1785,1957,2154,2340,2535,2684,2930,3073,3286,3473,3662,3835,4042,4255,4433,4574,4767,4972,5120,5347,5480,5662,5839,6040,6259,6412,6601,6921,7094,7365,7569,7689,7903,8073,8263,8444,8551, 241,142,124,108,110,120,154,137,144,129,104,162,120,170,117,130,139,136,121,131,118,115,139,149,146,147,130,107,142,107,129,116,102,123,278,121,270,120,119,141,114,121,139,76,80, 318,496,654,817,1221,1397,1614,1764,1929,2086,2258,2502,2655,2854,3047,3203,3425,3609,3783,3966,4160,4370,4572,4723,4913,5119,5250,5454,5622,5769,5968,6156,6361,6535,6879,7042,7364,7485,7688,7830,8017,8194,8402,8520, 36,34,55,294,56,63,13,21,28,68,82,33,29,76,26,83,48,53,52,76,95,63,2,44,59,1,97,26,40,70,72,103,51,66,42,52,1,84,1,73,56,69,42,31, . . . 20,23,26,28,30,59,61,65,69,73,76,318,330,332,338,339,353,496,500,506,510,529,654,657,661,663,665,667,670,672,680,682,686,689,701,708,817,839,842,843,848,850,852,856,859,862,865,868,873,874,877,882,889,893,896,902,912,920,923,930,938,940,942,1000,1002,1016,1018,1020,1023,1029,1031,1040,1042,1046,1054,1058,1059,1063,1065,1067,1069,1070,1074,1102,1108,1110,1221,1225,1228,1234,1252,1255,1268,1272,1276,1397,1400,1403,1406,1410,1421,1426,1431,1432,1442,1446,1450,1457,1459,1614,1618,1623,1626,1764,1775,1777,1779,1782,1784,1929,1931,1934,1945,1948,1954,1956,2035,2086,2089,2094,2096,2100,2102,2114,2117,2119,2125,2128,2133,2136,2140,2141,2144,2147,2151,2153,2258,2269,2275,2281,2283,2286,2296,2298,2300,2302,2304,2306,2311,2312,2331,2336,2339,2502,2504,2512,2514,2523,2526,2534,2655,2667,2669,2671,2675,2677,2680,2683,2854,2856,2859,2861,2873,2876,2890,2900,2903,2908,2914,2929,3047,3049,3065,3068,3072,3203,3234,3239,3242,3250,3251,3256,3271,3277,3285,3384,3425,3427,3429,3435,3437,3442,3444,3447,3451,3456,3460,3462,3464,3466,3472,3609,3610,3615,3617,3620,3624,3637,3648,3650,3655,3658,3661,3783,3786,3789,3795,3798,3804,3805,3808,3811,3812,3813,3816,3819,3821,3827,3828,3830,3834,3966,3969,3979,3983,3984,3986,3989,3990,3994,4009,4019,4021,4033,4041,4160,4162,4166,4169,4171,4173,4177,4178,4183,4184,4186,4192,4196,4200,4202,4205,4207,4210,4215,4218,4220,4237,4239,4242,4245,4254,4370,4387,4395,4396,4400,4407,4411,4416,4421,4423,4425,4431,4432,4526,4572,4573,4723,4730,4734,4736,4739,4742,4747,4754,4762,4763,4766,4913,4922,4924,4926,4930,4932,4942,4946,4949,4958,4968,4971,5119,5250,5254,5256,5260,5263,5266,5268,5270,5280,5282,5285,5288,5291,5296,5299,5301,5303,5321,5346,5454,5456,5458,5459,5462,5463,5465,5471,5476,5479,5622,5640,5642,5644,5646,5647,5650,5653,5654,5658,5661,5769,5776,5782,5784,5788,5791,5793,5794,5797,5800,5806,5809,5811,5813,5816,5826,5828,5838,5968,5980,5985,5986,5990,5993,5996,6003,6009,6013,6018,6020,6026,6029,6039,6156,6159,6180,6185,6193,6216,6218,6231,6235,6236,6258,6361,6367,6370,6374,6383,6385,6388,6391,6409,6411,6535,6537,6549,6550,6553,6555,6562,6566,6568,6569,6572,6575,6577,6579,6580,6584,6585,6587,6589,6591,6593,6594,6597,6600,6879,6881,6885,6901,6904,6907,6920,7042,7045,7054,7056,7057,7063,7067,7070,7073,7076,7078,7080,7087,7093,7364,7485,7507,7509,7515,7517,7519,7521,7524,7529,7533,7541,7544,7549,7551,7559,7565,7568,7688,7830,7832,7835,7838,7842,7843,7845,7847,7855,7870,7886,7896,7899,7902,8017,8022,8024,8035,8043,8045,8046,8061,8063,8072,8194,8211,8218,8230,8234,8235,8238,8243,8245,8250,8256,8262,8402,8403,8405,8407,8409,8410,8418,8433,8443,8520,8528,8538,8541,8550,8631,8633,8640,8645,8647,8653,8655,8658,8662,8665,8667,8671,8673,8682,8683,8713,8717,8723,8726,8730,8762,8768,8780,8786,8788,8794,8806,8808,8812,8814,8816,8821, +chr19 47506953 47527720 m84008_230107_003043_s1/212800855/ccs 177,375,576,1159,1343,1603,1690,2033,2327,2976,3468,3995,4209,4737,5001,5144,5313,5532,5726,5912,6383,6859,7025,7166,7366,7544,7928,8768,8886,9260,9742,10110,10307,10439,10626,10921,11085,11519,11721,11837,11973,12164,12395,12579,12890,13125,13322,13479,13683,13867,14197,14369,14725,14984,15360,15532,15756,15926,16147,16450,16614,16766,16970,17197,17550,17904,18477,18658,18819,19005,19206,19476,19605,19997,20185,20359, 131,168,149,130,137,86,156,75,243,141,142,140,128,112,132,161,107,110,143,128,147,146,140,178,139,123,127,113,183,440,153,136,116,133,294,160,137,201,98,135,167,152,153,298,80,116,117,142,154,152,171,181,142,144,138,82,146,154,145,148,76,169,115,141,153,161,180,148,185,200,188,128,184,173,160,151, 308,543,725,1289,1480,1689,1846,2108,2570,3117,3610,4135,4337,4849,5133,5305,5420,5642,5869,6040,6530,7005,7165,7344,7505,7667,8055,8881,9069,9700,9895,10246,10423,10572,10920,11081,11222,11720,11819,11972,12140,12316,12548,12877,12970,13241,13439,13621,13837,14019,14368,14550,14867,15128,15498,15614,15902,16080,16292,16598,16690,16935,17085,17338,17703,18065,18657,18806,19004,19205,19394,19604,19789,20170,20345, 67,33,434,54,123,1,187,219,406,351,385,74,400,152,11,8,112,84,43,343,329,20,1,22,39,261,713,5,191,42,215,61,16,54,1,4,297,1,18,1,24,79,31,13,155,81,40,62,30,178,1,175,117,232,34,142,24,67,158,16,76,35,112,212,201,412,1,13,1,1,82,1,208,15,14, . . . 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+chr19 47507279 47524132 m64076_210328_012155/147784005/ccs 77,163,295,710,827,1193,1376,1591,2283,2486,2676,2846,3054,3241,3432,3794,4011,4229,4405,4605,4842,5087,5427,5532,5752,5924,6074,6233,6420,6788,6868,7111,7286,7592,8520,8738,9061,9247,9434,9650,9846,10008,10185,10384,10666,11016,11153,11355,11521,11835,12197,12382,12538,12766,12903,13093,13282,13650,13849,14070,14278,14455,14631,14846,15052,15193,15386,15562,16074,16282,16482, 85,123,330,105,301,143,156,652,137,135,169,154,149,161,337,161,179,169,162,145,244,284,104,184,156,142,129,150,367,79,188,129,305,79,217,282,171,181,136,129,128,121,117,164,268,136,135,137,289,317,166,143,153,136,152,132,349,159,132,127,119,131,126,114,134,132,137,507,166,167,150, 162,286,625,815,1128,1336,1532,2243,2420,2621,2845,3000,3203,3402,3769,3955,4190,4398,4567,4750,5086,5371,5531,5716,5908,6066,6203,6383,6787,6867,7056,7240,7591,7671,8737,9020,9232,9428,9570,9779,9974,10129,10302,10548,10934,11152,11288,11492,11810,12152,12363,12525,12691,12902,13055,13225,13631,13809,13981,14197,14397,14586,14757,14960,15186,15325,15523,16069,16240,16449,16632, 1,9,85,12,65,40,59,40,66,55,1,54,38,30,25,56,39,7,38,92,1,56,1,36,16,8,30,37,1,1,55,46,1,849,1,41,15,6,80,67,34,56,82,118,82,1,67,29,25,45,19,13,75,1,38,57,19,40,89,81,58,45,89,92,7,61,39,5,42,33,49, . . . 76,162,286,288,292,294,625,628,680,706,709,815,817,824,826,1128,1131,1145,1149,1170,1173,1178,1185,1192,1336,1354,1358,1375,1532,1542,1546,1550,1562,1566,1583,1584,1587,1590,2243,2254,2257,2261,2282,2420,2423,2432,2439,2448,2451,2455,2458,2477,2484,2485,2621,2644,2653,2675,2845,3000,3053,3203,3210,3213,3220,3222,3228,3237,3240,3293,3372,3402,3407,3424,3427,3430,3431,3769,3779,3783,3793,3892,3955,3980,3982,3987,3989,3992,3995,3998,4002,4006,4010,4190,4228,4398,4404,4567,4573,4604,4750,4781,4829,4832,4841,5086,5371,5395,5397,5399,5401,5403,5405,5411,5415,5418,5422,5426,5531,5716,5725,5729,5739,5746,5749,5751,5792,5908,5914,5921,5923,5956,6018,6056,6066,6073,6203,6229,6232,6383,6387,6390,6391,6393,6397,6399,6401,6402,6415,6418,6419,6787,6867,7056,7061,7071,7092,7107,7110,7240,7243,7246,7257,7263,7278,7285,7591,7671,7675,7707,7709,7715,7719,7724,7726,7728,7730,7736,7749,7750,7752,7754,7756,7757,7765,7776,7780,7786,7790,7801,7805,7806,7825,7839,7849,7852,7867,7875,7877,7886,7889,7898,7909,7911,7913,7916,7918,7926,7944,7968,7969,7976,7979,7981,7983,7985,7991,7996,7998,8000,8001,8004,8006,8009,8013,8018,8022,8024,8027,8028,8032,8033,8034,8038,8040,8041,8066,8070,8072,8073,8076,8079,8082,8083,8086,8089,8092,8095,8096,8099,8102,8105,8110,8115,8121,8139,8166,8168,8170,8172,8175,8177,8182,8184,8186,8188,8190,8193,8195,8197,8200,8209,8222,8224,8226,8229,8234,8237,8258,8261,8263,8274,8277,8283,8284,8285,8290,8294,8298,8299,8300,8301,8304,8306,8310,8311,8313,8316,8351,8355,8356,8361,8371,8372,8374,8376,8380,8385,8390,8391,8393,8396,8406,8408,8410,8412,8415,8416,8417,8419,8427,8428,8431,8433,8434,8436,8446,8450,8456,8463,8465,8466,8470,8473,8477,8498,8502,8508,8510,8511,8513,8515,8516,8517,8519,8737,9020,9039,9046,9050,9055,9057,9060,9232,9240,9246,9428,9433,9570,9574,9591,9594,9605,9610,9612,9621,9623,9627,9628,9631,9635,9640,9642,9649,9779,9782,9785,9786,9790,9792,9799,9802,9805,9806,9810,9820,9823,9826,9839,9845,9974,9977,9979,10000,10007,10129,10140,10142,10145,10149,10161,10167,10171,10173,10184,10302,10326,10328,10355,10365,10375,10376,10381,10383,10548,10552,10553,10554,10558,10565,10569,10572,10573,10576,10581,10587,10589,10591,10593,10596,10600,10602,10604,10607,10608,10609,10611,10615,10625,10627,10630,10654,10659,10662,10665,10934,10938,10940,10944,10950,10953,10955,10957,10961,10977,10978,10984,10985,10989,11015,11152,11288,11292,11296,11297,11304,11311,11316,11320,11323,11326,11332,11334,11335,11339,11340,11345,11346,11349,11351,11354,11446,11492,11514,11517,11520,11810,11822,11824,11827,11831,11834,12152,12155,12158,12162,12164,12169,12171,12181,12186,12190,12196,12363,12370,12372,12381,12525,12530,12537,12691,12708,12715,12718,12722,12727,12730,12732,12734,12738,12740,12746,12751,12765,12902,13055,13063,13067,13068,13069,13071,13074,13092,13225,13229,13231,13232,13261,13262,13268,13271,13274,13281,13631,13632,13646,13649,13809,13812,13815,13818,13822,13824,13826,13828,13836,13841,13845,13847,13848,13981,13998,14002,14007,14011,14019,14023,14029,14033,14038,14041,14043,14048,14051,14052,14054,14060,14063,14064,14069,14197,14201,14206,14219,14222,14224,14229,14233,14245,14247,14249,14253,14266,14272,14277,14397,14405,14413,14422,14426,14441,14444,14446,14454,14586,14599,14602,14606,14618,14630,14663,14757,14777,14787,14797,14801,14803,14805,14807,14810,14811,14816,14817,14830,14845,14960,14981,14988,14993,14996,14998,15001,15002,15019,15020,15025,15032,15036,15039,15043,15051,15157,15186,15188,15192,15325,15328,15350,15352,15355,15359,15369,15375,15380,15381,15383,15385,15492,15523,15525,15527,15529,15531,15533,15537,15539,15541,15547,15551,15556,15561,16069,16073,16240,16243,16264,16266,16270,16274,16276,16281,16390,16449,16450,16453,16465,16474,16476,16477,16479,16481,16632,16634,16640,16655,16657,16660,16677,16680, +chr19 47507325 47527172 m84039_230401_034725_s4/174002742/ccs 168,383,729,897,1092,1269,1426,1589,1756,1893,2084,2243,2429,2600,2752,2951,3127,3309,3497,3638,3784,3969,4288,4406,4643,4987,5156,5250,5528,5725,5856,5947,6064,6183,6326,6487,6635,6832,7054,7191,7362,7531,8406,8588,8773,8973,9123,9314,9455,9642,9826,9925,10164,10325,10582,10744,11140,11257,11461,11617,11900,12074,12225,12424,12599,12771,12943,13166,13316,13505,13852,14076,14472,14612,14828,14988,15177,15368,15530,15950,16148,16294,16497,16696,16898,17181,17310,17501,17680,17844,18016,18103,18179,18375,18555,18704,18885,19063,19254,19472, 129,105,126,134,126,146,117,139,136,156,113,109,134,131,109,122,137,97,122,120,184,318,117,218,107,131,93,194,108,116,90,105,94,122,119,115,125,114,102,128,128,111,98,134,128,144,129,109,140,142,98,184,160,237,129,102,116,164,140,259,136,79,166,125,116,138,138,97,94,137,103,93,111,124,95,133,146,111,419,176,119,156,124,116,135,87,124,127,98,147,86,75,143,105,128,164,122,146,151,131, 136,297,488,855,1031,1218,1415,1543,1728,1892,2049,2197,2352,2563,2731,2861,3073,3264,3406,3619,3758,3968,4287,4405,4624,4750,5118,5249,5444,5636,5841,5946,6052,6158,6305,6445,6602,6760,6946,7156,7319,7490,7642,8504,8722,8901,9117,9252,9423,9595,9784,9924,10109,10324,10562,10711,10846,11256,11421,11601,11876,12036,12153,12391,12549,12715,12909,13081,13263,13410,13642,13955,14169,14583,14736,14923,15121,15323,15479,15949,16126,16267,16450,16621,16812,17033,17268,17434,17628,17778,17991,18102,18178,18322,18480,18683,18868,19007,19209,19405,19603, 32,86,241,42,61,51,11,46,28,1,35,46,77,37,21,90,54,45,91,19,26,1,1,1,19,237,38,1,84,89,15,1,12,25,21,42,33,72,108,35,43,41,764,84,51,72,6,62,32,47,42,1,55,1,20,33,294,1,40,16,24,38,72,33,50,56,34,85,53,95,210,121,303,29,92,65,56,45,51,1,22,27,47,75,86,148,42,67,52,66,25,1,1,53,75,21,17,56,45,67,31, . . . 2,5,6,29,136,139,147,148,151,154,167,297,305,310,314,320,328,332,333,337,341,344,348,360,363,366,373,376,382,488,495,502,512,514,521,529,546,556,608,616,621,667,671,674,676,677,680,684,688,695,700,703,708,720,724,728,855,857,861,863,871,873,887,891,893,896,972,1031,1034,1037,1041,1048,1050,1052,1055,1057,1063,1064,1070,1073,1074,1077,1091,1218,1220,1221,1227,1229,1236,1238,1246,1253,1256,1257,1262,1263,1268,1415,1418,1421,1425,1543,1549,1555,1557,1560,1570,1578,1580,1585,1588,1728,1736,1742,1744,1746,1748,1755,1892,2049,2051,2056,2058,2060,2083,2197,2199,2204,2209,2211,2214,2222,2232,2234,2237,2238,2242,2352,2353,2360,2372,2379,2388,2395,2398,2408,2411,2417,2425,2428,2563,2565,2566,2580,2585,2598,2599,2731,2741,2751,2809,2861,2890,2897,2917,2925,2930,2933,2950,3073,3080,3083,3091,3102,3111,3126,3264,3296,3304,3308,3406,3430,3445,3447,3449,3453,3454,3459,3468,3472,3483,3486,3494,3496,3619,3635,3637,3758,3760,3770,3778,3783,3968,4287,4347,4351,4405,4624,4642,4699,4750,4780,4783,4787,4793,4795,4798,4803,4811,4814,4817,4836,4838,4844,4897,4907,4928,4933,4936,4941,4943,4961,4963,4968,4974,4977,4983,4986,5037,5118,5137,5138,5144,5149,5155,5249,5444,5461,5464,5468,5475,5491,5493,5498,5504,5511,5514,5527,5636,5642,5654,5658,5660,5663,5668,5670,5675,5678,5680,5682,5686,5689,5691,5693,5707,5710,5711,5712,5724,5841,5844,5847,5850,5855,5946,6002,6052,6063,6158,6161,6170,6182,6305,6320,6325,6445,6446,6447,6453,6460,6462,6464,6467,6478,6483,6486,6602,6617,6621,6624,6634,6760,6769,6777,6780,6784,6787,6792,6794,6799,6801,6804,6805,6808,6815,6816,6819,6824,6831,6899,6927,6946,6954,6956,6976,6983,6987,6989,6995,6998,7001,7006,7012,7015,7017,7019,7023,7034,7037,7039,7053,7156,7167,7170,7174,7176,7180,7184,7190,7319,7331,7337,7344,7346,7354,7359,7361,7454,7490,7492,7499,7502,7525,7530,7603,7619,7642,7646,7650,7651,7653,7657,7676,7677,7679,7681,7683,7684,7688,7692,7710,7713,7717,7728,7732,7766,7769,7776,7779,7781,7794,7802,7804,7815,7834,7838,7841,7843,7850,7851,7852,7858,7861,7865,7868,7892,7893,7900,7905,7907,7909,7919,7921,7923,7927,7929,7932,7936,7939,7945,7947,7950,7951,7955,7956,7957,7961,7963,7964,7975,7987,7991,7993,7994,7997,8000,8003,8004,8007,8010,8023,8026,8031,8036,8042,8054,8060,8062,8068,8077,8078,8080,8082,8086,8088,8092,8097,8102,8108,8113,8115,8117,8120,8129,8138,8142,8144,8146,8149,8154,8156,8157,8178,8181,8183,8190,8191,8192,8194,8195,8197,8199,8200,8203,8204,8205,8210,8212,8214,8218,8221,8224,8225,8226,8230,8231,8233,8236,8242,8246,8250,8252,8254,8260,8262,8265,8268,8269,8271,8274,8276,8281,8283,8288,8291,8293,8295,8297,8299,8302,8303,8309,8314,8316,8319,8320,8322,8330,8349,8352,8364,8368,8372,8374,8379,8384,8388,8399,8405,8504,8506,8520,8523,8524,8526,8528,8535,8537,8539,8541,8544,8546,8556,8566,8569,8577,8585,8587,8722,8725,8728,8733,8738,8740,8743,8744,8749,8756,8759,8765,8767,8772,8901,8914,8916,8918,8928,8930,8932,8938,8942,8945,8947,8950,8953,8956,8964,8972,9117,9122,9252,9255,9257,9259,9262,9263,9266,9282,9290,9292,9293,9297,9299,9301,9304,9305,9308,9312,9313,9423,9434,9447,9453,9454,9527,9595,9598,9601,9604,9609,9614,9623,9625,9628,9634,9640,9641,9784,9786,9791,9793,9796,9806,9808,9809,9811,9825,9924,9983,10109,10118,10163,10324,10562,10566,10581,10621,10711,10717,10724,10743,10846,10849,10851,10865,10867,10877,10882,10883,10887,10889,10896,10897,10903,10908,10911,10927,10936,10938,10941,10944,10965,10968,10972,10996,10999,11006,11017,11021,11024,11025,11030,11032,11033,11038,11044,11049,11051,11053,11055,11063,11065,11067,11078,11079,11081,11083,11090,11096,11097,11098,11099,11101,11112,11115,11122,11124,11139,11256,11421,11425,11429,11432,11436,11441,11445,11446,11448,11460,11601,11616,11876,11880,11890,11899,12036,12039,12047,12048,12050,12052,12055,12056,12057,12060,12061,12063,12066,12069,12073,12153,12160,12200,12211,12213,12217,12224,12290,12353,12360,12391,12392,12397,12399,12409,12423,12549,12551,12553,12563,12566,12567,12575,12578,12598,12715,12721,12726,12736,12741,12745,12752,12760,12770,12882,12909,12912,12915,12942,13081,13082,13085,13088,13094,13097,13099,13103,13107,13109,13112,13115,13123,13135,13140,13165,13263,13265,13270,13272,13274,13277,13280,13287,13293,13296,13301,13302,13307,13315,13410,13418,13452,13462,13474,13478,13480,13484,13486,13491,13492,13504,13642,13644,13646,13650,13658,13668,13672,13675,13678,13694,13704,13774,13779,13781,13785,13802,13807,13821,13824,13826,13832,13833,13837,13840,13846,13851,13955,13975,13981,14010,14011,14013,14018,14023,14024,14026,14033,14035,14039,14041,14046,14051,14059,14064,14068,14071,14075,14169,14175,14180,14209,14213,14216,14217,14224,14227,14230,14232,14235,14236,14241,14245,14249,14252,14257,14262,14268,14273,14275,14276,14280,14283,14293,14295,14316,14349,14366,14368,14376,14379,14386,14393,14395,14398,14401,14404,14411,14412,14416,14418,14421,14424,14434,14436,14438,14443,14450,14451,14456,14462,14465,14471,14583,14593,14597,14609,14611,14736,14748,14760,14762,14778,14780,14783,14785,14787,14790,14794,14798,14803,14806,14811,14812,14815,14816,14824,14827,14923,14947,14960,14961,14963,14974,14979,14980,14983,14985,14987,15121,15135,15136,15140,15152,15155,15157,15176,15323,15326,15327,15340,15343,15351,15352,15355,15357,15367,15442,15479,15488,15509,15513,15516,15520,15526,15529,15949,16126,16147,16267,16286,16293,16450,16454,16458,16463,16468,16478,16483,16485,16488,16496,16621,16630,16631,16633,16635,16642,16646,16648,16651,16654,16658,16660,16666,16669,16670,16672,16680,16695,16727,16812,16816,16817,16824,16830,16832,16834,16838,16846,16867,16877,16880,16883,16888,16890,16897,16962,17033,17035,17039,17040,17051,17053,17055,17066,17097,17101,17115,17177,17178,17180,17268,17272,17275,17279,17283,17286,17291,17294,17297,17309,17434,17444,17447,17450,17455,17460,17463,17466,17470,17474,17477,17500,17628,17635,17654,17656,17659,17664,17673,17679,17778,17787,17789,17796,17816,17828,17834,17839,17843,17991,17996,18008,18011,18015,18102,18178,18322,18325,18328,18339,18347,18349,18350,18352,18355,18358,18363,18365,18369,18371,18374,18480,18483,18498,18508,18517,18519,18524,18527,18529,18539,18546,18548,18554,18683,18703,18868,18872,18884,19007,19023,19027,19038,19044,19047,19050,19051,19055,19062,19209,19211,19219,19224,19229,19231,19238,19245,19253,19405,19410,19415,19467,19471,19603,19626,19633,19796,19803,19807,19809,19810,19814,19823,19826,19828, +chr19 47507405 47523090 m54329U_210326_192251/77267415/ccs 100,298,424,650,922,1079,1220,1416,1551,1740,2063,2249,2441,2618,2792,2990,3136,3294,3465,3624,3808,3965,4144,4321,4461,4635,4782,4939,5060,5232,5479,5610,5796,5930,6114,6248,6408,6565,6778,6938,7061,7244,7454,8314,8491,8635,8776,8894,9038,9198,9365,9510,9679,9811,10043,10212,10362,10527,10791,11071,11359,11724,11947,12104,12263,12376,12534,12729,12969,13108,13280,13451,13602,13784,14014,14346,14501,14649,14829,15062,15202,15386, 106,121,136,221,127,130,141,134,148,302,132,140,112,145,119,115,147,158,124,138,120,121,150,130,150,146,134,120,140,122,80,137,129,154,113,126,107,110,83,112,117,111,80,83,114,104,117,143,129,114,129,123,130,144,105,120,105,118,164,119,244,113,88,76,112,148,110,137,92,140,133,134,99,92,90,116,99,96,115,112,124,101, 73,206,419,560,871,1049,1209,1361,1550,1699,2042,2195,2389,2553,2763,2911,3105,3283,3452,3589,3762,3928,4086,4294,4451,4611,4781,4916,5059,5200,5354,5559,5747,5925,6084,6227,6374,6515,6675,6861,7050,7178,7355,7534,8397,8605,8739,8893,9037,9167,9312,9494,9633,9809,9955,10148,10332,10467,10645,10955,11190,11603,11837,12035,12180,12375,12524,12644,12866,13061,13248,13413,13585,13701,13876,14104,14462,14600,14745,14944,15174,15326,15487, 27,92,5,90,51,30,11,55,1,41,21,54,52,65,29,79,31,11,13,35,46,37,58,27,10,24,1,23,1,32,125,51,49,5,30,21,34,50,103,77,11,66,99,780,94,30,37,1,1,31,53,16,46,2,88,64,30,60,146,116,169,121,110,69,83,1,10,85,103,47,32,38,17,83,138,242,39,49,84,118,28,60,37, . . . 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+chr19 47507794 47513324 m84039_230404_003541_s3/99686134/ccs 107,326,522,708,927,1114,1488,1663,1770,1904,2063,2283,2478,2856,3071,3254,3455,3630,3893,4104,4331,4528,4776,4946,5245, 182,127,185,216,138,349,174,106,83,141,196,176,377,214,168,188,149,174,162,174,169,167,148,277,185, 85,289,453,707,924,1065,1463,1662,1769,1853,2045,2259,2459,2855,3070,3239,3442,3604,3804,4055,4278,4500,4695,4924,5223, 22,37,69,1,3,49,25,1,1,51,18,24,19,1,1,15,13,26,89,49,53,28,81,22,22, . . . 0,1,5,85,88,93,106,289,294,325,453,467,492,509,521,707,924,926,1065,1109,1113,1463,1476,1478,1487,1662,1688,1696,1769,1853,1871,1874,1883,1884,1891,1894,1899,1903,2045,2048,2057,2062,2259,2264,2282,2459,2467,2477,2855,3070,3239,3253,3442,3454,3604,3624,3629,3804,3811,3824,3837,3850,3853,3855,3871,3872,3874,3886,3892,4055,4067,4070,4081,4095,4098,4103,4278,4282,4283,4286,4289,4290,4296,4307,4309,4312,4315,4325,4330,4451,4500,4506,4509,4527,4695,4702,4705,4709,4713,4716,4718,4722,4775,4924,4928,4945,5223,5225,5241,5244,5430,5433,5443,5445,5519,5520,5522, +chr19 47507921 47523781 m84039_230404_003541_s3/109972366/ccs 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+chr19 47508710 47528217 m54329U_210810_004956/105973473/ccs 77,264,457,784,979,1158,1360,1531,1828,2173,2341,2514,2715,2912,3125,3283,3465,3623,3831,3967,4127,4335,4495,4637,4856,5061,5269,5406,5568,5781,5984,6117,7024,7263,7484,7652,7797,7956,8138,8271,8480,8691,8917,9371,9772,9953,10088,10266,10450,10752,10940,11118,11284,11674,11808,12016,12231,12421,12625,12809,12986,13185,13350,13518,13730,13894,14209,14355,14581,14767,14885,15129,15328,15484,15711,15891,16113,16323,16524,16879,17099,17264,17442,17636,17806,18002,18196,18408,18583,18809,18983,19153, 146,140,318,136,148,130,148,296,305,152,140,142,137,146,132,127,127,134,129,140,131,130,141,159,128,118,109,144,160,134,132,128,125,158,126,117,137,152,116,144,138,119,391,104,126,134,176,151,272,144,142,143,314,115,171,148,172,146,138,122,138,145,138,158,108,262,145,148,185,98,169,136,134,173,157,136,128,162,354,186,164,177,193,169,191,193,145,147,147,145,160,170, 223,404,775,920,1127,1288,1508,1827,2133,2325,2481,2656,2852,3058,3257,3410,3592,3757,3960,4107,4258,4465,4636,4796,4984,5179,5378,5550,5728,5915,6116,6245,7149,7421,7610,7769,7934,8108,8254,8415,8618,8810,9308,9475,9898,10087,10264,10417,10722,10896,11082,11261,11598,11789,11979,12164,12403,12567,12763,12931,13124,13330,13488,13676,13838,14156,14354,14503,14766,14865,15054,15265,15462,15657,15868,16027,16241,16485,16878,17065,17263,17441,17635,17805,17997,18195,18341,18555,18730,18954,19143,19323, 41,53,9,59,31,72,23,1,40,16,33,59,60,67,26,55,31,74,7,20,77,30,1,60,77,90,28,18,53,69,1,779,114,63,42,28,22,30,17,65,73,107,63,297,55,1,2,33,30,44,36,23,76,19,37,67,18,58,46,55,61,20,30,54,56,53,1,78,1,20,75,63,22,54,23,86,82,39,1,34,1,1,1,1,5,1,67,28,79,29,10,1, . . . 28,33,36,39,43,45,48,52,56,59,61,63,68,69,76,137,223,227,231,236,238,242,243,245,247,251,254,262,263,404,406,415,418,420,426,428,431,436,438,446,449,456,775,778,783,920,921,930,935,936,940,955,958,978,1127,1132,1138,1143,1144,1149,1157,1183,1288,1299,1303,1311,1318,1320,1322,1328,1330,1337,1340,1346,1349,1351,1353,1359,1508,1530,1827,2133,2136,2148,2157,2158,2160,2169,2172,2325,2326,2331,2336,2340,2481,2488,2492,2506,2510,2513,2656,2669,2671,2681,2683,2685,2691,2695,2697,2700,2714,2852,2857,2861,2862,2865,2867,2874,2877,2880,2891,2894,2895,2898,2900,2911,3058,3061,3064,3067,3070,3073,3077,3083,3088,3092,3096,3098,3102,3106,3109,3124,3257,3267,3273,3282,3410,3412,3414,3417,3422,3425,3430,3432,3436,3443,3447,3455,3457,3464,3592,3615,3618,3622,3757,3758,3770,3775,3783,3785,3790,3793,3797,3800,3801,3804,3806,3808,3810,3821,3830,3960,3962,3964,3966,4107,4112,4113,4115,4126,4258,4264,4267,4271,4276,4280,4282,4285,4292,4297,4300,4302,4306,4308,4311,4313,4315,4319,4324,4326,4329,4332,4333,4334,4465,4494,4636,4796,4798,4804,4810,4812,4813,4817,4823,4824,4828,4831,4843,4846,4847,4850,4853,4855,4984,5008,5010,5012,5018,5020,5022,5024,5028,5030,5033,5041,5057,5060,5179,5197,5200,5210,5216,5228,5238,5262,5268,5378,5383,5386,5400,5405,5515,5550,5558,5562,5567,5728,5730,5733,5736,5740,5743,5745,5753,5757,5761,5775,5780,5915,5922,5928,5930,5933,5937,5943,5944,5955,5959,5961,5968,5970,5974,5978,5983,6116,6245,6258,6260,6264,6266,6270,6274,6275,6277,6279,6281,6300,6301,6303,6305,6307,6308,6312,6316,6318,6327,6331,6334,6337,6341,6352,6356,6357,6393,6400,6405,6426,6428,6439,6448,6458,6460,6462,6465,6467,6475,6476,6477,6483,6485,6486,6488,6493,6517,6518,6525,6528,6530,6532,6534,6539,6544,6546,6548,6549,6552,6554,6557,6561,6564,6566,6573,6576,6577,6581,6582,6583,6587,6589,6590,6613,6617,6619,6623,6626,6629,6630,6633,6636,6639,6643,6644,6646,6649,6652,6657,6662,6668,6681,6687,6689,6695,6704,6705,6707,6709,6713,6715,6717,6719,6722,6724,6731,6737,6765,6769,6771,6773,6774,6776,6781,6783,6784,6787,6788,6790,6805,6808,6810,6817,6819,6821,6824,6826,6830,6831,6832,6837,6838,6839,6841,6845,6848,6851,6852,6853,6857,6860,6863,6890,6895,6908,6910,6915,6917,6918,6920,6922,6924,6930,6931,6933,6937,6944,6947,6950,6952,6956,6958,6961,6963,6965,6977,6979,6980,6992,6996,7000,7001,7007,7012,7016,7019,7023,7149,7152,7153,7155,7157,7160,7166,7168,7170,7173,7175,7176,7177,7181,7195,7198,7206,7214,7216,7217,7220,7224,7226,7229,7231,7234,7238,7244,7246,7250,7252,7254,7256,7260,7262,7295,7388,7421,7424,7425,7429,7431,7433,7435,7437,7439,7453,7454,7455,7460,7474,7477,7479,7483,7610,7617,7621,7629,7635,7651,7696,7769,7776,7779,7784,7790,7792,7794,7796,7934,7938,7952,7955,8108,8111,8113,8119,8124,8131,8134,8137,8254,8257,8263,8270,8415,8420,8422,8425,8429,8435,8438,8440,8444,8446,8448,8450,8452,8454,8467,8469,8471,8476,8479,8618,8628,8632,8635,8641,8643,8647,8649,8656,8659,8660,8662,8665,8667,8670,8683,8690,8810,8819,8822,8824,8829,8831,8835,8839,8841,8843,8847,8849,8853,8857,8859,8861,8865,8867,8869,8871,8874,8875,8877,8916,9308,9328,9331,9333,9336,9337,9341,9345,9347,9350,9354,9357,9358,9361,9370,9475,9481,9485,9492,9495,9499,9503,9505,9507,9514,9517,9519,9526,9527,9531,9533,9538,9541,9542,9546,9548,9549,9551,9552,9556,9557,9563,9564,9566,9568,9570,9571,9573,9574,9575,9577,9578,9580,9581,9582,9583,9585,9587,9588,9592,9595,9598,9601,9602,9604,9607,9610,9615,9617,9619,9629,9631,9633,9636,9639,9645,9647,9651,9654,9663,9674,9681,9683,9685,9689,9692,9693,9695,9697,9698,9699,9701,9704,9705,9708,9709,9711,9713,9714,9715,9717,9720,9722,9726,9727,9729,9731,9737,9742,9744,9745,9748,9752,9762,9769,9771,9898,9952,10059,10087,10264,10265,10417,10422,10424,10426,10431,10433,10449,10722,10731,10737,10744,10751,10896,10905,10909,10914,10920,10923,10925,10928,10932,10935,10936,10939,11082,11085,11089,11096,11100,11111,11113,11117,11261,11265,11270,11273,11275,11283,11598,11604,11610,11612,11615,11616,11627,11630,11631,11633,11637,11639,11641,11644,11646,11663,11668,11673,11789,11792,11794,11802,11804,11807,11979,11996,12015,12164,12166,12168,12172,12173,12178,12183,12186,12188,12190,12195,12196,12198,12205,12213,12215,12230,12403,12405,12410,12412,12416,12420,12567,12576,12583,12586,12592,12594,12597,12598,12603,12606,12612,12624,12763,12775,12777,12781,12783,12786,12787,12800,12806,12808,12931,12956,12966,12975,12978,12980,12985,13124,13126,13163,13169,13184,13330,13334,13336,13338,13340,13343,13349,13488,13491,13514,13517,13676,13679,13680,13682,13684,13688,13690,13692,13698,13699,13704,13712,13714,13717,13723,13729,13838,13859,13865,13873,13878,13886,13893,14156,14159,14184,14187,14191,14196,14208,14354,14503,14505,14515,14527,14531,14534,14536,14542,14547,14580,14766,14865,14881,14884,15054,15060,15068,15071,15073,15076,15079,15082,15084,15086,15090,15095,15097,15100,15107,15110,15115,15117,15120,15124,15128,15161,15265,15267,15272,15280,15283,15286,15292,15298,15301,15302,15304,15306,15312,15327,15462,15464,15466,15478,15483,15657,15665,15680,15681,15685,15687,15688,15692,15705,15707,15710,15868,15872,15880,15887,15890,16027,16029,16032,16033,16045,16047,16049,16057,16061,16064,16067,16073,16077,16080,16081,16083,16085,16088,16107,16112,16241,16267,16269,16271,16287,16289,16292,16293,16297,16301,16306,16310,16312,16322,16485,16489,16493,16507,16510,16519,16523,16878,17065,17066,17072,17077,17098,17263,17375,17441,17635,17805,17997,18001,18195,18341,18352,18359,18362,18369,18371,18373,18376,18377,18382,18384,18386,18389,18391,18394,18407,18555,18561,18573,18582,18730,18737,18751,18754,18759,18762,18770,18776,18779,18781,18784,18787,18795,18808,18954,18958,18968,18970,18974,18976,18982,19143,19146,19152,19323,19468,19492,19495,19498, +chr19 47509060 47513962 m84039_230401_031619_s3/221582713/ccs 176,329,461,661,798,956,1089,1486,1628,1818,2001,2169,2340,2519,2747,3295,3412,3714,3893,4095,4280,4408, 133,131,129,109,118,119,123,76,110,83,109,115,118,100,116,83,212,108,111,100,109,106, 137,309,460,590,770,916,1075,1212,1562,1738,1901,2110,2284,2458,2619,2863,3378,3624,3822,4004,4195,4389,4514, 39,20,1,71,28,40,14,274,66,80,100,59,56,61,128,432,34,90,71,91,85,19,244, . . . 0,2,3,5,137,146,155,158,159,161,175,309,315,317,320,326,328,460,590,593,602,622,624,634,638,645,657,659,660,770,774,786,792,797,916,925,935,947,953,955,1075,1080,1088,1127,1212,1216,1267,1306,1308,1324,1336,1339,1346,1347,1349,1353,1357,1368,1375,1433,1461,1465,1466,1468,1485,1562,1578,1579,1580,1582,1585,1589,1590,1592,1595,1604,1608,1609,1611,1613,1621,1627,1677,1738,1740,1749,1752,1757,1758,1760,1762,1766,1768,1770,1771,1772,1775,1776,1779,1781,1784,1786,1787,1789,1793,1796,1805,1808,1811,1817,1901,1912,1914,1922,1923,1925,1928,1933,1937,1938,1974,1979,1980,1984,1991,1998,2000,2110,2114,2115,2117,2132,2143,2144,2154,2168,2284,2289,2300,2305,2308,2312,2317,2319,2324,2329,2333,2336,2339,2458,2460,2471,2474,2475,2476,2481,2484,2487,2488,2491,2495,2497,2500,2518,2619,2621,2627,2639,2644,2645,2647,2649,2671,2682,2683,2684,2686,2718,2719,2725,2740,2742,2746,2798,2841,2863,2872,2878,2882,2888,2891,2909,2912,2945,2947,2976,2979,2992,2996,2998,3000,3001,3005,3007,3008,3011,3017,3018,3021,3024,3028,3031,3034,3035,3039,3054,3075,3103,3105,3148,3150,3152,3157,3161,3163,3164,3167,3172,3174,3178,3179,3181,3182,3184,3186,3188,3189,3192,3195,3196,3200,3203,3207,3208,3210,3213,3217,3228,3230,3235,3238,3239,3241,3244,3249,3250,3253,3254,3262,3265,3269,3272,3290,3293,3294,3378,3380,3382,3385,3387,3388,3391,3394,3398,3399,3404,3405,3407,3411,3624,3657,3659,3662,3663,3665,3673,3674,3676,3677,3678,3680,3683,3685,3688,3692,3694,3695,3700,3701,3703,3704,3706,3707,3710,3712,3713,3733,3791,3822,3824,3828,3832,3835,3836,3839,3841,3843,3845,3847,3848,3852,3853,3858,3864,3867,3871,3872,3873,3879,3880,3882,3885,3889,3890,3892,4004,4006,4007,4010,4015,4016,4018,4022,4023,4024,4029,4032,4036,4037,4039,4042,4044,4046,4047,4051,4054,4057,4061,4063,4066,4075,4081,4083,4087,4088,4090,4093,4094,4195,4197,4199,4203,4205,4208,4210,4215,4219,4221,4224,4226,4231,4238,4241,4244,4247,4248,4254,4255,4257,4260,4262,4264,4271,4279,4340,4389,4405,4407,4514,4518,4519,4522,4524,4530,4531,4535,4538,4540,4541,4543,4545,4547,4551,4552,4554,4556,4558,4562,4567,4568,4569,4570,4574,4575,4579,4581,4582,4584,4586,4589,4590,4592,4594,4596,4598,4601,4614,4617,4620,4622,4667,4675,4677,4699,4700,4704,4707,4714,4722,4726,4729,4731,4733,4736,4740,4742,4743,4747,4752,4755,4757,4881,4884,4886,4889,4890,4892,4895, +chr19 47509233 47523608 m54329U_210326_192251/88801936/ccs 146,311,615,818,989,1192,1394,1569,1760,1918,2116,2292,2432,2629,2841,3020,3183,3356,3541,3760,3954,4095,4316,4450,4632,4758,4915,5106,5318,5398,5615,6433,6597,6764,6946,7069,7215,7367,7532,7709,7871,8027,8417,8738,9061,9235,9458,9608,9936,10114,10309,10454,10691,10860,11028,11208,11434,11595,11775,11995,12177,12360,12552,12757,12952,13138,13367,13516,13671,13811, 100,286,140,146,140,134,138,164,138,129,136,116,157,146,115,136,129,143,129,128,98,157,111,163,115,133,134,106,79,216,103,158,155,127,122,134,127,141,157,123,121,389,293,275,147,222,77,309,146,125,139,185,120,152,148,138,139,129,153,145,127,138,152,145,151,144,90,147,139,138, 246,597,755,964,1129,1326,1532,1733,1898,2047,2252,2408,2589,2775,2956,3156,3312,3499,3670,3888,4052,4252,4427,4613,4747,4891,5049,5212,5397,5614,5718,6591,6752,6891,7068,7203,7342,7508,7689,7832,7992,8416,8710,9013,9208,9457,9535,9917,10082,10239,10448,10639,10811,11012,11176,11346,11573,11724,11928,12140,12304,12498,12704,12902,13103,13282,13457,13663,13810,13949, 65,18,63,25,63,68,37,27,20,69,40,24,40,66,64,27,44,42,90,66,43,64,23,19,11,24,57,106,1,1,715,6,12,55,1,12,25,24,20,39,35,1,28,48,27,1,73,19,32,70,6,52,49,16,32,88,22,51,67,37,56,54,53,50,35,85,59,8,1,34, . . . 145,246,271,276,282,285,287,289,292,297,299,302,310,597,609,614,755,759,770,774,782,789,792,793,797,799,801,806,817,964,971,974,988,1129,1131,1135,1139,1142,1144,1147,1150,1152,1159,1162,1164,1170,1176,1191,1326,1330,1332,1333,1335,1338,1350,1353,1354,1358,1383,1385,1393,1532,1540,1541,1546,1547,1549,1559,1561,1563,1565,1568,1733,1759,1898,1904,1907,1908,1911,1917,2047,2050,2053,2060,2064,2069,2071,2075,2077,2080,2084,2087,2091,2115,2252,2255,2257,2264,2268,2275,2291,2408,2422,2431,2589,2608,2614,2616,2620,2623,2628,2775,2795,2798,2809,2811,2815,2817,2819,2824,2840,2956,2958,2960,2962,2963,2967,2969,2976,2980,2983,3001,3003,3011,3014,3015,3019,3156,3159,3182,3312,3316,3318,3322,3326,3329,3330,3332,3336,3349,3352,3355,3499,3516,3517,3519,3520,3522,3525,3528,3529,3537,3540,3670,3676,3679,3691,3697,3701,3704,3707,3709,3712,3717,3719,3723,3726,3735,3739,3741,3744,3751,3756,3759,3888,3896,3900,3901,3903,3906,3907,3909,3911,3916,3918,3922,3924,3925,3928,3931,3933,3947,3949,3953,4052,4065,4073,4075,4082,4086,4092,4094,4252,4256,4258,4262,4264,4270,4272,4273,4277,4299,4310,4315,4427,4430,4437,4440,4443,4444,4449,4613,4615,4623,4627,4629,4631,4747,4757,4891,4902,4907,4909,4914,5049,5058,5065,5069,5070,5071,5072,5075,5077,5080,5083,5101,5105,5212,5216,5220,5227,5234,5239,5242,5243,5247,5248,5250,5256,5257,5259,5263,5267,5270,5273,5274,5276,5288,5293,5295,5297,5304,5314,5317,5397,5614,5718,5720,5727,5731,5735,5736,5738,5740,5742,5748,5761,5762,5764,5766,5768,5769,5773,5779,5788,5792,5795,5798,5802,5813,5817,5818,5825,5828,5829,5832,5835,5837,5839,5845,5850,5851,5854,5861,5864,5865,5866,5880,5888,5890,5898,5901,5920,5922,5924,5927,5929,5937,5938,5945,5948,5950,5954,5961,5962,5967,5969,5978,5979,5986,5989,5991,5993,5995,6002,6007,6009,6011,6012,6015,6017,6020,6027,6029,6033,6035,6038,6039,6043,6044,6045,6049,6051,6052,6076,6080,6082,6083,6086,6089,6092,6093,6096,6099,6102,6105,6106,6107,6109,6112,6115,6120,6125,6131,6143,6149,6151,6157,6167,6168,6170,6172,6176,6178,6180,6182,6185,6187,6192,6194,6196,6198,6200,6203,6205,6210,6231,6233,6235,6236,6238,6243,6245,6246,6267,6270,6272,6283,6285,6287,6288,6290,6296,6298,6303,6305,6307,6311,6313,6314,6317,6318,6319,6323,6324,6326,6329,6361,6362,6375,6377,6384,6385,6387,6389,6391,6393,6398,6406,6414,6417,6432,6557,6591,6593,6596,6752,6753,6755,6757,6761,6763,6891,6897,6919,6926,6928,6929,6932,6934,6937,6940,6943,6945,7068,7167,7203,7210,7214,7342,7344,7347,7351,7352,7354,7355,7360,7361,7364,7366,7508,7516,7518,7520,7526,7527,7531,7689,7692,7695,7698,7708,7832,7835,7845,7848,7851,7854,7857,7858,7861,7863,7865,7870,7992,7998,8006,8014,8018,8022,8023,8026,8416,8710,8713,8737,9013,9018,9019,9025,9026,9028,9030,9032,9033,9037,9042,9044,9047,9049,9054,9057,9060,9208,9211,9214,9215,9217,9219,9234,9457,9535,9549,9552,9556,9558,9583,9585,9598,9607,9917,9923,9925,9929,9935,10082,10104,10107,10113,10239,10246,10253,10257,10261,10264,10268,10270,10274,10277,10279,10283,10285,10289,10291,10292,10299,10300,10305,10308,10448,10453,10639,10645,10649,10652,10661,10663,10664,10681,10690,10811,10831,10835,10838,10843,10853,10854,10856,10859,11012,11018,11027,11176,11179,11183,11191,11193,11199,11205,11207,11346,11348,11355,11360,11363,11370,11373,11376,11379,11384,11385,11399,11402,11403,11406,11407,11412,11416,11417,11419,11421,11423,11425,11427,11430,11433,11573,11574,11586,11594,11724,11738,11741,11743,11745,11748,11755,11758,11761,11774,11928,11930,11933,11940,11941,11942,11946,11952,11956,11961,11963,11965,11968,11970,11973,11983,11985,11990,11994,12140,12145,12149,12156,12160,12161,12165,12176,12304,12312,12315,12319,12321,12336,12340,12353,12359,12498,12501,12504,12518,12523,12527,12533,12542,12545,12551,12704,12708,12712,12720,12731,12737,12749,12756,12902,12905,12921,12925,12931,12932,12936,12951,13103,13105,13109,13116,13137,13282,13285,13299,13303,13306,13309,13312,13317,13326,13332,13334,13337,13341,13347,13349,13354,13356,13361,13362,13364,13366,13457,13466,13473,13477,13503,13507,13509,13515,13634,13663,13666,13668,13670,13810,13847,13879,13885,13949,13951,13961,13967,13968,13977,13980,13982,14301,14305,14307,14309,14310,14313,14323,14325,14328,14331,14334, +chr19 47509612 47524347 m84039_230401_034725_s4/123339260/ccs 74,581,769,1706,2204,2754,3393,3528,3724,4169,4523,4852,5213,5517,5650,6473,7304,7648,8226,9139,9558,10021,10888,11185,11596,12077,12246,12603,12822,13218,13384,13562,13744,14181,14305, 506,187,936,497,490,638,134,155,444,339,328,312,285,132,822,776,343,577,912,418,454,866,200,410,480,168,356,218,395,165,108,181,436,123,231, 580,768,1705,2203,2694,3392,3527,3683,4168,4508,4851,5164,5498,5649,6472,7249,7647,8225,9138,9557,10012,10887,11088,11595,12076,12245,12602,12821,13217,13383,13492,13743,14180,14304,14536, 1,1,1,1,60,1,1,41,1,15,1,49,19,1,1,55,1,1,1,1,9,1,97,1,1,1,1,1,1,1,70,1,1,1,1, . . . 0,1,5,6,73,580,768,1705,2203,2694,2722,2725,2753,3392,3527,3683,3723,4168,4508,4522,4851,5164,5212,5498,5516,5606,5649,6472,7249,7302,7303,7647,8225,9138,9557,10012,10020,10887,11088,11129,11184,11595,12076,12173,12245,12602,12821,13217,13383,13492,13498,13561,13675,13743,14180,14224,14304,14536,14723,14725,14727, +chr19 47509937 47521574 m54329U_210323_190418/72353082/ccs 121,302,506,698,895,1120,1292,1382,1538,1736,1907,2107,2281,2463,2753,3219,3399,3588,3764,3900,4179,4580,4743,4912,5799,6021,6325,6507,6689,6862,7042,7329,7515,7683,8084,8292,8500,8699,9194,9395,9586,9906,10088,10275,10452,10588,10784,10961,11166,11365, 158,149,185,174,200,151,89,86,155,152,186,122,161,285,465,179,188,130,135,278,269,134,127,129,136,260,133,179,165,140,282,182,167,362,201,151,198,481,192,109,297,161,174,147,135,195,174,147,141,140, 82,279,451,691,872,1095,1271,1381,1468,1693,1888,2093,2229,2442,2748,3218,3398,3587,3718,3899,4178,4448,4714,4870,5041,5935,6281,6458,6686,6854,7002,7324,7511,7682,8045,8285,8443,8698,9180,9386,9504,9883,10067,10262,10422,10587,10783,10958,11108,11307,11505, 39,23,55,7,23,25,21,1,70,43,19,14,52,21,5,1,1,1,46,1,1,132,29,42,758,86,44,49,3,8,40,5,4,1,39,7,57,1,14,9,82,23,21,13,30,1,1,3,58,58,46, . . . 81,85,89,96,112,120,279,280,285,292,294,301,451,454,463,469,475,476,479,482,499,505,691,693,697,769,872,889,890,892,894,1095,1097,1099,1101,1105,1119,1230,1271,1285,1289,1291,1381,1468,1471,1477,1480,1483,1486,1491,1496,1500,1506,1507,1511,1515,1517,1518,1531,1536,1537,1693,1697,1700,1703,1707,1709,1713,1720,1735,1775,1888,1892,1895,1906,2093,2106,2229,2234,2242,2244,2250,2253,2254,2275,2280,2323,2442,2449,2454,2456,2460,2462,2748,2750,2752,3218,3338,3398,3587,3718,3733,3736,3740,3742,3745,3763,3899,4178,4448,4453,4456,4458,4464,4472,4475,4486,4488,4495,4496,4497,4499,4501,4509,4511,4518,4519,4521,4526,4528,4531,4539,4541,4544,4552,4556,4567,4574,4579,4607,4714,4717,4721,4725,4727,4729,4732,4742,4870,4876,4911,5010,5041,5047,5060,5062,5066,5068,5072,5077,5079,5083,5089,5102,5103,5105,5107,5109,5110,5115,5118,5119,5130,5134,5135,5137,5138,5141,5145,5156,5160,5161,5188,5197,5205,5231,5233,5242,5245,5254,5264,5266,5271,5273,5280,5281,5282,5288,5298,5322,5323,5330,5335,5338,5340,5345,5350,5352,5355,5360,5366,5371,5375,5377,5380,5381,5385,5386,5387,5392,5395,5407,5423,5425,5429,5432,5436,5439,5442,5449,5450,5452,5455,5458,5463,5468,5474,5486,5501,5511,5512,5514,5516,5522,5524,5526,5529,5554,5563,5574,5576,5578,5588,5590,5591,5593,5614,5616,5623,5625,5627,5628,5632,5636,5638,5643,5644,5645,5647,5654,5659,5663,5666,5714,5723,5724,5726,5728,5730,5745,5747,5750,5762,5764,5767,5771,5783,5788,5798,5935,5939,5941,5958,5970,6020,6281,6296,6324,6458,6481,6506,6686,6688,6814,6854,6861,7002,7008,7010,7013,7025,7030,7031,7035,7041,7324,7328,7511,7514,7682,8045,8049,8051,8064,8067,8072,8080,8083,8285,8291,8443,8445,8461,8468,8469,8471,8474,8476,8477,8482,8493,8499,8698,9180,9182,9185,9193,9386,9394,9504,9527,9561,9566,9585,9883,9886,9888,9892,9893,9895,9898,9901,9905,10067,10075,10082,10087,10262,10266,10274,10422,10427,10428,10433,10451,10587,10783,10958,10960,11108,11110,11115,11122,11125,11133,11139,11141,11151,11165,11307,11335,11340,11352,11357,11364,11505,11517,11524,11525,11529,11540,11550, +chr19 47510024 47533653 m54329U_210326_192251/104792639/ccs 158,402,565,754,942,1140,1346,1511,1716,1875,2018,2165,2381,2544,2750,2924,3108,3258,3444,3627,3798,3962,4168,4320,4459,4646,4818,5654,5736,5919,6166,6388,6651,6906,7084,7245,7409,7567,7707,7902,8467,8576,8782,8923,9091,9271,9389,9585,9852,10007,10188,10340,10544,10712,10901,11057,11293,11445,11693,11876,12035,12252,12429,12734,12897,13378,13578,13760,13951,14163,14383,14582,14791,14962,15192,15346,15515,15686,15903,16038,16259,16445,16629,16817,16972,17196,17389,17552,17719,17879,18098,18296,18430,18634,18873,19090,19269,19414,19605,19760,19954,20201,20361,20559,20739,20902,21127,21333,21552,21754,21938,22157,22354,22536,22720,22920,23117,23281,23449, 131,100,138,109,131,128,112,100,96,81,127,105,111,146,135,146,112,128,136,141,131,123,121,121,140,111,100,81,173,134,113,181,134,123,122,116,86,128,132,269,108,166,140,138,130,114,144,223,125,174,121,145,129,158,139,115,115,132,118,117,151,130,257,145,475,122,136,148,161,167,128,141,123,156,104,162,148,139,134,182,139,150,175,150,169,150,157,162,127,135,139,97,122,140,133,118,124,131,126,116,115,156,157,134,156,162,145,147,146,119,141,130,134,138,136,129,150,159,140, 80,289,502,703,863,1073,1268,1458,1611,1812,1956,2145,2270,2492,2690,2885,3070,3220,3386,3580,3768,3929,4085,4289,4441,4599,4757,4918,5735,5909,6053,6279,6569,6785,7029,7206,7361,7495,7695,7839,8171,8575,8742,8922,9061,9221,9385,9533,9808,9977,10181,10309,10485,10673,10870,11040,11172,11408,11577,11811,11993,12186,12382,12686,12879,13372,13500,13714,13908,14112,14330,14511,14723,14914,15118,15296,15508,15663,15825,16037,16220,16398,16595,16804,16967,17141,17346,17546,17714,17846,18014,18237,18393,18552,18774,19006,19208,19393,19545,19731,19876,20069,20357,20518,20693,20895,21064,21272,21480,21698,21873,22079,22287,22488,22674,22856,23049,23267,23440, 78,113,63,51,79,67,78,53,105,63,62,20,111,52,60,39,38,38,58,47,30,33,83,31,18,47,61,736,1,10,113,109,82,121,55,39,48,72,12,63,296,1,40,1,30,50,4,52,44,30,7,31,59,39,31,17,121,37,116,65,42,66,47,48,18,6,78,46,43,51,53,71,68,48,74,50,7,23,78,1,39,47,34,13,5,55,43,6,5,33,84,59,37,82,99,84,61,21,60,29,78,132,4,41,46,7,63,61,72,56,65,78,67,48,46,64,68,14,9, . . . 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+chr19 47510045 47522679 m84039_230404_003541_s3/205851410/ccs 80,263,443,655,827,1034,1452,1660,1810,1992,2168,2382,2871,3034,3163,3448,3600,3773,3962,4171,4548,4673,4789,5588,5791,5982,6178,6365,6687,6860,7331,7538,7865,8031,8383,8518,8656,8785,9153,9360,9578,9736,9929,10328,10532,10746,10969,11156,11358,11603,11769,12008,12240, 119,157,140,91,159,161,140,149,181,118,133,171,99,107,165,125,132,110,133,229,84,105,118,124,159,149,123,288,136,407,153,266,136,142,134,137,128,327,113,111,112,132,291,128,159,152,109,130,144,111,144,83,111, 199,420,583,746,986,1195,1592,1809,1991,2110,2301,2553,2970,3141,3328,3573,3732,3883,4095,4400,4632,4778,4907,5712,5950,6131,6301,6653,6823,7267,7484,7804,8001,8173,8517,8655,8784,9112,9266,9471,9690,9868,10220,10456,10691,10898,11078,11286,11502,11714,11913,12091,12351, 64,23,72,81,48,257,68,1,1,58,81,318,64,22,120,27,41,79,76,148,41,11,681,79,32,47,64,34,37,64,54,61,30,210,1,1,1,41,94,107,46,61,108,76,55,71,78,72,101,55,95,149,83, . . . 4,6,13,26,28,36,38,39,53,67,79,199,204,262,420,424,428,429,432,435,439,442,583,591,603,610,611,613,625,629,630,632,634,654,746,763,800,802,805,817,826,986,994,995,1000,1001,1005,1009,1012,1021,1023,1033,1195,1202,1207,1209,1210,1214,1216,1219,1222,1225,1229,1231,1233,1236,1249,1255,1279,1282,1297,1305,1310,1380,1385,1388,1403,1406,1411,1413,1416,1419,1451,1592,1594,1607,1610,1614,1626,1629,1639,1641,1647,1659,1778,1809,1991,2110,2122,2143,2160,2165,2167,2212,2301,2313,2317,2320,2321,2324,2326,2328,2331,2339,2341,2356,2359,2370,2378,2381,2553,2556,2580,2586,2587,2589,2594,2597,2616,2624,2626,2628,2630,2633,2637,2641,2661,2664,2666,2671,2676,2680,2697,2702,2705,2709,2711,2712,2717,2718,2720,2721,2723,2724,2726,2727,2737,2741,2744,2754,2763,2764,2771,2777,2779,2784,2790,2792,2796,2797,2800,2802,2804,2810,2812,2817,2819,2822,2823,2826,2828,2835,2839,2841,2845,2849,2860,2862,2869,2870,2970,2973,2975,2977,2990,2993,2996,2997,2998,3002,3007,3010,3012,3033,3083,3129,3141,3148,3152,3154,3155,3158,3161,3162,3328,3332,3338,3340,3342,3347,3349,3352,3357,3361,3363,3365,3370,3372,3384,3391,3392,3395,3404,3406,3407,3409,3418,3422,3424,3447,3573,3575,3579,3592,3596,3599,3732,3733,3739,3743,3746,3748,3750,3753,3757,3769,3772,3883,3892,3926,3929,3936,3944,3952,3955,3961,4095,4102,4106,4113,4116,4118,4127,4134,4142,4149,4152,4170,4400,4415,4444,4452,4453,4455,4458,4461,4462,4464,4468,4472,4475,4478,4481,4493,4498,4500,4502,4503,4509,4513,4518,4519,4522,4527,4530,4536,4538,4543,4547,4632,4649,4663,4666,4671,4672,4778,4780,4788,4907,4909,4924,4928,4934,4939,4945,4964,4965,4967,4969,4971,4972,4980,4982,4991,4995,4998,5001,5005,5016,5020,5021,5028,5031,5035,5038,5042,5048,5054,5057,5064,5067,5069,5082,5090,5092,5100,5103,5112,5122,5124,5126,5129,5131,5138,5146,5149,5151,5153,5163,5164,5169,5171,5180,5188,5193,5195,5197,5207,5209,5211,5212,5215,5220,5227,5229,5233,5235,5238,5239,5243,5244,5245,5249,5251,5252,5275,5279,5281,5285,5288,5291,5292,5295,5298,5306,5308,5311,5314,5324,5330,5342,5348,5350,5356,5365,5366,5368,5370,5374,5376,5378,5380,5383,5385,5390,5392,5394,5398,5401,5403,5405,5408,5430,5432,5434,5435,5437,5442,5445,5449,5451,5466,5469,5471,5482,5485,5487,5493,5498,5500,5502,5509,5512,5513,5514,5518,5521,5569,5571,5576,5579,5581,5583,5585,5587,5712,5717,5718,5728,5731,5741,5744,5749,5751,5758,5761,5779,5787,5790,5950,5952,5956,5974,5981,6131,6134,6137,6175,6177,6301,6308,6311,6358,6364,6653,6656,6659,6660,6668,6674,6676,6680,6682,6686,6823,6824,6826,6830,6834,6838,6841,6852,6859,7267,7327,7330,7484,7501,7507,7509,7517,7519,7521,7523,7525,7527,7529,7531,7534,7535,7537,7804,7831,7836,7849,7852,7864,8001,8007,8010,8014,8017,8030,8136,8173,8177,8179,8180,8186,8193,8198,8206,8208,8209,8211,8212,8217,8223,8224,8226,8228,8230,8231,8234,8235,8237,8238,8242,8247,8248,8252,8255,8258,8261,8262,8264,8267,8270,8277,8279,8299,8305,8307,8320,8322,8334,8338,8380,8382,8517,8546,8655,8784,9112,9117,9123,9125,9129,9152,9266,9279,9283,9286,9293,9294,9297,9300,9302,9305,9308,9310,9314,9326,9329,9337,9338,9347,9353,9359,9471,9475,9478,9486,9493,9509,9513,9517,9533,9541,9544,9546,9550,9556,9559,9560,9562,9568,9572,9575,9577,9690,9693,9718,9726,9730,9731,9733,9735,9767,9868,9870,9877,9891,9894,9913,9924,9928,10220,10253,10260,10274,10276,10279,10280,10297,10300,10301,10303,10305,10308,10316,10325,10327,10388,10456,10466,10468,10471,10474,10482,10484,10492,10500,10502,10514,10520,10525,10530,10531,10691,10695,10703,10707,10711,10725,10731,10733,10745,10898,10902,10906,10909,10915,10930,10935,10937,10939,10954,10956,10958,10965,10968,11078,11093,11095,11100,11106,11107,11108,11117,11119,11125,11130,11133,11139,11142,11144,11147,11154,11155,11286,11309,11316,11317,11322,11332,11334,11339,11344,11346,11349,11352,11357,11429,11502,11509,11517,11520,11523,11525,11528,11529,11532,11534,11538,11542,11547,11549,11550,11553,11559,11566,11572,11573,11576,11580,11584,11586,11588,11593,11602,11714,11731,11736,11743,11744,11762,11768,11913,11927,11931,11935,11941,11964,11971,12006,12007,12091,12101,12117,12120,12131,12133,12136,12140,12142,12146,12147,12151,12154,12157,12162,12166,12169,12171,12173,12175,12177,12180,12184,12185,12186,12189,12192,12194,12198,12202,12203,12204,12208,12209,12212,12216,12221,12228,12239,12351,12355,12358,12361,12362,12367,12375,12380,12382,12384,12386,12389,12392,12393,12398,12405,12410,12417,12428,12433,12627,12630, +chr19 47510306 47526564 m54329U_210323_190418/99550444/ccs 69,254,388,578,751,921,1124,1288,1511,1702,2051,2238,2424,2643,2808,3015,3191,3355,3518,3840,4033,4170,4300,4416,4535,5384,5669,5846,6004,6152,6353,6545,6691,6879,7205,7424,7584,7716,8178,8336,8499,8668,8836,8999,9161,9349,9506,9666,9836,10032,10226,10451,10643,10805,11046,11220,11455,11626,11762,11925,12143,12331,12515,12742,12865,13038,13151,13409,13588,13793,13964,14174,14372,14614,14781,14914,15141,15352,15541,15708,15924, 124,133,151,93,137,142,116,131,104,97,108,119,106,102,127,116,131,105,303,118,92,104,78,84,84,246,104,102,141,145,152,132,160,295,118,125,118,124,84,123,121,165,121,128,94,113,108,94,132,118,140,96,103,114,79,95,80,135,123,143,122,102,117,76,130,109,141,86,78,117,102,109,105,114,124,147,127,130,154,193,122, 193,387,539,671,888,1063,1240,1419,1615,1799,2159,2357,2530,2745,2935,3131,3322,3460,3821,3958,4125,4274,4378,4500,4619,5630,5773,5948,6145,6297,6505,6677,6851,7174,7323,7549,7702,7840,8262,8459,8620,8833,8957,9127,9255,9462,9614,9760,9968,10150,10366,10547,10746,10919,11125,11315,11535,11761,11885,12068,12265,12433,12632,12818,12995,13147,13292,13495,13666,13910,14066,14283,14477,14728,14905,15061,15268,15482,15695,15901,16046, 61,1,39,80,33,61,48,92,87,252,79,67,113,63,80,60,33,58,19,75,45,26,38,35,765,39,73,56,7,56,40,14,28,31,101,35,14,338,74,40,48,3,42,34,94,44,52,76,64,76,85,96,59,127,95,140,91,1,40,75,66,82,110,47,43,4,117,93,127,54,108,89,137,53,9,80,84,59,13,23,61, . . . 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54,40,34,12,62,35,79,64,28,7,89,19,75,26,62,57,1,35,4,96,1,127,602,126,71,21,28,1,71,116,5,1,34,37,510,52,19,9,44,68,47,71,33,40,16,32,60,47,71,48,30,62,24,27,75,10,32,61,34,7,45,69,31,48,81,55,31,50,37,46,27,73,39,60,71,109,90,51,93,40,59,48,4,1,40,69,126,54,73,151,29,72,125,101,54,26,57,39,72,33,60,77,105,43,23,1,35,60,31,74,46,3,67,1,25,33,69,65,20,7,28,26,43,43, . . . 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18000,18135,18140,18148,18151,18154,18161,18168,18203,18334,18337,18340,18344,18347,18349,18355,18357,18358,18378,18381,18383,18386,18387,18389,18412,18414,18416,18429,18432,18445,18447,18459,18574,18589,18590,18602,18604,18605,18611,18617,18620,18625,18627,18779,18780,18784,18793,18794,18796,18805,18810,18815,18822,18828,18851,18948,18957,18973,18989,18992,18993,19007,19009,19019,19023,19026,19031,19034,19039,19044,19061,19064,19083,19087,19093,19095,19098,19219,19233,19247,19357,19361,19375,19381,19391,19394,19407,19411,19418,19428,19537,19547,19571,19581,19593,19595,19596,19597,19600,19602,19603,19608,19610,19615,19622,19625,19627,19648,19661,19783,19787,19789,19791,19805,19809,19812,19814,19817,19819,19823,19824,19826,19829,19834,19836,19838,19851,19856,19858,19870,19873,19877,19883,19989,19997,20000,20002,20005,20008,20013,20015,20016,20042,20176,20185,20197,20201,20341,20349,20358,20367,20370,20373,20397,20536,20541,20553,20555,20559,20561,20569,20574,20715,20717,20720,20721,20726,20730,20732,20733,20736,20737,20740,20745,20752,20753,20755,20759,20761,20762,20765,20767,20773,20786,20940,20942,20945,20949,20960,20967,20970,20972,21111,21134,21135,21140,21145,21165,21170,21273,21280,21287,21290,21294,21295,21297,21301,21304,21307,21308,21312,21315,21319,21324,21328,21349,21458,21464,21470,21480,21482,21487,21494,21496,21499,21501,21502,21507,21520,21522,21524,21534,21562,21699,21718,21721,21723,21725,21727,21737,21741,21885,21887,21891,21897,21900,21902,21906,21907,22408,22546,22562,22565,22567,22569,22580,22712,22721,22731,22737,22745,22754,22771,22902,22907,22912,22916,22922,22932,22938,22998,23036,23039,23090,23093,23102,23109,23221,23222,23224,23227,23231,23253,23260,23266,23410,23412,23547,23557,23561,23573,23577,23578,23581,23600,23605,23613,23742,23947,23952,23954,23955,23960,23964,23966,23971,24018,24126,24133,24152,24154,24158,24327,24380,24395,24687,24694,24714,24717,24725,24748,24751,24872,24891,25089,25095,25259,25262,25280,25283,25286,25463,25466,25468,25471,25488,25620,25640,25642,25644,25648,25651,25654,25656,25659,25662,25809,25815,25820,25826,25832,25834,25836,25846,25851,26003,26017,26025,26032,26040,26045, +chr19 47510518 47527257 m84039_230401_034725_s4/117245222/ccs 109,309,434,575,838,917,1306,1716,1993,2199,2393,2776,2976,3087,3420,3614,3841,4003,4201,4303,4454,4711,4904,5482,5665,5793,5888,5987,6084,6197,6417,6743,6848,7097,7583,7825,8076,8260,8357,8495,8630,9029,9138,9285,9505,9657,9778,9902,10012,10206,10398,10640,10794,10875,11167,11303,11471,11684,11855,12064,12259,12450,12643,12738,12988,13130,13235,13386,13550,13765,13968,14239,14381,14548,14705,14920,15273,15384,15746,15901,15990,16173,16295,16451, 152,120,105,262,78,381,345,239,176,137,163,101,110,326,142,226,161,197,101,150,139,160,572,77,127,94,98,96,112,191,325,104,156,437,186,222,137,96,137,134,166,94,103,190,151,120,87,109,94,191,149,153,77,194,88,97,129,170,168,119,103,137,94,142,141,103,105,155,141,154,125,141,158,128,214,352,110,361,154,86,166,105,155,177, 108,261,429,539,837,916,1298,1651,1955,2169,2336,2556,2877,3086,3413,3562,3840,4002,4200,4302,4453,4593,4871,5476,5559,5792,5887,5986,6083,6196,6388,6742,6847,7004,7534,7769,8047,8213,8356,8494,8629,8796,9123,9241,9475,9656,9777,9865,10011,10106,10397,10547,10793,10871,11069,11255,11400,11600,11854,12023,12183,12362,12587,12737,12880,13129,13233,13340,13541,13691,13919,14093,14380,14539,14676,14919,15272,15383,15745,15900,15987,16156,16278,16450,16628, 1,48,5,36,1,1,8,65,38,30,57,220,99,1,7,52,1,1,1,1,1,118,33,6,106,1,1,1,1,1,29,1,1,93,49,56,29,47,1,1,1,233,15,44,30,1,1,37,1,100,1,93,1,4,98,48,71,84,1,41,76,88,56,1,108,1,2,46,9,74,49,146,1,9,29,1,1,1,1,1,3,17,17,1,1, . . . 0,1,4,9,108,261,300,308,429,433,539,546,548,554,574,837,916,1298,1302,1305,1651,1687,1692,1705,1712,1715,1955,1992,2169,2197,2198,2264,2289,2336,2392,2556,2606,2610,2624,2659,2693,2710,2744,2764,2775,2780,2834,2877,2880,2909,2953,2955,2975,3023,3025,3086,3413,3419,3451,3531,3562,3580,3586,3604,3611,3613,3840,3900,3947,4002,4200,4259,4283,4302,4453,4511,4593,4596,4611,4621,4655,4660,4702,4709,4710,4744,4804,4821,4871,4903,5476,5477,5479,5481,5559,5562,5567,5589,5661,5664,5746,5792,5887,5986,6083,6196,6388,6391,6408,6416,6742,6770,6847,7004,7059,7096,7534,7582,7769,7773,7824,8047,8069,8074,8075,8213,8239,8259,8356,8452,8494,8573,8629,8796,8821,8873,8875,8884,8925,8934,8937,8999,9018,9028,9123,9134,9137,9241,9255,9273,9280,9284,9475,9504,9560,9606,9656,9728,9777,9865,9879,9892,9901,9966,9985,10011,10106,10113,10156,10173,10175,10176,10205,10267,10325,10397,10460,10512,10547,10620,10639,10793,10871,10874,10913,10997,11069,11133,11148,11152,11166,11255,11268,11278,11302,11400,11416,11436,11447,11470,11600,11611,11659,11663,11683,11751,11854,11951,12023,12029,12055,12060,12063,12143,12183,12188,12205,12240,12254,12256,12258,12304,12310,12362,12366,12382,12386,12387,12405,12444,12449,12476,12512,12554,12587,12608,12632,12642,12737,12880,12884,12891,12895,12952,12956,12964,12987,13129,13188,13233,13234,13274,13312,13340,13341,13342,13385,13541,13549,13691,13699,13726,13755,13757,13761,13764,13881,13919,13946,13964,13967,14034,14093,14106,14109,14153,14161,14163,14228,14238,14332,14380,14539,14547,14640,14676,14704,14919,15272,15346,15383,15745,15846,15900,15987,15989,16048,16156,16172,16278,16291,16294,16356,16410,16450,16527,16555,16628,16642,16671,16733,16735,16736, +chr19 47510580 47527139 m84039_230404_003541_s3/257819209/ccs 243,353,585,830,932,1232,1435,1885,2006,2279,2439,2684,2810,3061,3242,3408,3579,3818,4120,5057,5296,5606,5767,6149,6347,6686,6872,7005,7172,7333,7521,7893,8396,8590,8865,9047,9243,9416,9740,9946,10097,10278,10501,10695,10880,11083,11256,11457,11639,11849,12733,12845,13069,13286,13492,13680,13870,14057,14249,14429,14613,14785,14878,15009,15184,15343,15531,15710,15913,16116, 104,166,128,85,117,89,101,77,89,100,144,76,150,100,137,138,127,123,108,106,150,160,128,130,145,107,85,135,138,144,86,129,112,140,77,112,96,108,133,146,129,124,105,87,118,100,119,99,106,105,111,147,121,113,117,136,130,112,122,113,119,92,102,110,101,133,136,101,108,118, 107,347,519,713,915,1049,1321,1536,1962,2095,2379,2583,2760,2960,3161,3379,3546,3706,3941,4228,5163,5446,5766,5895,6279,6492,6793,6957,7140,7310,7477,7607,8022,8508,8730,8942,9159,9339,9524,9873,10092,10226,10402,10606,10782,10998,11183,11375,11556,11745,11954,12844,12992,13190,13399,13609,13816,14000,14169,14371,14542,14732,14877,14980,15119,15285,15476,15667,15811,16021,16234, 136,6,66,117,17,183,114,349,44,184,60,101,50,101,81,29,33,112,179,829,133,160,1,254,68,194,79,48,32,23,44,286,374,82,135,105,84,77,216,73,5,52,99,89,98,85,73,82,83,104,779,1,77,96,93,71,54,57,80,58,71,53,1,29,65,58,55,43,102,95,194, . . . 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+chr19 47510789 47515778 m84039_230404_003541_s3/81792247/ccs 74,395,586,767,906,1161,1313,1514,1632,1752,1917,2478,2772,2906,3307,3446,3599,3739,3884,4037,4633, 110,110,110,94,108,76,115,106,119,119,121,106,92,87,111,114,110,123,118,109,131, 184,505,696,861,1014,1237,1428,1620,1751,1871,2038,2584,2864,2993,3418,3560,3709,3862,4002,4146,4764, 211,81,71,45,147,76,86,12,1,46,440,188,42,314,28,39,30,22,35,487,79, . . . 2,3,5,8,11,15,19,21,24,26,27,29,31,34,35,37,39,49,52,56,58,61,63,73,184,189,193,197,200,202,206,210,214,215,217,219,222,225,226,230,235,237,240,242,244,246,250,251,265,333,351,355,357,361,365,368,374,376,382,387,391,392,394,505,508,511,514,519,522,527,529,533,535,538,542,545,549,553,555,558,561,566,568,573,577,582,585,696,702,704,708,709,713,716,718,723,725,729,736,738,741,742,744,746,754,759,762,765,766,861,863,865,866,868,872,877,878,884,885,887,897,899,905,1014,1026,1028,1032,1035,1050,1052,1055,1060,1070,1080,1083,1086,1088,1090,1092,1094,1100,1102,1105,1108,1111,1114,1116,1119,1121,1126,1141,1160,1237,1247,1253,1254,1257,1259,1261,1264,1267,1270,1274,1276,1278,1279,1283,1285,1286,1289,1296,1299,1309,1312,1428,1445,1450,1456,1460,1462,1464,1474,1478,1481,1485,1495,1513,1620,1631,1751,1871,1873,1875,1881,1885,1887,1889,1891,1894,1898,1902,1916,2011,2038,2040,2045,2053,2057,2063,2065,2068,2071,2073,2074,2078,2080,2083,2084,2087,2089,2091,2093,2096,2100,2102,2106,2110,2113,2121,2123,2125,2126,2130,2136,2142,2145,2149,2151,2157,2158,2160,2163,2170,2201,2205,2207,2215,2217,2222,2225,2227,2229,2231,2233,2234,2236,2238,2241,2243,2244,2249,2252,2254,2257,2258,2259,2263,2266,2268,2271,2273,2275,2277,2279,2282,2284,2285,2293,2300,2302,2307,2310,2315,2325,2384,2394,2397,2407,2422,2427,2430,2432,2434,2439,2443,2446,2449,2451,2456,2458,2460,2463,2465,2466,2469,2471,2473,2475,2477,2584,2586,2595,2597,2599,2603,2608,2618,2622,2638,2645,2708,2721,2723,2729,2735,2737,2742,2745,2747,2753,2756,2771,2864,2867,2878,2879,2884,2892,2895,2896,2898,2900,2902,2905,2993,2994,3000,3004,3007,3009,3011,3025,3033,3081,3083,3089,3106,3108,3109,3111,3124,3126,3131,3142,3144,3148,3151,3155,3159,3161,3163,3164,3165,3167,3170,3176,3180,3185,3187,3188,3191,3220,3222,3225,3233,3256,3259,3260,3262,3268,3272,3280,3281,3293,3295,3306,3418,3429,3431,3445,3560,3574,3582,3584,3590,3598,3709,3715,3718,3721,3725,3729,3732,3738,3862,3864,3865,3876,3880,3882,3883,4002,4005,4016,4029,4036,4146,4155,4163,4165,4167,4170,4172,4178,4180,4184,4186,4190,4194,4195,4197,4201,4220,4221,4223,4225,4227,4228,4236,4238,4247,4251,4272,4284,4287,4288,4291,4294,4296,4298,4299,4304,4309,4310,4313,4323,4346,4348,4359,4378,4385,4387,4395,4419,4437,4444,4447,4449,4451,4453,4463,4465,4467,4468,4471,4476,4494,4505,4519,4531,4535,4537,4541,4544,4547,4548,4612,4626,4630,4632,4664,4764,4767,4769,4773,4774,4776,4779,4785,4789,4811,4824,4826,4842,4971,4980,4982,4984, +chr19 47510878 47527135 m84008_230107_003043_s1/179442349/ccs 201,384,567,756,960,1092,1279,1429,1579,1734,2020,2320,2475,2666,2854,3016,3182,3483,3686,3805,3953,4867,5011,5130,5288,5471,5661,5846,6034,6247,6387,6644,6841,6985,7171,7618,7885,7991,8151,8442,8624,8786,8941,9128,9263,9487,9649,9842,10080,10229,10442,10620,10813,11013,11182,11356,11538,11680,11865,12061,12208,12417,12591,12758,12974,13177,13361,13575,13774,13958,14089,14308,14480,14705,14902,15077,15271,15414,15601,15824,15977, 147,147,126,132,116,127,100,136,110,107,225,115,156,122,137,138,253,121,109,140,118,115,118,133,141,139,166,119,142,92,116,106,86,83,125,266,105,134,242,113,96,114,117,112,160,118,139,131,134,125,121,138,128,136,154,133,141,117,139,124,167,125,140,181,124,153,150,124,86,97,153,116,150,172,87,124,106,129,107,110,132, 146,348,531,693,888,1076,1219,1379,1565,1689,1841,2245,2435,2631,2788,2991,3154,3435,3604,3795,3945,4071,4982,5129,5263,5429,5610,5827,5965,6176,6339,6503,6750,6927,7068,7296,7884,7990,8125,8393,8555,8720,8900,9058,9240,9423,9605,9788,9973,10214,10354,10563,10758,10941,11149,11336,11489,11679,11797,12004,12185,12375,12542,12731,12939,13098,13330,13511,13699,13860,14055,14242,14424,14630,14877,14989,15201,15377,15543,15708,15934,16109, 55,36,36,63,72,16,60,50,14,45,179,75,40,35,66,25,28,48,82,10,8,796,29,1,25,42,51,19,69,71,48,141,91,58,103,322,1,1,26,49,69,66,41,70,23,64,44,54,107,15,88,57,55,72,33,20,49,1,68,57,23,42,49,27,35,79,31,64,75,98,34,66,56,75,25,88,70,37,58,116,43,20, . . . 8,15,16,146,157,161,162,179,186,188,200,348,374,377,381,383,531,533,536,539,542,544,547,550,552,556,563,566,660,693,701,703,727,730,734,736,755,862,888,890,893,894,897,900,903,909,913,919,924,928,930,932,934,938,942,959,1076,1079,1083,1085,1091,1219,1235,1238,1242,1246,1248,1250,1253,1258,1260,1263,1265,1266,1269,1278,1379,1395,1400,1404,1415,1422,1425,1428,1565,1567,1578,1644,1689,1707,1720,1723,1726,1733,1841,1846,1850,1852,1867,1870,1872,1875,1880,1881,1882,1887,1888,1890,1891,1893,1894,1896,1900,1902,1906,1907,1911,1912,1914,1916,1917,1920,1924,1929,1934,1941,1946,1947,1949,1954,1955,1957,1960,1962,1963,1966,1967,1970,1972,1974,1977,1980,1982,1983,1989,1992,1993,1996,1998,2000,2002,2005,2015,2019,2245,2251,2254,2271,2275,2276,2278,2281,2282,2285,2287,2292,2294,2298,2300,2301,2304,2307,2309,2312,2317,2319,2435,2442,2448,2450,2452,2455,2459,2463,2469,2471,2474,2631,2633,2639,2640,2645,2647,2648,2652,2654,2659,2663,2665,2788,2802,2805,2808,2810,2812,2815,2819,2825,2832,2835,2838,2841,2843,2847,2853,2991,2993,2997,3001,3015,3154,3157,3159,3178,3181,3435,3442,3449,3452,3454,3460,3465,3474,3476,3482,3604,3611,3619,3624,3627,3630,3633,3634,3636,3644,3650,3653,3665,3670,3672,3675,3681,3685,3795,3804,3902,3945,3952,4071,4083,4094,4096,4100,4102,4106,4110,4111,4113,4117,4136,4137,4139,4141,4143,4144,4148,4152,4154,4170,4173,4177,4188,4192,4193,4200,4203,4204,4207,4210,4212,4214,4215,4220,4225,4226,4229,4236,4239,4254,4262,4264,4272,4275,4284,4294,4296,4298,4301,4303,4310,4311,4312,4318,4321,4323,4325,4331,4335,4336,4341,4343,4345,4352,4353,4360,4365,4367,4369,4374,4381,4399,4401,4405,4407,4410,4411,4415,4416,4417,4421,4424,4435,4447,4451,4453,4457,4460,4463,4467,4473,4476,4477,4478,4480,4483,4486,4491,4496,4502,4514,4520,4537,4538,4540,4546,4548,4550,4552,4555,4557,4562,4573,4577,4580,4589,4602,4604,4606,4609,4617,4638,4641,4643,4650,4652,4654,4657,4659,4663,4664,4665,4670,4674,4681,4684,4685,4686,4690,4693,4696,4741,4743,4750,4751,4753,4755,4757,4759,4764,4770,4772,4775,4777,4780,4781,4783,4787,4791,4798,4807,4810,4813,4815,4829,4833,4834,4849,4866,4916,4966,4982,4985,4990,4993,4997,4999,5010,5129,5263,5265,5267,5271,5273,5287,5328,5400,5425,5429,5431,5436,5439,5442,5459,5462,5463,5470,5610,5619,5630,5641,5660,5827,5833,5834,5839,5842,5845,5965,5982,5987,5989,5992,5995,5998,6000,6002,6004,6005,6008,6012,6015,6017,6026,6031,6033,6176,6179,6180,6197,6200,6201,6208,6213,6216,6219,6225,6233,6238,6240,6246,6339,6348,6351,6353,6356,6358,6360,6366,6372,6374,6376,6377,6381,6382,6386,6503,6508,6510,6511,6514,6516,6519,6523,6529,6531,6532,6535,6537,6539,6541,6543,6549,6550,6557,6563,6565,6566,6571,6592,6594,6600,6603,6604,6606,6608,6611,6612,6615,6618,6625,6629,6643,6750,6769,6770,6772,6776,6777,6780,6784,6787,6807,6808,6815,6820,6840,6927,6939,6940,6944,6946,6947,6948,6951,6962,6971,6984,7068,7092,7096,7097,7100,7102,7108,7112,7115,7116,7128,7130,7131,7134,7136,7138,7166,7169,7170,7296,7303,7309,7314,7325,7328,7330,7339,7340,7346,7352,7353,7359,7360,7364,7366,7371,7374,7375,7379,7380,7381,7382,7385,7389,7390,7396,7397,7399,7401,7403,7404,7407,7408,7410,7411,7413,7414,7415,7416,7418,7420,7425,7434,7435,7437,7440,7443,7448,7450,7452,7454,7457,7459,7462,7464,7466,7469,7472,7480,7484,7487,7488,7490,7493,7495,7496,7501,7502,7507,7511,7512,7514,7516,7518,7520,7521,7522,7526,7528,7530,7531,7534,7537,7538,7541,7542,7544,7546,7550,7553,7555,7556,7559,7560,7564,7570,7572,7575,7577,7578,7581,7584,7585,7587,7589,7591,7592,7597,7602,7604,7608,7617,7884,7990,8125,8130,8150,8393,8411,8413,8415,8419,8421,8422,8426,8431,8434,8436,8441,8555,8570,8574,8579,8592,8594,8595,8601,8603,8610,8623,8720,8726,8729,8738,8742,8745,8747,8753,8756,8761,8766,8769,8785,8900,8905,8909,8910,8912,8915,8922,8929,8933,8940,9058,9063,9066,9083,9089,9091,9094,9106,9108,9116,9127,9240,9258,9262,9423,9430,9436,9438,9443,9444,9446,9449,9450,9456,9478,9486,9605,9620,9623,9626,9628,9644,9647,9648,9788,9792,9796,9797,9803,9805,9807,9810,9813,9816,9818,9825,9830,9834,9835,9841,9973,9975,9981,10005,10009,10010,10015,10018,10020,10022,10026,10030,10037,10045,10047,10068,10076,10079,10214,10221,10225,10228,10354,10357,10374,10378,10381,10384,10386,10396,10399,10400,10408,10415,10417,10420,10424,10426,10430,10435,10441,10563,10567,10572,10578,10581,10585,10588,10591,10592,10595,10599,10611,10613,10615,10619,10758,10771,10772,10776,10779,10782,10784,10788,10794,10801,10807,10810,10812,10906,10941,10943,10945,10946,10948,10956,10958,10965,10968,10969,10972,10974,10975,10978,10979,10981,10984,10986,10988,10991,10992,10993,10998,11002,11008,11012,11149,11153,11163,11167,11169,11171,11173,11181,11336,11343,11355,11489,11491,11495,11504,11509,11512,11517,11521,11523,11525,11532,11537,11679,11797,11810,11816,11826,11828,11829,11831,11832,11836,11837,11839,11847,11849,11860,11864,12004,12007,12012,12017,12020,12021,12023,12024,12029,12054,12060,12185,12207,12375,12383,12384,12386,12388,12389,12395,12399,12405,12408,12413,12416,12542,12546,12547,12549,12552,12562,12565,12568,12572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+chr19 47510884 47527565 m54329U_210813_020940/103744027/ccs 182,338,503,691,930,1116,1280,1480,1641,1808,1995,2163,2300,2459,2642,2838,3121,3275,3595,3841,3960,4794,5036,5273,5595,5788,6357,6550,6750,6991,7224,7369,7620,7828,7993,8277,8695,9295,9463,9640,9851,10039,10230,10398,10574,10774,10946,11107,11281,11450,11650,12205,12352,12521,12680,12923,13132,13307,13478,13663,13871,14042,14218,14398,14565,14768,14993,15411,15599,15765,15937,16107,16277,16464, 116,117,131,207,116,109,103,124,137,171,110,126,137,126,131,247,116,90,93,84,100,118,148,102,118,121,108,105,120,117,103,102,121,83,283,136,124,130,133,131,150,117,83,119,139,115,127,147,122,138,127,100,136,123,128,112,114,120,135,139,122,127,151,128,202,132,417,160,135,118,131,156,146,118, 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+chr19 47511145 47534069 m64076_221119_202646/33490605/ccs 118,314,490,706,861,1214,1769,2289,2489,2643,2812,2972,3128,3620,3883,3978,4140,4245,4474,4800,5147,5488,5729,5904,6118,6315,6533,6717,7092,7281,7627,7779,7908,8108,8249,8448,8654,8755,9754,9916,10133,10511,11157,11349,11521,11710,12135,12347,12505,12688,12842,13176,13316,13556,13805,13976,14143,14380,14584,14896,15089,15276,15444,15615,15750,15991,16279,16449,16620,16964,17159,17328,17546,17704,18183,18542,18835,19003,19337,19532,19694,19927,20123,20267,20628,20973,21138,21353,21610,21727,21916,22484, 158,140,215,104,308,518,480,165,150,168,156,155,362,232,94,161,78,128,287,311,307,180,139,143,161,136,150,288,122,256,151,128,181,140,193,205,80,957,154,83,290,628,163,139,149,424,211,93,162,145,333,130,161,156,152,166,168,192,311,143,162,151,170,129,196,162,148,167,307,162,161,152,157,429,326,292,153,322,194,161,172,154,138,360,327,164,193,256,116,169,561,168, 112,276,454,705,810,1169,1732,2249,2454,2639,2811,2968,3127,3490,3852,3977,4139,4218,4373,4761,5111,5454,5668,5868,6047,6279,6451,6683,7005,7214,7537,7778,7907,8089,8248,8442,8653,8734,9712,9908,9999,10423,11139,11320,11488,11670,12134,12346,12440,12667,12833,13175,13306,13477,13712,13957,14142,14311,14572,14895,15039,15251,15427,15614,15744,15946,16153,16427,16616,16927,17126,17320,17480,17703,18133,18509,18834,18988,19325,19531,19693,19866,20081,20261,20627,20955,21137,21331,21609,21726,21896,22477,22652, 6,38,36,1,51,45,37,40,35,4,1,4,1,130,31,1,1,27,101,39,36,34,61,36,71,36,82,34,87,67,90,1,1,19,1,6,1,21,42,8,134,88,18,29,33,40,1,1,65,21,9,1,10,79,93,19,1,69,12,1,50,25,17,1,6,45,126,22,4,37,33,8,66,1,50,33,1,15,12,1,1,61,42,6,1,18,1,22,1,1,20,7,22, . . . 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+chr19 47511426 47524219 m54329U_210326_192251/44827220/ccs 215,472,660,844,1012,1209,1413,1603,1777,1961,2135,2312,2457,2621,2839,2980,3357,4240,4387,4611,4769,4923,5093,5301,5521,5688,5925,6064,6260,6493,6659,6852,7072,7329,7478,7662,7886,8068,8274,8437,8624,8811,9021,9191,9346,9526,9733,9916,10068,10271,10450,10630,10793,10968,11197,11471,11643,11806,12186,12403,12596, 157,106,148,145,138,130,132,135,118,123,160,136,103,136,106,376,168,119,116,146,117,139,168,143,119,140,113,144,135,136,109,122,137,123,131,170,135,141,157,128,148,145,130,147,171,132,129,143,122,128,138,123,142,126,191,142,150,319,149,137,148, 165,372,578,808,989,1150,1339,1545,1738,1895,2084,2295,2448,2560,2757,2945,3356,3525,4359,4503,4757,4886,5062,5261,5444,5640,5828,6038,6208,6395,6629,6768,6974,7209,7452,7609,7832,8021,8209,8431,8565,8772,8956,9151,9338,9517,9658,9862,10059,10190,10399,10588,10753,10935,11094,11388,11613,11793,12125,12335,12540, 50,100,82,36,23,59,74,58,39,66,51,17,9,61,82,35,1,715,28,108,12,37,31,40,77,48,97,26,52,98,30,84,98,120,26,53,54,47,65,6,59,39,65,40,8,9,75,54,9,81,51,42,40,33,103,83,30,13,61,68,56, . . . 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+chr19 47511448 47535018 m84039_230401_034725_s4/159777178/ccs 92,271,624,808,927,1094,1464,1702,1836,1946,2128,2288,2445,2676,2947,3269,4317,4614,4827,5306,5481,5653,5823,6044,6205,6419,6570,6923,7120,7334,7516,7669,7960,8079,8238,8405,8620,8707,8879,9077,9300,9502,9719,9854,10021,10214,10381,10540,10711,10896,11226,11670,11806,11977,12478,12638,12809,12959,13140,13326,13567,13737,13877,14078,14174,14296,14466,14687,15070,15215,15524,15800,16055,16201,16383,16518,16706,16868,16954,17240,17431,17585,17828,18025,18204,18378,18564,18810,18950,19112,19326,19485,19685,19829,19927,20035,20204,20583,20740,20955,21131,21280,21480,21638,21807,22011,22172,22349,22518,22627,22886,23108,23267, 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+chr19 47511839 47526360 m54329U_210323_190418/33229501/ccs 119,278,445,627,797,987,1199,1393,1563,1750,1918,2233,2398,2619,2809,3004,3894,4073,4256,4395,4582,4772,4948,5291,5453,5616,5800,6013,6235,6416,6653,6878,7023,7171,7352,7564,7718,8111,8287,8522,8696,8914,9091,9296,9491,9960,10098,10319,10497,10664,10848,11021,11196,11383,11747,11964,12164,12358,12576,12806,12991,13189,13372,13568,13951,14041, 132,123,137,136,159,125,115,127,139,167,293,137,145,111,83,100,116,125,128,154,167,131,284,119,120,114,143,139,134,121,174,144,147,160,157,138,339,140,156,141,157,144,133,125,264,123,168,115,145,132,97,119,147,299,139,135,165,149,107,117,115,122,154,348,89,265, 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+chr19 47512947 47530027 m84039_230404_003541_s3/133760457/ccs 266,488,1454,1921,3169,3758,4515,4684,5475,5995,6551,6908,7095,7846,7978,8179,9200,9549,10320,10541,10726,11282,11437,11834,12210,12409,12638,12997,13781,13963,14338,14499,14674,14844,15022,15200,15368,15555,15737,15922,16104,16489,16698,16874, 108,107,110,111,102,101,102,142,117,105,95,120,113,131,156,117,115,87,101,134,103,116,101,81,142,110,104,129,122,89,150,139,124,99,98,104,115,135,100,103,149,116,111,144, 374,595,1564,2032,3271,3859,4617,4826,5592,6100,6646,7028,7208,7977,8134,8296,9315,9636,10421,10675,10829,11398,11538,11915,12352,12519,12742,13126,13903,14052,14488,14638,14798,14943,15120,15304,15483,15690,15837,16025,16253,16605,16809, 114,859,357,1137,487,656,67,649,403,451,262,67,638,1,45,904,234,684,120,51,453,39,296,295,57,119,255,655,60,286,11,36,46,79,80,64,72,47,85,79,236,93,65, . . . 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+chr19 47513489 47534420 m64076_210328_012155/11535850/ccs 81,436,606,778,981,1185,1346,2160,2428,2591,2787,2939,3357,3586,3755,3970,4176,4364,4578,4800,4996,5356,5580,5695,5979,6114,6348,6549,6729,6924,7130,7340,7568,7755,7927,8115,8294,8518,8718,8910,9134,9322,9491,9673,9830,10022,10186,10385,10602,10796,11133,11329,11488,11658,11824,11991,12373,12562,12757,12969,13173,13347,13551,13745,13938,14137,14334,14499,14671,14859,15065,15272,15463,15660,15938,16093,16293,16492,16666,16861,17063,17256,17440,17635,17794,18010,18260,18473,18684,18890,19121,19282,19455,19618,20298,20530,20705, 301,124,129,138,114,129,143,153,118,105,129,400,144,140,159,128,131,143,128,119,317,139,114,154,83,145,140,179,159,157,140,124,123,126,122,120,145,134,154,128,120,140,118,135,127,156,134,129,154,281,142,141,127,149,151,325,139,179,168,161,173,162,145,172,141,151,102,140,133,148,163,150,159,155,77,150,143,155,178,174,151,144,162,155,172,131,113,151,136,98,127,126,126,626,98,126,102, 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+chr19 47514095 47525362 m84039_230401_031619_s3/45484832/ccs 141,306,429,602,1532,1769,1900,2098,2221,2378,2564,2814,3180,3384,3598,3718,3858,3979,4403,4597,4757,4876,4995,5543,5628,5739,5950,6137,6390,6526,6698,6900,7051,7225,7367,7493,7696,8059,8199,8329,8515,8626,8807,8971,9075,9214,9630,9769,9923,10137,10377,10492,10704,10904, 115,122,155,123,105,122,124,78,154,116,121,129,126,113,111,118,83,97,145,148,103,118,98,84,110,80,134,100,80,130,131,109,126,139,125,132,158,100,107,135,110,126,115,103,138,177,124,143,151,154,77,127,100,123, 256,428,584,725,1637,1891,2024,2176,2375,2494,2685,2943,3306,3497,3709,3836,3941,4076,4548,4745,4860,4994,5093,5627,5738,5819,6084,6237,6470,6656,6829,7009,7177,7364,7492,7625,7854,8159,8306,8464,8625,8752,8922,9074,9213,9391,9754,9912,10074,10291,10454,10619,10804,11027, 50,1,18,807,132,9,74,45,3,70,129,237,78,101,9,22,38,327,49,12,16,1,450,1,1,131,53,153,56,42,71,42,48,3,1,71,205,40,23,51,1,55,49,1,1,239,15,11,63,86,38,85,100,41, . . . 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+chr19 47514312 47539335 m54329U_210810_004956/145688885/ccs 137,351,440,654,1333,1509,1728,1887,2213,2372,2587,2775,2963,3158,3325,3527,3714,4202,4340,4567,4823,5061,5255,5406,5624,5799,5959,6102,6282,6425,6768,6979,7149,7323,7545,7729,8198,8306,8576,8891,9207,9422,9613,9790,9960,10156,10406,10578,10716,10874,11104,11419,11592,11753,11965,12121,12311,12521,12723,12914,13090,13326,13494,13672,13886,14104,14266,14462,14658,14840,15038,15194,15396,15570,15770,15962,16132,16317,16520,16656,16881,17438,17643,17806,17978,18189,18379,18599,18777,18966,19155,19333,19491,19713,19921,20123,20361,20747,20906,21110,21345,21547,21742,21905,22114,22297,22504,22783,22985,23170,23395,23600,23899,24093,24235,24433,24634, 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+chr19 47514327 47528440 m84039_230401_034725_s4/169282444/ccs 131,300,521,1342,1534,1748,1896,2124,2283,2476,2621,2770,2903,3009,3184,3391,3531,3682,4156,4463,4619,4830,5234,5530,5763,5935,6298,6513,6661,7071,7241,7412,7648,7785,7987,8168,8374,8494,8668,8838,9174,9630,9787,9976,10168,10360,10574,10856,10991,11173,11353,11559,11702,11909,12129,12307,12532,12682,12887,13081,13261,13444,13642,13835, 125,111,89,105,128,104,130,129,101,120,117,132,105,146,109,89,93,123,123,106,142,108,105,143,129,97,101,128,110,108,122,141,111,94,144,121,86,143,101,235,113,106,128,115,127,126,139,112,134,102,128,138,143,115,86,149,105,140,133,109,134,139,107,131, 256,411,610,1447,1662,1852,2026,2253,2384,2596,2738,2902,3008,3155,3293,3480,3624,3805,4279,4569,4761,4938,5339,5673,5892,6032,6399,6641,6771,7179,7363,7553,7759,7879,8131,8289,8460,8637,8769,9073,9287,9736,9915,10091,10295,10486,10713,10968,11125,11275,11481,11697,11845,12024,12215,12456,12637,12822,13020,13190,13395,13583,13749, 44,110,732,87,86,44,98,30,92,25,32,1,1,29,98,51,58,351,184,50,69,296,191,90,43,266,114,20,300,62,49,95,26,108,37,85,34,31,69,101,343,51,61,77,65,88,143,23,48,78,78,5,64,105,92,76,45,65,61,71,49,59,86, . . . 1,3,6,27,31,42,45,47,53,60,61,63,65,74,76,80,81,85,87,89,91,96,97,99,102,106,107,108,109,113,115,118,121,125,126,128,130,256,258,263,288,293,299,411,416,424,427,429,433,440,447,450,454,458,460,462,465,469,472,474,476,481,484,493,498,518,520,610,611,623,627,631,634,642,650,654,658,659,661,663,665,671,684,685,687,689,691,692,702,711,721,736,740,741,784,802,810,812,820,823,842,846,849,851,858,859,860,866,868,869,871,876,900,901,908,911,915,917,922,927,929,931,935,937,940,944,947,949,953,955,958,959,963,964,969,971,972,983,995,999,1001,1002,1005,1008,1011,1012,1015,1018,1025,1026,1028,1031,1034,1039,1044,1050,1062,1068,1070,1076,1085,1088,1090,1094,1096,1098,1100,1103,1105,1110,1112,1114,1116,1118,1123,1128,1137,1150,1152,1154,1157,1162,1165,1171,1189,1191,1198,1199,1200,1202,1203,1205,1207,1212,1218,1219,1222,1232,1233,1234,1238,1241,1244,1284,1289,1291,1296,1298,1299,1301,1303,1305,1311,1319,1330,1341,1357,1407,1447,1450,1460,1462,1463,1468,1469,1470,1477,1480,1487,1488,1493,1498,1504,1506,1509,1513,1515,1525,1529,1533,1572,1662,1665,1667,1669,1673,1686,1687,1689,1691,1692,1693,1696,1699,1700,1709,1711,1713,1716,1721,1724,1725,1729,1732,1735,1747,1852,1861,1870,1872,1876,1885,1887,1893,1895,1922,1951,2021,2026,2029,2031,2033,2035,2040,2043,2049,2050,2051,2056,2060,2064,2065,2067,2069,2070,2071,2073,2074,2080,2081,2092,2095,2096,2107,2108,2118,2121,2123,2253,2255,2257,2260,2262,2271,2274,2277,2282,2384,2403,2415,2424,2426,2428,2429,2431,2433,2439,2440,2444,2446,2452,2454,2458,2472,2475,2551,2596,2597,2601,2604,2607,2620,2738,2741,2745,2749,2760,2766,2769,2902,2929,2955,3008,3043,3155,3160,3161,3164,3183,3293,3302,3311,3314,3318,3319,3320,3322,3328,3330,3338,3342,3343,3345,3349,3350,3351,3357,3362,3363,3369,3381,3390,3480,3484,3486,3487,3504,3506,3508,3511,3515,3517,3519,3523,3530,3624,3640,3648,3670,3671,3674,3676,3678,3681,3719,3805,3807,3811,3813,3815,3818,3820,3842,3847,3848,3851,3853,3857,3867,3869,3871,3875,3877,3878,3879,3884,3885,3886,3889,3891,3892,3898,3899,3903,3905,3910,3929,3935,4001,4003,4005,4008,4011,4016,4031,4034,4039,4040,4041,4046,4050,4052,4054,4056,4063,4064,4066,4068,4070,4072,4076,4079,4080,4082,4084,4088,4093,4098,4100,4102,4108,4109,4113,4115,4116,4122,4123,4125,4127,4131,4133,4135,4142,4146,4152,4155,4279,4304,4324,4325,4328,4330,4336,4340,4353,4364,4367,4368,4370,4372,4375,4377,4379,4382,4383,4386,4388,4392,4394,4397,4402,4405,4406,4411,4413,4417,4423,4427,4428,4431,4434,4439,4440,4443,4445,4448,4450,4462,4509,4562,4569,4570,4579,4589,4595,4598,4603,4618,4761,4763,4768,4770,4775,4776,4780,4781,4782,4786,4789,4791,4794,4796,4798,4803,4805,4815,4821,4827,4829,4938,4941,4944,4946,4949,4950,4952,4954,4958,4960,4961,4965,4966,4970,4973,4975,4978,4980,4983,4990,4991,4998,5001,5009,5017,5020,5022,5059,5099,5101,5130,5146,5149,5152,5155,5159,5162,5163,5166,5172,5174,5177,5181,5187,5190,5198,5202,5204,5205,5210,5212,5221,5233,5295,5339,5347,5349,5351,5355,5357,5362,5366,5370,5371,5372,5393,5448,5468,5472,5516,5520,5523,5525,5529,5673,5676,5677,5682,5684,5687,5696,5698,5700,5703,5706,5708,5712,5713,5715,5721,5723,5727,5728,5730,5732,5735,5737,5738,5743,5747,5751,5754,5762,5838,5892,5897,5899,5902,5905,5910,5913,5914,5916,5928,5934,6032,6057,6060,6063,6073,6075,6078,6082,6083,6086,6089,6092,6098,6104,6108,6166,6182,6185,6192,6238,6247,6254,6259,6264,6273,6297,6399,6404,6407,6411,6419,6426,6428,6429,6433,6435,6439,6444,6445,6449,6451,6453,6463,6467,6475,6479,6481,6482,6485,6487,6488,6490,6504,6509,6512,6577,6641,6643,6645,6660,6701,6771,6773,6778,6780,6784,6788,6799,6801,6806,6812,6814,6820,6823,6825,6831,6832,6836,6839,6850,6853,6860,6866,6869,6881,6883,6885,6888,6944,6951,6960,6965,6971,6974,6977,6980,6985,6986,6992,6998,7009,7010,7017,7043,7045,7065,7067,7070,7140,7151,7179,7181,7187,7189,7192,7199,7204,7205,7208,7212,7215,7216,7240,7278,7315,7363,7365,7367,7369,7371,7378,7385,7386,7387,7390,7392,7394,7397,7400,7411,7553,7570,7577,7583,7585,7593,7597,7633,7647,7759,7782,7784,7879,7881,7891,7934,7935,7938,7941,7945,7946,7951,7953,7957,7960,7962,7963,7982,7984,7986,8131,8134,8151,8154,8156,8157,8167,8289,8291,8312,8314,8316,8317,8320,8323,8327,8331,8333,8336,8340,8343,8344,8346,8347,8351,8352,8355,8357,8362,8365,8367,8368,8372,8373,8460,8478,8487,8493,8525,8637,8642,8643,8656,8659,8667,8737,8769,8785,8791,8794,8796,8800,8802,8806,8811,8813,8814,8817,8821,8834,8837,9073,9103,9104,9121,9123,9125,9134,9142,9152,9158,9160,9170,9173,9244,9287,9294,9298,9301,9313,9322,9324,9327,9331,9333,9335,9338,9339,9342,9343,9346,9355,9358,9364,9367,9369,9370,9372,9374,9375,9379,9384,9387,9395,9449,9453,9491,9526,9528,9534,9537,9548,9553,9560,9561,9563,9565,9570,9573,9575,9576,9579,9580,9584,9585,9587,9589,9592,9601,9608,9610,9615,9627,9629,9652,9726,9736,9743,9749,9752,9766,9768,9770,9772,9775,9778,9780,9783,9786,9874,9915,9918,9925,9936,9940,9943,9953,9956,9961,9964,9966,9975,10091,10109,10112,10126,10130,10133,10136,10137,10139,10144,10147,10149,10152,10160,10163,10167,10221,10295,10306,10309,10311,10313,10323,10326,10328,10331,10333,10335,10339,10345,10349,10351,10353,10357,10359,10419,10486,10488,10493,10495,10496,10498,10504,10511,10515,10519,10521,10522,10528,10529,10543,10545,10546,10549,10558,10564,10566,10568,10571,10572,10573,10713,10715,10716,10718,10726,10731,10736,10737,10739,10740,10742,10746,10751,10752,10754,10755,10758,10768,10770,10773,10806,10851,10855,10968,10974,10984,10985,10990,11125,11144,11157,11160,11172,11275,11300,11302,11316,11319,11327,11333,11341,11343,11346,11349,11352,11481,11489,11492,11496,11501,11502,11505,11513,11521,11523,11528,11530,11533,11535,11540,11556,11558,11670,11697,11698,11701,11845,11854,11863,11867,11869,11879,11883,11886,11894,11908,12024,12042,12045,12050,12057,12074,12078,12081,12082,12093,12095,12098,12100,12107,12119,12121,12128,12215,12228,12243,12244,12252,12255,12260,12261,12264,12268,12271,12274,12278,12285,12289,12290,12297,12299,12303,12305,12306,12456,12462,12466,12469,12470,12474,12475,12478,12481,12488,12491,12493,12505,12515,12531,12637,12662,12668,12677,12681,12822,12825,12833,12837,12838,12843,12845,12847,12848,12854,12856,12860,12863,12866,12869,12886,13020,13023,13026,13034,13037,13039,13041,13043,13046,13048,13049,13052,13069,13072,13076,13078,13080,13190,13203,13207,13211,13215,13236,13238,13240,13241,13244,13246,13248,13260,13301,13395,13405,13407,13410,13412,13417,13419,13427,13429,13434,13435,13438,13443,13470,13583,13591,13593,13594,13600,13604,13610,13618,13621,13625,13634,13641,13749,13764,13789,13791,13798,13799,13825,13830,13831,13834,13966,13968,13990,13992,13994,13996,13998,14001,14002,14004,14008,14043,14047,14087,14091, +chr19 47514355 47517971 m84008_230107_003043_s1/209457465/ccs 126,328,635,1131,1281,1504,1686,2266,2407,2618,2777,2936,3093, 139,248,140,119,116,145,579,140,136,100,110,150,138, 90,265,576,775,1250,1397,1649,2265,2406,2543,2718,2887,3086,3231, 36,63,59,356,31,107,37,1,1,75,59,49,7,1, . . . 90,93,97,98,100,102,108,110,114,118,125,265,266,272,277,279,283,285,287,290,294,298,300,301,312,316,318,319,325,327,576,583,584,592,594,595,596,600,602,604,609,615,617,621,623,627,631,632,634,698,775,805,833,873,881,884,886,888,890,895,900,902,905,908,910,913,917,920,922,926,928,978,1017,1023,1035,1041,1110,1119,1127,1130,1195,1211,1250,1252,1256,1257,1262,1264,1269,1280,1397,1400,1403,1405,1408,1410,1413,1419,1424,1437,1478,1480,1483,1487,1491,1499,1503,1649,1685,2265,2406,2543,2545,2550,2551,2553,2556,2564,2568,2573,2574,2578,2581,2584,2585,2587,2589,2590,2592,2597,2600,2611,2617,2718,2721,2724,2734,2737,2740,2743,2750,2754,2759,2767,2769,2771,2776,2887,2903,2907,2911,2912,2930,2935,3086,3092,3231,3604, +chr19 47514515 47519907 m84008_230107_003043_s1/130946739/ccs 153,314,1021,1340,1633,1845,1991,2153,2355,2520,2733,2904,3071,3309,3535,3694,3907,4074,4267,4417,4588,5024,5189, 84,118,318,281,155,111,152,162,155,140,103,138,188,147,137,159,142,133,109,132,134,132,136, 56,237,432,1339,1621,1788,1956,2143,2315,2510,2660,2836,3042,3259,3456,3672,3853,4049,4207,4376,4549,4722,5156, 97,77,589,1,12,57,35,10,40,10,73,68,29,50,79,22,54,25,60,41,39,302,33, . . . 55,65,69,71,76,80,84,86,88,91,93,98,99,100,101,105,106,112,113,115,123,125,127,130,152,237,253,260,267,273,275,279,282,285,287,289,293,294,297,306,313,432,440,442,444,455,457,461,463,467,471,472,474,478,497,498,500,502,504,505,509,513,515,524,528,529,531,534,538,549,553,554,615,623,625,633,636,645,655,657,659,662,664,671,672,673,679,682,684,686,689,692,696,697,702,704,705,713,714,721,724,726,728,730,735,740,742,744,748,753,757,760,762,766,768,771,772,776,777,778,782,784,785,796,808,812,814,818,821,824,825,828,831,834,837,838,839,841,844,847,852,857,863,875,881,883,889,898,899,901,903,907,909,911,913,916,918,923,925,927,929,931,934,936,938,941,950,959,963,965,967,968,970,975,978,984,999,1002,1004,1020,1339,1621,1624,1626,1630,1632,1788,1790,1795,1797,1798,1799,1803,1804,1810,1818,1822,1844,1956,1962,1969,1981,1984,1987,1990,2143,2148,2152,2315,2317,2320,2324,2327,2330,2346,2354,2510,2516,2519,2660,2689,2691,2698,2699,2711,2718,2732,2836,2842,2849,2853,2855,2860,2863,2865,2868,2874,2876,2879,2883,2891,2895,2897,2901,2903,3042,3052,3056,3058,3060,3062,3064,3068,3070,3259,3262,3268,3270,3271,3273,3274,3278,3280,3285,3299,3308,3424,3456,3457,3460,3468,3471,3472,3475,3476,3488,3490,3491,3494,3496,3498,3526,3529,3534,3672,3674,3685,3688,3690,3693,3853,3855,3856,3871,3872,3874,3878,3886,3888,3890,3891,3898,3904,3906,4049,4052,4057,4068,4073,4207,4209,4218,4223,4226,4234,4239,4244,4249,4255,4266,4376,4383,4390,4403,4416,4549,4552,4559,4562,4566,4569,4570,4573,4575,4581,4582,4585,4587,4722,4725,4733,4736,4738,4741,4744,4746,4751,4753,4759,4761,4762,4765,4767,4770,4771,4773,4775,4779,4781,4782,4786,4787,4790,4791,4794,4796,4799,4801,4805,4806,4811,4812,4814,4816,4822,4826,4830,4838,4851,4859,4862,4915,4924,4937,4942,4944,4961,4963,4967,4970,4973,4976,4980,4983,4989,4993,4995,4998,5008,5011,5023,5156,5170,5172,5176,5178,5183,5188,5325,5341,5344,5346,5350,5372,5376,5377,5382, +chr19 47514810 47540310 m84008_230107_003043_s1/189797755/ccs 1049,1144,1332,1495,1642,1853,2007,2158,2350,2524,2871,3040,3203,3450,3768,3934,4124,4281,4451,4644,4914,5121,5318,5496,5665,5830,6015,6247,6498,6659,6872,7025,7231,7419,7673,7896,8110,8270,8453,8631,8775,8991,9174,9371,9571,9763,9971,10170,10352,10515,10721,10901,11071,11430,11609,11791,11989,12165,12366,12567,12753,12944,13141,13331,13546,13707,14061,14260,14470,14668,14870,15118,15273,15450,15656,15820,16016,16183,16375,16566,16772,16909,17136,17345,17569,17775,18159,18362,18531,18749,18916,19109,19302,19516,19751,19897,20074,20268,20475,20636,20836,21024,21211,21420,21563,21752,21925,22094,22358,22563,22723,22922,23103,23314,23474,23670,23865,24099,24292,24437,24622,24787,25012,25174, 94,142,109,143,129,153,116,135,173,290,131,126,165,296,138,189,137,140,172,269,147,116,125,133,153,135,168,136,99,115,143,175,134,157,94,112,84,124,147,131,172,147,160,152,180,151,129,118,144,205,134,122,300,142,139,179,175,178,138,123,121,116,104,131,133,316,146,123,142,149,134,140,129,138,112,155,166,131,145,148,134,148,150,145,176,339,156,130,154,149,141,144,151,141,121,151,155,137,146,172,153,165,169,142,144,140,132,157,117,101,147,134,148,140,154,141,141,122,121,154,145,155,128,154, 147,1143,1286,1441,1638,1771,2006,2123,2293,2523,2814,3002,3166,3368,3746,3906,4123,4261,4421,4623,4913,5061,5237,5443,5629,5818,5965,6183,6383,6597,6774,7015,7200,7365,7576,7767,8008,8194,8394,8600,8762,8947,9138,9334,9523,9751,9914,10100,10288,10496,10720,10855,11023,11371,11572,11748,11970,12164,12343,12504,12690,12874,13060,13245,13462,13679,14023,14207,14383,14612,14817,15004,15258,15402,15588,15768,15975,16182,16314,16520,16714,16906,17057,17286,17490,17745,18114,18315,18492,18685,18898,19057,19253,19453,19657,19872,20048,20229,20405,20621,20808,20989,21189,21380,21562,21707,21892,22057,22251,22475,22664,22870,23056,23251,23454,23628,23811,24006,24221,24413,24591,24767,24942,25140,25328, 902,1,46,54,4,82,1,35,57,1,57,38,37,82,22,28,1,20,30,21,1,60,81,53,36,12,50,64,115,62,98,10,31,54,97,129,102,76,59,31,13,44,36,37,48,12,57,70,64,19,1,46,48,59,37,43,19,1,23,63,63,70,81,86,84,28,38,53,87,56,53,114,15,48,68,52,41,1,61,46,58,3,79,59,79,30,45,47,39,64,18,52,49,63,94,25,26,39,70,15,28,35,22,40,1,45,33,37,107,88,59,52,47,63,20,42,54,93,71,24,31,20,70,34,38, . . . 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+chr19 47514827 47529737 m84039_230404_003541_s3/181208974/ccs 894,1239,1538,1912,2234,2591,2779,3021,3134,3237,3440,3628,3942,4271,4461,4634,5117,5486,5869,6070,6278,6449,6645,6829,7024,7360,7595,7748,7910,8104,8257,8412,8616,8814,9048,9166,9392,9612,9784,9982,10140,10237,10355,10531,10766,10986,11174,11387,11585,11780,11982,12152,12230,12336,12692,12873,13063,13403,13576,13736,13941,14113,14318,14525, 136,284,349,296,350,144,197,112,84,171,150,305,299,151,124,453,355,359,147,150,149,159,127,148,307,154,139,140,193,148,154,180,197,128,117,178,170,138,127,139,96,78,140,222,188,187,212,175,171,191,169,77,86,349,165,162,287,164,155,164,151,170,192,168, 128,1030,1523,1887,2208,2584,2735,2976,3133,3218,3408,3590,3933,4241,4422,4585,5087,5472,5845,6016,6220,6427,6608,6772,6977,7331,7514,7734,7888,8103,8252,8411,8592,8813,8942,9165,9344,9562,9750,9911,10121,10236,10315,10495,10753,10954,11173,11386,11562,11756,11971,12151,12229,12316,12685,12857,13035,13350,13567,13731,13900,14092,14283,14510,14693, 766,209,15,25,26,7,44,45,1,19,32,38,9,30,39,49,30,14,24,54,58,22,37,57,47,29,81,14,22,1,5,1,24,1,106,1,48,50,34,71,19,1,40,36,13,32,1,1,23,24,11,1,1,20,7,16,28,53,9,5,41,21,35,15,39, . . . 1,128,143,155,160,162,164,166,185,186,190,192,193,201,203,212,216,219,222,237,241,242,275,278,303,311,313,320,323,332,342,349,351,358,366,376,384,400,401,408,411,413,415,417,422,427,429,431,435,440,455,458,459,465,469,471,495,501,505,508,511,512,515,518,525,526,528,531,534,544,550,562,568,585,588,590,596,603,623,628,637,646,654,657,662,671,686,689,729,732,733,734,739,741,789,791,796,807,812,820,823,829,831,834,835,837,839,844,854,858,861,863,873,877,881,893,1030,1033,1034,1041,1047,1049,1051,1058,1062,1073,1076,1135,1143,1168,1170,1172,1200,1202,1203,1212,1214,1216,1219,1235,1238,1523,1525,1528,1530,1533,1537,1887,1889,1911,2208,2217,2220,2222,2228,2233,2584,2590,2735,2778,2976,2978,2981,2989,2993,2996,3011,3013,3020,3133,3218,3223,3232,3236,3408,3413,3438,3439,3590,3595,3627,3933,3938,3941,4241,4251,4255,4258,4259,4262,4270,4422,4440,4451,4460,4585,4587,4604,4613,4626,4633,5087,5116,5472,5478,5481,5485,5845,5859,5862,5868,6016,6024,6069,6220,6223,6227,6230,6233,6236,6244,6246,6259,6270,6277,6427,6445,6448,6608,6616,6625,6644,6772,6778,6792,6795,6799,6805,6812,6817,6821,6828,6977,6981,6983,6987,6990,6992,7000,7005,7007,7009,7014,7023,7331,7336,7339,7352,7355,7359,7514,7533,7538,7540,7544,7574,7594,7734,7741,7744,7747,7802,7888,7909,8103,8252,8256,8411,8592,8597,8615,8813,8942,8944,8950,8958,8961,8982,9038,9047,9165,9344,9346,9348,9362,9364,9391,9562,9581,9611,9750,9754,9762,9774,9777,9783,9911,9931,9939,9943,9946,9959,9962,9963,9975,9978,9981,10121,10129,10135,10139,10236,10315,10318,10326,10331,10339,10343,10346,10349,10354,10441,10495,10498,10500,10506,10523,10526,10527,10530,10753,10765,10954,10958,10961,10967,10968,10970,10977,10985,11173,11386,11562,11565,11569,11584,11756,11763,11771,11774,11779,11971,11981,12151,12229,12316,12335,12685,12691,12857,12859,12865,12872,13035,13062,13350,13360,13374,13377,13380,13391,13402,13567,13575,13731,13735,13900,13902,13929,13939,13940,14092,14112,14283,14294,14303,14316,14317,14510,14516,14524,14693,14710,14712,14731,14906,14907,14909,14911,14912, +chr19 47515224 47527520 m54329U_210323_190418/97651167/ccs 431,613,965,1168,1328,1480,1712,1959,2096,2273,2450,2647,2795,2971,3141,3324,3721,3955,4127,4340,4517,4740,4957,5183,5341,5539,5757,5958,6176,6330,6486,6676,6891,7084,7277,7478,7676,7877,8051,8224,8401,8607,8824,8973,9183,9372,9581,9927,10110,10275,10446,10623,10821,10953,11217,11356,11433,11766,11961, 120,257,117,151,151,116,98,127,130,135,118,137,127,135,153,139,134,94,108,116,114,122,129,118,115,133,121,121,110,150,101,131,136,106,107,129,133,134,154,147,162,124,130,159,120,114,281,105,124,166,129,131,128,119,138,76,219,97,128, 551,870,1082,1319,1479,1596,1810,2086,2226,2408,2568,2784,2922,3106,3294,3463,3855,4049,4235,4456,4631,4862,5086,5301,5456,5672,5878,6079,6286,6480,6587,6807,7027,7190,7384,7607,7809,8011,8205,8371,8563,8731,8954,9132,9303,9486,9862,10032,10234,10441,10575,10754,10949,11072,11355,11432,11652,11863,12089, 62,95,86,9,1,116,149,10,47,42,79,11,49,35,30,258,100,78,105,61,109,95,97,40,83,85,80,97,44,6,89,84,57,87,94,69,68,40,19,30,44,93,19,51,69,95,65,78,41,5,48,67,4,145,1,1,114,98,53, . . . 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126,127,134,145,176,149,136,153,134,191,376,111,167,112,181,143,308,409,397,355,179,174,179,200,176,154,153,303,165,139,129,126,151,139,166,178,147,152,156,189,172,147,149,156,166,398,210,148,172,175,199,110,159,173,136,176,192,171,165,151,164,173,192,141,152,158,105,87,87,136,480,159,274,133,572,150,140,158,131,119,487,126,332,150,164,552,223,175,163,169,158,137,161,154,138,172,159,155,173,145,160,121,113,109,108,131,160,117,129,130,122,130,149,117,124,125,156,130,144,290,158,158,174,377,149,185,176,141,176, 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1,143,19,16,18,24,22,55,12,1,45,59,10,67,52,37,40,1,11,15,20,23,1,28,13,22,39,1,36,146,10,39,79,7,1,17,40,36,1,22,12,49,46,29,9,7,26,1,31,24,22,80,28,31,48,4,1,14,48,27,8,1,1,54,34,75,18,1,39,45,1,4,1,1,22,44,6,41,102,21,33,52,20,16,28,5,1,1,43,22,65,50,19,74,20,21,40,43,30,43,58,65,84,88,67,61,31,128,27,60,76,24,68,108,67,18,77,30,171,3,56,31,78,1,29,17,1,52,28, . . . 7,19,29,32,35,36,39,42,44,47,48,49,51,54,57,62,67,73,84,90,92,98,107,108,110,112,116,118,122,125,134,138,140,143,184,186,187,193,208,211,213,220,224,227,233,234,235,240,241,242,244,248,251,254,260,263,266,272,276,280,282,284,290,292,293,295,298,299,301,304,311,313,318,323,329,342,424,469,597,600,609,617,619,620,623,627,629,632,634,641,653,657,659,663,665,687,688,690,692,715,716,723,739,874,883,892,1038,1041,1043,1053,1230,1245,1247,1397,1400,1403,1404,1409,1418,1420,1557,1559,1562,1565,1570,1574,1575,1578,1732,1744,1746,1749,1750,1752,1757,1761,1770,1774,1786,1921,1927,1932,2124,2501,2503,2507,2513,2514,2518,2525,2526,2536,2538,2542,2545,2657,2682,2689,2704,2705,2710,2712,2715,2883,2892,3005,3022,3029,3032,3037,3039,3047,3055,3062,3068,3071,3253,3263,3265,3266,3268,3273,3276,3289,3304,3448,3450,3459,3463,3464,3466,3470,3484,3793,3825,3832,4242,4640,4650,5006,5020,5200,5212,5219,5394,5416,5596,5797,5824,6001,6013,6168,6175,6189,6343,6381,6685,6851,6879,6886,7026,7029,7031,7040,7044,7057,7059,7062,7064,7067,7068,7072,7074,7078,7083,7085,7087,7088,7092,7095,7096,7100,7104,7106,7108,7115,7120,7130,7133,7135,7141,7142,7146,7152,7159,7171,7301,7303,7310,7437,7444,7473,7475,7627,7635,7637,7639,7645,7646,7647,7649,7652,7653,7655,7656,7665,7670,7674,7676,7679,7681,7684,7689,7692,7694,7705,7845,7847,7851,8018,8197,8213,8361,8364,8378,8387,8397,8400,8553,8558,8564,8566,8574,8575,8588,8745,8935,8956,9129,9133,9140,9288,9292,9304,9307,9310,9312,9315,9319,9336,9486,9496,9499,9502,9504,9521,9526,9529,9531,9688,9706,9711,9712,9716,9883,9886,9891,10290,10292,10296,10507,10517,10522,10532,10681,10854,10865,10884,11060,11073,11083,11283,11304,11415,11416,11418,11464,11466,11469,11471,11474,11494,11654,11656,11681,11855,11862,11882,11885,12022,12049,12067,12069,12246,12249,12442,12614,12627,12793,12799,12809,12812,12815,12820,12833,12840,12992,13003,13007,13009,13018,13183,13186,13190,13364,13557,13699,13730,13732,13742,13750,13752,13905,13910,13922,13929,13933,13938,14097,14099,14118,14119,14123,14126,14144,14148,14153,14171,14277,14294,14382,14470,14473,14481,14483,14487,14502,14508,14553,14645,14648,14655,14675,14683,14686,14687,14689,15170,15330,15333,15608,15742,16315,16331,16336,16487,16497,16499,16501,16504,16509,16511,16514,16517,16530,16671,16676,16835,16850,16854,16872,16875,17007,17020,17022,17035,17039,17041,17054,17057,17077,17079,17088,17092,17095,17099,17108,17179,17228,17230,17236,17243,17248,17736,17741,17745,17747,17751,17754,17760,17766,17768,17866,17895,17898,17904,17908,17910,17915,17920,17922,17946,18279,18289,18294,18298,18380,18449,18460,18464,18629,18632,18636,18642,18646,18649,18653,18656,19209,19213,19437,19613,19777,19781,19785,19798,19801,19804,19808,19813,19819,19989,19991,19995,19996,19997,20000,20002,20006,20008,20010,20169,20171,20196,20197,20202,20206,20208,20211,20212,20214,20233,20371,20382,20406,20413,20414,20417,20420,20582,20588,20590,20600,20755,20777,20791,20803,20806,20825,20828,20967,20971,20986,21159,21179,21339,21342,21343,21349,21350,21356,21375,21378,21534,21554,21576,21750,21754,21779,21925,21938,21939,21946,21951,21957,21967,22128,22132,22135,22136,22142,22156,22162,22167,22171,22185,22307,22312,22316,22332,22338,22350,22363,22371,22485,22492,22495,22498,22500,22501,22525,22544,22549,22551,22554,22558,22568,22678,22684,22695,22702,22727,22731,22733,22735,22737,22741,22748,22752,22755,22757,22765,22809,22856,22874,22881,22888,22889,22891,22894,22897,22901,22909,22911,22915,22917,22920,22927,22933,22940,23027,23072,23076,23100,23102,23105,23109,23112,23114,23117,23129,23132,23293,23295,23300,23306,23315,23323,23441,23445,23451,23475,23478,23481,23487,23490,23493,23496,23500,23509,23513,23521,23526,23568,23669,23698,23704,23719,23720,23724,23855,23860,23866,23878,23885,23891,23894,23897,23903,23907,23914,24037,24043,24055,24059,24062,24064,24067,24069,24074,24084,24086,24088,24112,24243,24246,24257,24264,24266,24294,24416,24422,24441,24443,24445,24449,24452,24458,24459,24469,24472,24483,24601,24606,24608,24613,24615,24621,24623,24625,24626,24630,24633,24640,24644,24646,24649,24652,24667,24669,24683,24687,24689,24691,24693,24697,24698,24701,24705,24708,24833,24835,24840,24844,24846,24852,24859,24863,24867,24869,24884,24892,24899,25025,25029,25042,25199,25204,25218,25219,25221,25228,25230,25234,25237,25240,25265,25269,25271,25275,25406,25435,25580,25584,25587,25601,25619,25621,25622,25627,25628,25634,25640,25646,25650,25653,25655,25658,25669,25670,25672,25675,25676,25679,25682,25683,25685,25688,25692,25694,25696,25697,25703,25704,25714,25719,25729,25733,25750,26041,26043,26202,26215,26232,26234,26236,26238,26240,26243,26247,26249,26254,26257,26416,26420,26424,26428,26446,26621,26622,26632,26651,26654,26657,26662,26696,26698,27076,27226,27250,27254,27440,27446,27451,27456,27633,27775,27780,27800,27808,27814,27822,27826,28003,28005,28018,28030, +chr19 47515325 47525397 m64076_210328_012155/64620793/ccs 315,745,1096,1234,1386,1525,1738,1936,2353,2746,2939,3096,3293,3483,3629,3807,3955,4109,4337,4732,4908,5063,5234,5480,5602,5830,6013,6217,6389,6554,6748,6921,7070,7218,7430,7612,7771,7939,8136,8321,8503,8686,8869,9005,9235,9398,9592,9781, 101,197,122,117,129,129,123,107,107,124,81,129,134,145,133,109,153,107,81,106,101,121,132,99,86,103,98,77,108,145,134,123,134,91,96,116,134,162,147,138,152,129,132,165,116,138,139,118, 416,942,1218,1351,1515,1654,1861,2043,2460,2870,3020,3225,3427,3628,3762,3916,4108,4216,4418,4838,5009,5184,5366,5579,5688,5933,6111,6294,6497,6699,6882,7044,7204,7309,7526,7728,7905,8101,8283,8459,8655,8815,9001,9170,9351,9536,9731,9899, 329,154,16,35,10,84,75,310,286,69,76,68,56,1,45,39,1,121,314,70,54,50,114,23,142,80,106,95,57,49,39,26,14,121,86,43,34,35,38,44,31,54,4,65,47,56,50,77, . . . 8,11,14,15,18,21,24,27,28,31,34,37,42,47,53,66,73,75,81,93,95,123,128,133,142,155,157,159,162,167,170,172,176,195,197,204,205,206,208,209,211,213,217,218,219,228,232,233,234,235,238,239,240,244,245,247,250,251,252,253,254,256,257,260,264,266,268,274,276,277,279,282,283,285,288,289,290,296,303,305,308,310,312,314,416,433,436,439,441,444,446,447,449,451,453,455,457,460,469,470,472,473,478,479,480,487,489,490,492,497,498,503,514,516,519,523,525,527,530,532,535,542,617,620,622,629,635,637,639,641,643,645,647,648,649,651,653,670,671,674,676,677,679,681,685,687,698,699,703,704,705,709,712,721,723,725,744,942,956,963,968,971,974,976,977,981,985,987,990,992,994,995,996,998,1000,1001,1002,1004,1005,1007,1011,1013,1014,1015,1018,1019,1022,1023,1025,1027,1028,1033,1036,1038,1041,1043,1045,1047,1053,1062,1063,1064,1068,1069,1070,1073,1080,1095,1218,1225,1233,1351,1374,1385,1515,1520,1524,1654,1656,1663,1668,1676,1683,1689,1699,1709,1720,1721,1725,1737,1861,1863,1865,1867,1868,1870,1872,1873,1884,1885,1886,1890,1892,1894,1895,1896,1899,1900,1902,1904,1908,1909,1912,1914,1917,1919,1921,1924,1927,1928,1933,1935,1970,2043,2053,2054,2056,2059,2061,2064,2066,2069,2075,2077,2080,2084,2088,2090,2092,2093,2096,2106,2110,2132,2198,2201,2204,2210,2211,2213,2216,2218,2223,2225,2226,2227,2229,2233,2235,2237,2240,2241,2243,2247,2251,2253,2255,2257,2259,2261,2263,2265,2268,2269,2271,2286,2288,2290,2291,2292,2295,2296,2297,2298,2303,2304,2309,2310,2311,2313,2314,2316,2328,2330,2331,2333,2337,2338,2341,2344,2345,2348,2352,2460,2471,2472,2474,2475,2476,2479,2482,2483,2484,2486,2488,2489,2490,2493,2494,2500,2501,2505,2507,2508,2509,2512,2513,2518,2523,2525,2527,2529,2532,2536,2538,2540,2543,2545,2547,2553,2619,2623,2625,2645,2657,2658,2661,2665,2666,2669,2672,2673,2676,2677,2683,2684,2685,2688,2689,2691,2692,2695,2696,2697,2699,2702,2728,2731,2736,2745,2870,2874,2876,2878,2887,2890,2892,2894,2898,2901,2902,2903,2922,2934,2938,3020,3027,3029,3032,3035,3041,3043,3047,3050,3051,3052,3053,3056,3058,3059,3070,3075,3077,3079,3081,3089,3093,3095,3225,3226,3230,3231,3234,3236,3239,3248,3251,3253,3256,3258,3261,3262,3264,3265,3267,3269,3270,3272,3273,3277,3278,3281,3283,3284,3286,3289,3292,3427,3438,3448,3452,3453,3455,3456,3459,3463,3466,3468,3470,3472,3473,3475,3479,3482,3628,3762,3765,3777,3787,3797,3799,3804,3805,3806,3916,3925,3936,3947,3949,3954,4108,4216,4220,4222,4226,4228,4229,4231,4234,4236,4237,4238,4240,4243,4244,4246,4247,4251,4255,4258,4267,4268,4273,4275,4276,4278,4280,4284,4286,4288,4290,4293,4294,4296,4297,4302,4306,4309,4311,4315,4317,4320,4325,4332,4336,4418,4422,4433,4436,4442,4444,4445,4450,4473,4476,4479,4493,4541,4554,4576,4578,4581,4586,4587,4588,4590,4593,4594,4596,4602,4604,4605,4606,4609,4611,4612,4614,4615,4617,4619,4620,4622,4625,4627,4628,4630,4631,4641,4642,4647,4651,4653,4655,4658,4662,4663,4664,4665,4667,4670,4672,4674,4678,4686,4695,4698,4701,4702,4704,4705,4707,4709,4712,4714,4715,4719,4721,4723,4728,4731,4838,4842,4846,4855,4857,4858,4859,4862,4864,4865,4868,4869,4894,4907,5009,5011,5014,5015,5017,5026,5029,5030,5032,5035,5036,5038,5040,5041,5043,5045,5046,5051,5060,5062,5184,5187,5190,5192,5195,5196,5199,5200,5202,5205,5208,5211,5216,5218,5228,5230,5233,5366,5367,5369,5371,5374,5377,5380,5382,5383,5388,5393,5394,5396,5398,5399,5405,5410,5412,5413,5415,5416,5418,5423,5425,5429,5430,5432,5433,5434,5437,5440,5441,5445,5449,5450,5452,5454,5459,5461,5465,5467,5477,5479,5579,5584,5601,5688,5690,5708,5713,5719,5721,5725,5729,5731,5735,5737,5738,5740,5742,5745,5757,5759,5761,5766,5768,5769,5774,5777,5778,5780,5782,5785,5789,5792,5793,5799,5806,5808,5812,5816,5829,5933,5938,5942,5948,5950,5954,5955,5960,5970,5971,5973,5975,5980,5982,5985,5989,5991,5992,5995,6000,6003,6012,6111,6114,6116,6122,6124,6128,6132,6141,6143,6145,6146,6147,6150,6153,6155,6156,6157,6160,6164,6168,6169,6170,6172,6174,6176,6178,6180,6183,6184,6197,6201,6203,6205,6215,6216,6294,6301,6303,6307,6308,6311,6315,6319,6321,6333,6336,6337,6341,6344,6347,6349,6353,6356,6357,6358,6359,6363,6365,6366,6368,6372,6375,6380,6382,6385,6388,6407,6426,6497,6506,6508,6511,6513,6516,6521,6523,6525,6530,6533,6539,6549,6551,6553,6699,6702,6706,6708,6712,6714,6718,6732,6734,6736,6747,6882,6886,6889,6901,6904,6920,7044,7049,7050,7054,7069,7121,7204,7209,7210,7213,7217,7309,7314,7315,7320,7343,7348,7351,7354,7357,7358,7362,7364,7367,7371,7375,7377,7382,7383,7386,7388,7393,7395,7396,7398,7399,7403,7404,7406,7411,7414,7416,7417,7419,7420,7429,7526,7545,7548,7552,7554,7558,7561,7563,7565,7566,7569,7573,7582,7586,7589,7590,7592,7593,7611,7665,7728,7736,7739,7743,7747,7750,7752,7754,7756,7762,7765,7770,7905,7924,7933,7936,7938,8101,8102,8107,8112,8116,8117,8119,8133,8135,8283,8286,8309,8320,8459,8462,8470,8475,8478,8481,8484,8486,8488,8492,8502,8655,8664,8682,8685,8815,8818,8820,8823,8826,8831,8840,8854,8864,8866,8868,9001,9004,9170,9173,9176,9177,9179,9182,9184,9187,9189,9192,9194,9198,9200,9203,9207,9213,9215,9216,9221,9222,9228,9229,9231,9233,9234,9351,9361,9366,9368,9371,9373,9375,9379,9381,9384,9389,9391,9393,9395,9397,9536,9544,9551,9553,9555,9557,9559,9561,9562,9565,9566,9568,9569,9573,9586,9589,9591,9731,9739,9745,9749,9753,9755,9756,9758,9761,9763,9766,9780,9899,9906,9909,9912,9915,9921,9923,9927,9930,9938,9940,9943,9945,9952,9965,9975, +chr19 47515526 47530633 m64076_210328_012155/70713469/ccs 110,243,659,1164,1400,1629,1798,1959,2203,2360,2546,2727,2886,3079,3233,3399,3593,3778,3930,4139,4334,4506,4687,4882,5097,5292,5439,5647,5867,6037,6177,6386,6548,6724,6950,7096,7240,7397,7598,7743,7940,8094,8313,8519,8743,8832,9049,9302,9483,9667,9856,10069,10224,10448,10583,10798,10983,11172,11417,11602,11788,12208,12418,12579,12786,12978,13121,13370,13554,13752,13971,14172,14375,14523,14733,14913, 116,415,498,215,224,163,137,135,127,158,123,156,138,142,160,149,136,120,140,139,114,180,135,125,129,107,148,131,124,139,143,128,142,147,145,89,127,143,135,149,127,165,117,135,88,179,176,117,110,109,112,123,149,132,153,133,157,176,104,91,137,129,143,148,125,132,130,132,136,94,125,105,101,178,146,153, 226,658,1157,1379,1624,1792,1935,2094,2330,2518,2669,2883,3024,3221,3393,3548,3729,3898,4070,4278,4448,4686,4822,5007,5226,5399,5587,5778,5991,6176,6320,6514,6690,6871,7095,7185,7367,7540,7733,7892,8067,8259,8430,8654,8831,9011,9225,9419,9593,9776,9968,10192,10373,10580,10736,10931,11140,11348,11521,11693,11925,12337,12561,12727,12911,13110,13251,13502,13690,13846,14096,14277,14476,14701,14879,15066, 17,1,7,21,5,6,24,109,30,28,58,3,55,12,6,45,49,32,69,56,58,1,60,90,66,40,60,89,46,1,66,34,34,79,1,55,30,58,10,48,27,54,89,89,1,38,77,64,74,80,101,32,75,3,62,52,32,69,81,95,283,81,18,59,67,11,119,52,62,125,76,98,47,32,34,16, . . . 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+chr19 47515617 47528492 m84039_230404_003541_s3/134221345/ccs 148,325,767,1029,1213,1473,1670,1883,2025,2138,2338,2677,2911,3047,3249,3380,3577,3776,3962,4111,4318,4488,4650,4840,4982,5310,5651,5815,6022,6237,6420,6599,6744,6951,7097,7298,7454,7636,7814,7988,8171,8363,8623,8862,9010,9192,9367,9524,9727,9895,10069,10239,10390,10620,10922,11067,11248,11464,11650,11859,12055,12293,12396,12575, 111,119,109,172,128,85,100,124,112,173,92,112,123,111,130,79,75,136,104,114,111,137,154,139,128,113,102,122,102,122,134,138,142,100,155,124,131,143,131,113,98,126,117,97,101,126,116,119,116,162,115,150,124,144,121,112,163,106,150,130,114,102,149,143, 112,259,444,876,1201,1341,1558,1770,2007,2137,2311,2430,2789,3034,3158,3379,3459,3652,3912,4066,4225,4429,4625,4804,4979,5110,5423,5753,5937,6124,6359,6554,6737,6886,7051,7252,7422,7585,7779,7945,8101,8269,8489,8740,8959,9111,9318,9483,9643,9843,10057,10184,10389,10514,10764,11043,11179,11411,11570,11800,11989,12169,12395,12545,12718, 36,66,323,153,12,132,112,113,18,1,27,247,122,13,91,1,118,124,50,45,93,59,25,36,3,200,228,62,85,113,61,45,7,65,46,46,32,51,35,43,70,94,134,122,51,81,49,41,84,52,12,55,1,106,158,24,69,53,80,59,66,124,1,30,33, . . . 0,2,19,112,136,147,217,259,261,263,278,288,291,294,307,310,313,317,324,444,447,450,455,460,462,465,466,470,471,478,481,487,492,526,528,585,600,622,623,625,626,643,645,649,651,653,659,663,668,671,674,677,680,683,684,688,690,693,695,697,698,707,710,714,716,718,721,722,725,726,728,730,731,746,748,750,764,766,833,876,877,886,896,899,923,933,934,935,946,964,970,972,975,977,986,1008,1021,1025,1028,1201,1212,1341,1343,1346,1350,1352,1356,1358,1364,1372,1376,1377,1379,1404,1406,1412,1415,1416,1420,1424,1425,1427,1429,1432,1433,1440,1444,1446,1450,1457,1469,1472,1558,1581,1585,1591,1594,1595,1599,1604,1609,1612,1619,1622,1623,1628,1630,1632,1634,1637,1638,1642,1646,1649,1655,1657,1664,1669,1730,1757,1770,1773,1777,1785,1789,1791,1793,1797,1799,1801,1804,1819,1820,1868,1882,2007,2008,2024,2137,2311,2313,2321,2334,2337,2430,2439,2442,2455,2458,2464,2468,2471,2475,2490,2492,2495,2514,2518,2520,2531,2591,2604,2610,2617,2626,2630,2633,2635,2636,2640,2641,2647,2648,2652,2654,2655,2658,2662,2666,2671,2676,2789,2795,2804,2806,2807,2810,2815,2825,2827,2828,2831,2835,2837,2852,2863,2866,2878,2881,2887,2889,2910,3034,3046,3158,3162,3165,3168,3170,3173,3177,3199,3201,3202,3204,3206,3207,3212,3214,3219,3232,3240,3243,3248,3379,3459,3467,3513,3522,3523,3531,3534,3545,3547,3551,3574,3576,3652,3662,3670,3675,3683,3685,3688,3690,3693,3694,3708,3711,3716,3719,3721,3722,3724,3727,3730,3732,3736,3740,3743,3748,3756,3759,3760,3762,3767,3768,3769,3772,3775,3912,3914,3922,3928,3929,3936,3953,3961,4066,4073,4078,4081,4083,4104,4105,4110,4150,4225,4227,4240,4262,4264,4266,4267,4272,4273,4274,4276,4279,4280,4283,4288,4292,4295,4297,4301,4317,4429,4433,4449,4455,4457,4459,4466,4484,4487,4625,4643,4649,4685,4804,4819,4823,4837,4839,4943,4979,4981,5110,5122,5134,5143,5144,5147,5149,5152,5155,5158,5163,5177,5189,5193,5195,5196,5201,5202,5204,5210,5219,5221,5223,5224,5225,5227,5233,5235,5243,5248,5250,5253,5271,5273,5288,5291,5309,5357,5423,5426,5430,5433,5435,5439,5455,5456,5461,5464,5465,5467,5469,5472,5476,5479,5521,5563,5568,5596,5600,5603,5605,5608,5617,5620,5625,5632,5635,5637,5638,5650,5753,5755,5758,5765,5767,5770,5772,5773,5778,5780,5782,5798,5800,5808,5810,5814,5937,5940,5945,5948,5949,5954,5967,5969,5970,5992,5996,6000,6021,6092,6113,6124,6127,6130,6133,6146,6150,6155,6159,6162,6163,6165,6167,6173,6174,6177,6181,6183,6187,6190,6192,6194,6195,6197,6200,6205,6207,6209,6221,6223,6224,6230,6232,6234,6236,6269,6359,6361,6364,6379,6382,6385,6389,6391,6395,6397,6401,6411,6415,6417,6419,6554,6558,6560,6564,6565,6569,6572,6575,6584,6587,6589,6595,6598,6737,6743,6886,6891,6895,6901,6910,6911,6915,6918,6924,6926,6950,7051,7055,7068,7073,7075,7076,7078,7079,7083,7086,7091,7094,7096,7218,7252,7268,7271,7272,7289,7297,7422,7426,7430,7433,7435,7447,7449,7453,7480,7585,7591,7611,7614,7616,7622,7625,7635,7702,7779,7785,7786,7813,7945,7946,7949,7959,7961,7964,7987,8101,8104,8108,8112,8137,8140,8156,8159,8162,8164,8166,8170,8269,8288,8291,8294,8297,8298,8302,8305,8307,8310,8314,8319,8326,8328,8332,8333,8339,8342,8343,8345,8362,8489,8490,8492,8496,8497,8500,8503,8507,8508,8522,8523,8525,8528,8541,8543,8545,8549,8561,8562,8578,8588,8591,8599,8601,8609,8622,8740,8759,8764,8793,8795,8837,8861,8959,8966,8969,8971,8978,8984,8987,8991,9003,9006,9009,9111,9124,9126,9128,9140,9143,9146,9156,9159,9162,9167,9172,9175,9178,9186,9189,9191,9318,9332,9334,9342,9346,9350,9353,9366,9483,9487,9512,9523,9550,9643,9647,9649,9651,9653,9671,9676,9678,9681,9691,9693,9696,9700,9701,9702,9707,9719,9726,9843,9847,9860,9873,9876,9894,10057,10060,10062,10065,10068,10184,10208,10211,10227,10229,10238,10275,10389,10514,10517,10538,10541,10544,10573,10619,10764,10794,10837,10847,10849,10898,10921,11043,11045,11056,11061,11062,11066,11179,11183,11218,11220,11221,11223,11232,11234,11236,11240,11247,11348,11411,11412,11414,11415,11418,11420,11422,11424,11436,11440,11445,11447,11456,11458,11460,11462,11463,11518,11570,11593,11602,11611,11613,11625,11635,11637,11639,11647,11649,11675,11800,11806,11810,11813,11820,11823,11835,11847,11857,11858,11989,12000,12008,12025,12032,12036,12048,12052,12054,12169,12173,12186,12195,12198,12201,12205,12214,12221,12224,12230,12241,12257,12261,12271,12275,12292,12335,12395,12545,12559,12571,12574,12617,12674,12704,12718,12728,12740,12750,12841,12855,12856,12857,12859,12860,12861, +chr19 47515639 47536773 m64076_210328_012155/69403730/ccs 86,252,496,722,915,1116,1281,1673,1869,2108,2384,2886,3255,3358,3537,3991,4135,4299,4484,4653,4896,5062,5241,5458,5648,5843,6267,6413,6639,6844,6998,7138,7281,7690,7822,7997,8217,8432,8657,8896,9053,9222,9405,9614,9775,9971,10164,10333,10521,10715,10902,11066,11219,11406,11607,11796,11960,12125,12338,12531,12860,13037,13208,13452,13648,13841,14015,14247,14416,14592,14698,14834,15019,15193,15335,15534,15715,15866,16062,16659,16868,17058,17291,17483,17643,17797,18031,18246,18437,18643,18845,19053,19203,19390,19555,19752,19982,20168,20516,20655,20825,20997, 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+chr19 47516059 47529030 m84039_230404_003541_s3/82513978/ccs 232,392,562,925,1117,1207,1320,1521,1700,1901,2093,2295,2664,2833,3074,3269,3640,3801,4033,4207,4395,4630,4832,5014,5232,5389,5540,5751,5994,6143,6379,6543,6794,6922,7124,7308,7459,7632,7902,8115,8295,8510,8735,8956,9265,9435,9520,9763,10152,10359,10550,10967,11146,11313,11493,11728,11876,12059,12257,12449,12634, 159,168,339,129,89,77,153,170,180,179,163,328,158,189,176,370,133,172,173,157,177,161,162,142,141,150,160,158,128,162,132,169,99,171,183,119,159,181,136,156,180,166,141,157,169,84,205,379,206,138,371,130,163,179,201,147,182,145,156,158,153, 206,391,560,901,1054,1206,1284,1473,1691,1880,2080,2256,2623,2822,3022,3250,3639,3773,3973,4206,4364,4572,4791,4994,5156,5373,5539,5700,5909,6122,6305,6511,6712,6893,7093,7307,7427,7618,7813,8038,8271,8475,8676,8876,9113,9434,9519,9725,10142,10358,10497,10921,11097,11309,11492,11694,11875,12058,12204,12413,12607,12787, 26,1,2,24,63,1,36,48,9,21,13,39,41,11,52,19,1,28,60,1,31,58,41,20,76,16,1,51,85,21,74,32,82,29,31,1,32,14,89,77,24,35,59,80,152,1,1,38,10,1,53,46,49,4,1,34,1,1,53,36,27,43, . . . 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+chr19 47516423 47523540 m84008_230107_003043_s1/127407090/ccs 215,368,528,692,860,1068,1258,1410,1584,1837,1988,2163,2359,2479,2676,2869,3099,3274,3436,3621,3807,4008,4209,4397,4596,4789,5007,5177,5313,5570,5851,6075,6263,6561, 126,136,138,160,140,141,133,167,127,105,163,122,112,175,172,147,146,146,140,175,136,142,138,166,133,147,114,121,175,131,97,131,262,354, 132,341,504,666,852,1000,1209,1391,1577,1711,1942,2151,2285,2471,2654,2848,3016,3245,3420,3576,3796,3943,4150,4347,4563,4729,4936,5121,5298,5488,5701,5948,6206,6525,6915, 83,27,24,26,8,68,49,19,7,126,46,12,74,8,22,21,83,29,16,45,11,65,59,50,33,60,71,56,15,82,150,127,57,36,1, . . . 131,158,162,164,169,195,198,207,210,212,214,341,347,352,354,356,362,367,504,508,511,514,515,527,666,669,672,675,681,683,691,852,859,1000,1021,1049,1053,1057,1060,1067,1209,1225,1227,1257,1391,1409,1577,1578,1583,1711,1723,1741,1747,1748,1753,1754,1757,1759,1763,1769,1772,1774,1803,1804,1809,1812,1836,1942,1953,1960,1972,1976,1978,1987,2151,2162,2285,2291,2305,2310,2331,2347,2353,2356,2358,2471,2478,2654,2657,2669,2673,2675,2848,2852,2858,2868,3016,3023,3058,3065,3068,3078,3080,3083,3098,3214,3245,3255,3257,3261,3263,3273,3420,3426,3431,3435,3462,3576,3579,3581,3582,3587,3611,3618,3620,3796,3801,3803,3806,3943,3947,3948,3950,3957,3982,3986,3992,3996,4001,4003,4007,4150,4157,4162,4169,4176,4181,4208,4347,4375,4390,4396,4563,4566,4570,4573,4576,4595,4729,4730,4748,4764,4770,4774,4788,4936,4948,4950,4953,4961,4969,4975,4981,5006,5121,5127,5129,5132,5149,5165,5176,5298,5312,5488,5508,5522,5526,5530,5533,5534,5543,5549,5551,5554,5566,5569,5701,5722,5738,5744,5746,5748,5753,5779,5783,5787,5789,5792,5803,5811,5819,5843,5850,5948,5952,5959,5990,5998,6010,6017,6021,6023,6046,6048,6050,6074,6152,6206,6211,6214,6225,6227,6230,6234,6237,6238,6245,6251,6262,6525,6560,6915,7048,7064, +chr19 47516482 47530674 m84039_230401_031619_s3/178849005/ccs 69,305,438,665,752,894,1104,1243,1384,1580,1995,2124,2316,2416,2573,2723,2863,3058,3216,3365,3541,3720,3898,4091,4288,4467,4650,4859,4995,5187,5363,5534,5746,5912,6083,6451,6596,6804,6963,7169,7540,7714,8103,8464,8690,8871,9040,9258,9422,9571,9803,10152,10343,10539,10718,10901,11072,11338,11472,11617,11777,11990,12163,12441,12551,12775,12969,13162,13315,13495,13670,13850, 117,113,114,75,141,145,104,112,110,130,111,93,92,136,144,139,171,119,148,110,124,102,118,118,117,88,85,103,93,77,120,106,111,132,87,109,128,118,125,85,131,110,92,101,125,142,140,105,113,144,80,128,140,110,150,94,265,101,144,76,127,111,117,87,146,121,105,110,101,125,79,120, 186,418,552,740,893,1039,1208,1355,1494,1710,2106,2217,2408,2552,2717,2862,3034,3177,3364,3475,3665,3822,4016,4209,4405,4555,4735,4962,5088,5264,5483,5640,5857,6044,6170,6560,6724,6922,7088,7254,7671,7824,8195,8565,8815,9013,9180,9363,9535,9715,9883,10280,10483,10649,10868,10995,11337,11439,11616,11693,11904,12101,12280,12528,12697,12896,13074,13272,13416,13620,13749,13970, 119,20,113,12,1,65,35,29,86,285,18,99,8,21,6,1,24,39,1,66,55,76,75,79,62,95,124,33,99,99,51,106,55,39,281,36,80,41,81,286,43,279,269,125,56,27,78,59,36,88,269,63,56,69,33,77,1,33,1,84,86,62,161,23,78,73,88,43,79,50,101,45, . . . 0,3,4,6,11,57,58,68,132,167,186,199,218,220,223,225,226,227,230,232,234,235,238,240,241,243,244,247,249,250,253,256,259,262,265,268,271,272,276,279,281,283,304,418,426,429,435,436,437,552,553,564,566,569,570,572,577,583,587,590,594,601,606,609,615,618,624,631,639,664,740,751,779,893,1039,1048,1050,1055,1058,1061,1065,1067,1069,1073,1075,1079,1085,1087,1089,1093,1097,1101,1103,1170,1201,1208,1213,1214,1220,1224,1231,1233,1240,1242,1355,1357,1359,1361,1364,1370,1377,1379,1383,1454,1494,1504,1520,1522,1523,1526,1528,1530,1533,1546,1556,1558,1561,1562,1566,1570,1572,1575,1579,1710,1717,1720,1722,1728,1731,1732,1737,1738,1744,1745,1751,1752,1756,1758,1763,1766,1767,1771,1772,1774,1776,1777,1781,1782,1788,1789,1791,1793,1795,1796,1799,1800,1802,1803,1805,1806,1807,1810,1812,1817,1820,1823,1826,1827,1829,1835,1836,1840,1842,1844,1846,1849,1851,1854,1856,1858,1861,1864,1872,1876,1879,1880,1885,1887,1888,1893,1899,1903,1904,1906,1908,1910,1914,1918,1920,1922,1923,1924,1926,1930,1933,1934,1936,1938,1945,1947,1948,1951,1952,1953,1954,1956,1962,1963,1964,1967,1970,1973,1977,1981,1994,2106,2111,2117,2120,2123,2217,2220,2239,2250,2254,2255,2258,2263,2266,2270,2283,2284,2287,2298,2301,2315,2408,2415,2552,2554,2558,2572,2717,2722,2862,2924,3008,3034,3049,3055,3057,3177,3192,3200,3208,3210,3215,3364,3475,3495,3498,3500,3511,3519,3520,3526,3529,3530,3537,3540,3665,3669,3673,3682,3687,3713,3719,3790,3813,3822,3839,3840,3843,3844,3846,3855,3857,3861,3863,3865,3866,3868,3876,3885,3886,3887,3892,3897,4016,4018,4022,4026,4028,4031,4037,4038,4042,4044,4052,4054,4055,4059,4062,4067,4071,4073,4074,4080,4082,4085,4090,4209,4224,4231,4233,4236,4239,4241,4255,4260,4263,4276,4287,4405,4416,4427,4430,4435,4437,4458,4466,4555,4557,4568,4571,4574,4577,4585,4587,4594,4595,4600,4603,4604,4606,4611,4615,4618,4619,4625,4627,4642,4649,4735,4742,4744,4747,4756,4761,4764,4768,4771,4774,4776,4777,4780,4786,4789,4795,4796,4800,4805,4807,4810,4814,4816,4819,4820,4828,4831,4834,4837,4846,4858,4932,4957,4962,4978,4985,4994,5088,5094,5113,5119,5126,5132,5133,5136,5140,5144,5146,5148,5153,5161,5162,5169,5178,5186,5264,5265,5274,5277,5287,5289,5291,5296,5300,5304,5306,5309,5318,5322,5324,5328,5331,5333,5335,5336,5341,5346,5348,5350,5355,5362,5483,5487,5491,5495,5501,5506,5531,5533,5571,5620,5640,5659,5665,5677,5680,5696,5700,5707,5711,5714,5717,5726,5729,5733,5737,5745,5857,5869,5874,5879,5881,5885,5892,5894,5895,5905,5911,6044,6054,6058,6061,6067,6069,6082,6170,6176,6179,6180,6193,6199,6205,6210,6215,6217,6221,6225,6228,6233,6242,6246,6249,6251,6253,6295,6341,6347,6375,6384,6387,6390,6394,6402,6407,6410,6411,6413,6414,6419,6431,6442,6444,6446,6450,6513,6560,6568,6575,6577,6579,6586,6589,6591,6595,6623,6724,6726,6728,6738,6765,6773,6782,6803,6922,6932,6936,6937,6939,6944,6949,6952,6953,6955,6958,6962,7001,7088,7093,7094,7101,7103,7106,7116,7125,7127,7129,7140,7144,7146,7157,7160,7165,7168,7254,7269,7276,7279,7282,7290,7293,7298,7301,7304,7306,7308,7312,7317,7319,7322,7329,7330,7332,7337,7339,7342,7346,7349,7350,7354,7356,7359,7361,7369,7371,7379,7430,7440,7452,7461,7467,7468,7470,7474,7475,7481,7484,7485,7489,7494,7495,7496,7498,7500,7502,7505,7508,7511,7514,7523,7524,7526,7528,7534,7539,7671,7674,7678,7684,7686,7688,7694,7702,7713,7824,7829,7835,7845,7848,7852,7855,7857,7859,7861,7866,7868,7873,7874,7876,7879,7883,7884,7887,7889,7890,7897,7899,7907,7909,7918,7920,7925,7929,7932,7943,7951,8002,8007,8018,8020,8023,8027,8033,8036,8041,8043,8048,8049,8051,8054,8063,8081,8083,8086,8094,8102,8195,8201,8209,8211,8213,8217,8238,8240,8242,8249,8251,8254,8269,8271,8276,8279,8286,8289,8346,8356,8361,8364,8371,8373,8375,8379,8381,8382,8388,8389,8391,8401,8403,8406,8409,8411,8415,8418,8419,8424,8426,8428,8431,8433,8435,8439,8443,8446,8447,8449,8450,8453,8454,8457,8459,8461,8463,8471,8496,8565,8569,8573,8576,8578,8581,8583,8586,8591,8593,8599,8600,8602,8606,8611,8614,8615,8618,8620,8622,8626,8628,8630,8632,8633,8642,8651,8655,8658,8660,8671,8679,8683,8686,8689,8815,8828,8835,8836,8838,8840,8845,8846,8849,8851,8857,8863,8870,9013,9021,9027,9031,9033,9039,9180,9188,9194,9205,9207,9210,9213,9215,9218,9220,9221,9224,9229,9230,9233,9245,9255,9257,9363,9374,9382,9384,9389,9391,9394,9396,9401,9403,9417,9421,9535,9554,9556,9559,9561,9570,9715,9724,9728,9730,9735,9740,9744,9747,9764,9769,9771,9774,9777,9782,9783,9793,9795,9802,9883,9885,9896,9900,9903,9906,9907,9911,9915,9918,9926,9928,9931,9935,9937,9939,9942,9943,9954,9956,9959,9961,9964,9968,9974,9982,9984,9986,9992,10049,10069,10078,10083,10084,10089,10096,10098,10104,10105,10112,10113,10116,10121,10122,10125,10129,10142,10146,10150,10151,10280,10314,10317,10320,10323,10327,10330,10331,10342,10441,10483,10485,10486,10493,10498,10506,10513,10523,10538,10649,10656,10663,10669,10672,10674,10677,10679,10681,10683,10686,10688,10694,10698,10699,10704,10706,10715,10717,10789,10868,10884,10887,10895,10900,10995,11020,11027,11033,11051,11057,11064,11067,11068,11071,11337,11400,11402,11439,11471,11616,11693,11716,11722,11733,11737,11740,11748,11759,11765,11774,11776,11904,11906,11914,11916,11922,11937,11939,11941,11943,11944,11948,11950,11962,11964,11965,11978,11980,11989,12015,12057,12101,12105,12117,12121,12124,12125,12137,12151,12154,12157,12159,12162,12280,12284,12296,12298,12301,12304,12309,12312,12315,12316,12329,12335,12337,12339,12341,12342,12344,12346,12348,12350,12355,12359,12361,12365,12368,12370,12374,12386,12393,12401,12418,12420,12439,12440,12528,12530,12540,12543,12545,12548,12550,12697,12702,12703,12707,12711,12714,12717,12719,12720,12726,12733,12735,12736,12738,12743,12745,12747,12752,12756,12774,12859,12896,12908,12915,12916,12923,12926,12928,12932,12940,12942,12944,12946,12949,12960,12968,13023,13074,13077,13091,13094,13096,13098,13099,13103,13107,13113,13116,13119,13121,13123,13127,13134,13146,13149,13161,13272,13278,13290,13292,13296,13298,13304,13307,13314,13416,13418,13441,13443,13444,13450,13451,13454,13460,13470,13476,13479,13482,13485,13494,13620,13622,13626,13631,13641,13649,13653,13654,13657,13659,13666,13669,13749,13774,13802,13811,13817,13821,13831,13833,13837,13842,13846,13849,13970,13980,13982,13986,13987,13999,14014,14179,14181,14185,14187, +chr19 47516511 47535109 m84039_230404_003541_s3/246354145/ccs 396,525,752,1160,1337,1556,1845,2105,2288,2664,2877,3017,3228,3599,3771,3974,4145,4227,4320,4533,4740,4923,5089,5290,5507,5702,6091,6301,6389,6572,7119,7292,7483,7663,7862,8024,8186,8384,8566,8758,8927,9205,9378,9897,10241,10407,10718,11178,11348,11664,11886,12046,12133,12240,12618,12802,12971,13167,13372,13541,13738,13882,15008,15131,15221,15396,15726,15889,16099,16468,16833,17383,17596,17781,17885,17989,18396, 128,179,366,153,112,75,157,161,334,152,139,156,321,150,192,147,81,75,169,149,121,135,160,168,145,272,208,84,149,458,127,166,175,163,161,159,197,163,115,137,277,132,518,343,165,246,453,169,315,182,145,86,77,332,139,160,159,147,160,116,143,1107,122,89,120,266,120,118,348,339,549,212,179,103,100,406,136, 351,524,704,1118,1313,1449,1631,2002,2266,2622,2816,3016,3173,3549,3749,3963,4121,4226,4302,4489,4682,4861,5058,5249,5458,5652,5974,6299,6385,6538,7030,7246,7458,7658,7826,8023,8183,8383,8547,8681,8895,9204,9337,9896,10240,10406,10653,11171,11347,11663,11846,12031,12132,12210,12572,12757,12962,13130,13314,13532,13657,13881,14989,15130,15220,15341,15662,15846,16007,16447,16807,17382,17595,17775,17884,17985,18395, 45,1,48,42,24,107,214,103,22,42,61,1,55,50,22,11,24,1,18,44,58,62,31,41,49,50,117,2,4,34,89,46,25,5,36,1,3,1,19,77,32,1,41,1,1,1,65,7,1,1,40,15,1,30,46,45,9,37,58,9,81,1,19,1,1,55,64,43,92,21,26,1,1,6,1,4,1, . . . 0,1,2,4,5,351,359,395,524,704,713,716,718,723,725,737,739,751,1118,1141,1145,1151,1159,1313,1321,1336,1449,1473,1496,1501,1506,1531,1534,1543,1545,1548,1552,1555,1631,1633,1639,1641,1644,1672,1673,1676,1678,1682,1689,1735,1738,1739,1743,1754,1761,1763,1765,1767,1768,1771,1774,1778,1784,1785,1789,1792,1795,1798,1799,1844,2002,2004,2009,2010,2014,2025,2026,2030,2031,2034,2049,2054,2056,2058,2061,2064,2067,2069,2072,2077,2081,2083,2086,2089,2104,2266,2270,2273,2279,2282,2287,2622,2624,2638,2639,2653,2655,2663,2784,2816,2817,2831,2832,2835,2838,2840,2843,2846,2852,2859,2864,2867,2876,3016,3173,3181,3219,3223,3227,3549,3554,3564,3577,3580,3596,3598,3749,3755,3761,3765,3770,3963,3968,3970,3973,4121,4143,4144,4226,4302,4308,4319,4489,4491,4496,4500,4509,4514,4520,4532,4682,4690,4701,4705,4710,4714,4717,4719,4739,4861,4867,4872,4879,4881,4884,4886,4887,4892,4922,4984,5058,5060,5063,5067,5069,5088,5249,5266,5271,5275,5289,5458,5476,5499,5506,5652,5655,5668,5671,5675,5686,5689,5692,5701,5974,6035,6043,6049,6053,6056,6059,6062,6083,6090,6299,6300,6385,6388,6538,6571,7030,7075,7077,7118,7246,7264,7272,7275,7282,7286,7291,7397,7458,7461,7463,7479,7482,7658,7662,7826,7829,7831,7857,7861,8023,8183,8185,8383,8547,8555,8565,8681,8689,8706,8732,8737,8739,8746,8757,8895,8910,8911,8926,9204,9337,9363,9368,9370,9373,9375,9377,9896,10240,10406,10653,10656,10664,10668,10717,11171,11177,11347,11663,11846,11850,11853,11855,11860,11867,11873,11875,11883,11885,12031,12036,12039,12042,12045,12132,12210,12212,12232,12237,12239,12572,12574,12578,12579,12591,12593,12596,12600,12617,12662,12757,12772,12774,12775,12786,12801,12962,12965,12970,13130,13155,13157,13166,13314,13329,13331,13338,13346,13348,13371,13495,13532,13534,13540,13657,13677,13687,13697,13701,13706,13711,13715,13718,13737,13881,14989,15000,15006,15007,15130,15220,15341,15342,15344,15346,15350,15354,15366,15369,15395,15662,15680,15697,15699,15701,15704,15725,15846,15868,15870,15873,15875,15877,15885,15886,15888,16007,16028,16029,16042,16064,16068,16075,16078,16083,16098,16447,16467,16807,16814,16820,16822,16824,16828,16832,17382,17595,17775,17780,17884,17985,17988,18395,18532,18540,18544,18546,18548,18560,18567,18574,18582,18585, +chr19 47516658 47520871 m84039_230401_034725_s4/172757415/ccs 186,335,523,722,929,1065,1256,1431,1698,1949,2208,2492,2729,2901,3104,3285,3461,3668,3850,4017, 117,121,119,96,134,137,128,95,216,152,283,200,141,132,127,147,186,127,145,107, 149,303,456,642,818,1063,1202,1384,1526,1914,2101,2491,2692,2870,3033,3231,3432,3647,3795,3995, 37,32,67,80,111,2,54,47,172,35,107,1,37,31,71,54,29,21,55,22, . . . 0,1,3,4,6,51,149,159,161,162,164,168,173,175,178,182,184,185,303,312,321,326,334,456,464,466,471,473,476,480,486,489,491,495,497,499,501,503,505,520,522,642,649,663,667,670,674,679,688,698,707,710,711,713,716,718,721,818,824,835,839,843,851,855,858,861,867,870,873,875,880,882,883,886,890,892,894,897,898,900,904,908,910,912,914,916,918,920,922,925,926,928,1063,1064,1202,1204,1208,1220,1223,1227,1239,1247,1249,1255,1302,1384,1387,1392,1398,1401,1405,1408,1416,1421,1430,1526,1529,1531,1535,1542,1545,1549,1553,1555,1557,1567,1569,1570,1576,1577,1581,1583,1588,1591,1592,1596,1599,1601,1606,1607,1614,1616,1618,1621,1624,1630,1631,1635,1642,1645,1648,1651,1652,1654,1657,1660,1697,1914,1930,1934,1942,1945,1948,2101,2112,2117,2123,2132,2137,2140,2160,2169,2171,2173,2174,2179,2181,2186,2187,2189,2195,2199,2202,2204,2207,2491,2692,2695,2698,2700,2704,2708,2711,2716,2719,2728,2870,2880,2883,2888,2890,2891,2896,2900,3033,3045,3071,3072,3075,3080,3083,3089,3103,3231,3247,3255,3258,3262,3264,3268,3270,3275,3281,3283,3284,3360,3432,3447,3448,3450,3453,3460,3647,3649,3667,3795,3812,3816,3820,3826,3830,3831,3843,3845,3849,3907,3995,4013,4016,4078,4112,4124,4142,4146,4154,4164,4166,4171,4172,4184,4188,4192,4198,4200,4206,4207,4208,4209,4211, +chr19 47516680 47530390 m84008_230107_003043_s1/83759496/ccs 204,357,501,716,854,1098,1239,1732,2068,2172,2331,2482,2674,2857,3054,3233,3421,3590,3760,3944,4158,4379,4525,4740,4947,5108,5280,5465,5667,5838,6016,6214,6385,6553,6750,6940,7184,7389,7550,7746,7929,8135,8323,8502,8706,8890,9004,9090,9458,9619,9764,9961,10135,10441,10632,10833,10991,11212,11387,11729,11905,12155,12377,12556,12731,12940,13137,13284,13459, 148,141,146,126,145,140,133,275,81,130,112,144,137,130,102,165,158,161,183,179,151,145,160,129,116,160,155,163,152,160,144,136,152,130,168,168,108,135,176,158,150,130,146,203,179,113,85,333,101,139,157,144,305,171,144,147,157,109,93,172,167,92,117,134,148,154,128,162,150, 176,352,498,647,842,999,1238,1372,2007,2149,2302,2443,2626,2811,2987,3156,3398,3579,3751,3943,4123,4309,4524,4685,4869,5063,5268,5435,5628,5819,5998,6160,6350,6537,6683,6918,7108,7292,7524,7726,7904,8079,8265,8469,8705,8885,9003,9089,9423,9559,9758,9921,10105,10440,10612,10776,10980,11148,11321,11480,11901,12072,12247,12494,12690,12879,13094,13265,13446, 28,5,3,69,12,99,1,360,61,23,29,39,48,46,67,77,23,11,9,1,35,70,1,55,78,45,12,30,39,19,18,54,35,16,67,22,76,97,26,20,25,56,58,33,1,5,1,1,35,60,6,40,30,1,20,57,11,64,66,249,4,83,130,62,41,61,43,19,13, . . . 7,22,25,29,34,37,38,43,176,182,184,187,190,199,203,352,355,356,498,500,582,647,649,661,664,676,685,688,689,691,715,842,853,999,1003,1008,1011,1017,1019,1023,1026,1027,1034,1042,1049,1065,1066,1070,1072,1079,1094,1097,1238,1372,1392,1397,1400,1402,1406,1410,1413,1415,1417,1421,1422,1424,1428,1437,1443,1449,1451,1452,1454,1456,1458,1460,1462,1466,1468,1470,1473,1475,1489,1502,1507,1511,1518,1521,1539,1542,1546,1552,1557,1564,1567,1568,1572,1575,1578,1583,1590,1592,1594,1597,1600,1601,1606,1608,1613,1614,1621,1624,1628,1665,1704,1719,1723,1725,1731,2007,2009,2012,2014,2026,2029,2040,2064,2065,2067,2149,2171,2302,2305,2318,2319,2323,2330,2443,2448,2450,2457,2469,2475,2481,2626,2628,2631,2633,2636,2643,2654,2659,2670,2673,2811,2818,2839,2842,2850,2856,2987,2991,3007,3009,3046,3053,3156,3166,3168,3175,3181,3193,3200,3203,3205,3207,3208,3229,3231,3232,3398,3420,3579,3585,3589,3751,3755,3759,3943,4123,4153,4157,4309,4311,4316,4323,4334,4336,4342,4346,4350,4352,4359,4361,4363,4366,4369,4372,4378,4524,4685,4692,4705,4714,4717,4720,4723,4728,4739,4869,4875,4881,4886,4907,4920,4925,4926,4946,5063,5066,5079,5081,5083,5088,5095,5096,5100,5107,5228,5268,5279,5435,5439,5443,5445,5448,5451,5460,5461,5464,5628,5630,5632,5666,5819,5822,5837,5998,5999,6002,6015,6160,6169,6178,6181,6184,6188,6213,6350,6365,6368,6370,6382,6384,6537,6552,6683,6685,6701,6713,6718,6743,6744,6746,6749,6918,6939,7108,7113,7128,7130,7133,7135,7137,7140,7141,7144,7146,7153,7163,7169,7177,7178,7183,7292,7298,7310,7313,7314,7318,7324,7329,7351,7353,7357,7366,7370,7380,7382,7388,7495,7524,7527,7528,7532,7534,7541,7549,7726,7728,7733,7741,7745,7839,7904,7907,7913,7917,7920,7924,7928,8079,8089,8095,8097,8100,8105,8134,8265,8283,8305,8322,8469,8476,8479,8497,8500,8501,8705,8885,8889,8926,9003,9089,9423,9452,9457,9559,9579,9592,9595,9598,9600,9608,9614,9618,9758,9763,9921,9933,9938,9941,9943,9949,9960,10105,10109,10112,10121,10124,10131,10134,10440,10612,10627,10631,10776,10782,10786,10787,10790,10793,10796,10798,10808,10814,10821,10825,10829,10832,10980,10990,11148,11151,11157,11177,11190,11192,11211,11321,11323,11345,11362,11386,11480,11494,11497,11505,11511,11518,11522,11526,11546,11552,11569,11574,11637,11657,11661,11664,11666,11669,11671,11679,11686,11698,11709,11718,11721,11723,11724,11728,11901,11904,12072,12076,12078,12081,12084,12086,12119,12121,12128,12132,12135,12148,12150,12154,12247,12253,12305,12307,12308,12312,12315,12328,12330,12333,12338,12356,12368,12373,12376,12494,12517,12519,12526,12532,12533,12537,12555,12690,12696,12701,12704,12707,12709,12710,12721,12723,12727,12730,12879,12888,12894,12897,12900,12904,12927,12930,12935,12939,13094,13108,13110,13112,13114,13125,13129,13131,13136,13183,13265,13283,13446,13455,13458,13609,13611,13617,13620,13661,13672, +chr19 47516962 47536525 m84008_230107_003043_s1/80221888/ccs 219,413,625,827,1029,1273,1443,1655,1870,2209,2412,2592,2799,2980,3187,3613,3849,4033,4385,4555,4762,4951,5107,5361,5550,5719,5936,6090,6290,6477,6677,6878,7087,7225,7420,7577,7736,7911,8070,8263,8464,8698,8874,9192,9314,9513,9707,9919,10128,10315,10543,10723,10920,11093,11265,11430,11641,11800,12013,12236,12418,12610,12812,13019,13185,13401,13607,13976,14195,14313,14584,14776,14962,15281,15501,15730,15916,16070,16230,16384,16553,16755,16990,17159,17336,17506,17681,17900,18101,18271,18391,18681,18877,19039,19235, 119,101,125,144,122,101,130,131,292,100,101,136,151,138,124,103,77,126,111,163,160,155,139,117,138,103,106,157,147,199,120,129,113,145,101,126,129,93,130,168,143,109,285,121,149,153,130,142,151,159,116,134,142,124,127,147,90,108,102,98,108,102,112,122,150,130,96,118,97,150,91,111,249,109,117,81,114,123,147,129,90,132,116,136,123,116,160,120,114,119,172,120,117,132,129, 217,338,514,750,971,1151,1374,1573,1786,2162,2309,2513,2728,2950,3118,3311,3716,3926,4159,4496,4718,4922,5106,5246,5478,5688,5822,6042,6247,6437,6676,6797,7007,7200,7370,7521,7703,7865,8004,8200,8431,8607,8807,9159,9313,9463,9666,9837,10061,10279,10474,10659,10857,11062,11217,11392,11577,11731,11908,12115,12334,12526,12712,12924,13141,13335,13531,13703,14094,14292,14463,14675,14887,15211,15390,15618,15811,16030,16193,16377,16513,16643,16887,17106,17295,17459,17622,17841,18020,18215,18390,18563,18801,18994,19171,19364, 2,75,111,77,58,122,69,82,84,47,103,79,71,30,69,302,133,107,226,59,44,29,1,115,72,31,114,48,43,40,1,81,80,25,50,56,33,46,66,63,33,91,67,33,1,50,41,82,67,36,69,64,63,31,48,38,64,69,105,121,84,84,100,95,44,66,76,273,101,21,121,101,75,70,111,112,105,40,37,7,40,112,103,53,41,47,59,59,81,56,1,118,76,45,64,84, . . . 216,218,338,363,365,366,370,388,407,412,514,520,522,525,526,529,531,532,538,547,551,554,557,563,566,569,571,576,578,579,582,586,588,590,593,594,596,604,606,608,614,616,618,622,624,750,752,754,760,781,784,788,790,810,812,815,823,826,971,977,981,983,987,994,997,1002,1005,1009,1010,1015,1028,1151,1162,1168,1173,1175,1177,1179,1181,1185,1187,1192,1194,1208,1215,1221,1224,1226,1229,1230,1237,1242,1244,1257,1258,1259,1262,1264,1265,1271,1272,1374,1392,1396,1399,1405,1407,1408,1413,1419,1423,1424,1426,1434,1438,1442,1573,1574,1578,1579,1584,1596,1597,1599,1601,1604,1606,1612,1615,1617,1618,1620,1625,1626,1631,1632,1634,1637,1640,1654,1786,1811,1814,1816,1818,1820,1821,1823,1824,1827,1830,1832,1835,1841,1848,1853,1863,1864,1866,1868,1869,2162,2167,2176,2190,2200,2202,2208,2309,2323,2333,2346,2348,2353,2363,2368,2379,2384,2390,2393,2411,2513,2525,2532,2539,2543,2571,2575,2577,2578,2591,2728,2735,2740,2766,2770,2772,2775,2778,2780,2798,2950,2953,2957,2959,2963,2965,2967,2968,2973,2976,2979,3118,3120,3130,3135,3142,3143,3145,3148,3152,3155,3157,3161,3162,3167,3170,3174,3176,3186,3311,3316,3320,3322,3328,3332,3340,3341,3343,3347,3349,3353,3355,3357,3360,3361,3364,3376,3378,3381,3384,3386,3391,3397,3418,3471,3477,3495,3497,3499,3500,3503,3506,3510,3514,3516,3517,3519,3524,3525,3537,3539,3542,3543,3546,3547,3549,3552,3558,3563,3583,3595,3612,3681,3716,3724,3727,3729,3730,3735,3740,3741,3754,3755,3757,3759,3760,3763,3772,3776,3777,3780,3781,3784,3786,3788,3791,3792,3796,3797,3799,3806,3808,3812,3814,3824,3826,3836,3848,3926,3929,3931,3933,3937,3946,3948,3952,3956,3958,3978,3979,3983,3987,3990,3992,3995,3996,3998,4001,4002,4006,4007,4008,4011,4018,4023,4024,4027,4030,4032,4062,4159,4163,4174,4181,4187,4200,4214,4223,4225,4228,4235,4307,4319,4326,4328,4331,4335,4337,4338,4340,4341,4346,4349,4352,4355,4367,4376,4378,4384,4496,4499,4501,4516,4520,4522,4524,4526,4537,4543,4547,4549,4551,4554,4718,4721,4726,4728,4731,4734,4753,4761,4922,4927,4944,4950,5106,5246,5251,5257,5264,5265,5278,5288,5289,5295,5296,5301,5308,5319,5320,5325,5327,5331,5334,5337,5353,5360,5478,5485,5497,5508,5509,5513,5525,5528,5546,5549,5688,5691,5694,5710,5714,5718,5822,5831,5840,5853,5859,5862,5875,5879,5883,5884,5885,5887,5890,5894,5900,5903,5905,5907,5908,5911,5923,5928,5932,5935,6042,6045,6078,6085,6089,6247,6249,6257,6262,6275,6278,6280,6286,6289,6437,6442,6460,6473,6476,6676,6797,6811,6822,6825,6829,6833,6838,6843,6850,6853,6865,6867,6870,6871,6875,6877,7007,7011,7016,7020,7022,7024,7027,7030,7034,7036,7042,7046,7056,7057,7061,7063,7071,7086,7200,7208,7216,7224,7370,7377,7381,7383,7385,7388,7391,7395,7398,7401,7405,7406,7409,7419,7521,7526,7529,7536,7545,7549,7555,7557,7558,7570,7571,7573,7575,7576,7703,7708,7710,7713,7715,7717,7721,7727,7731,7733,7735,7865,7868,7870,7875,7877,7880,7886,7895,7901,7910,8004,8028,8030,8035,8040,8044,8049,8053,8055,8060,8065,8069,8200,8204,8207,8210,8215,8219,8228,8231,8232,8236,8262,8431,8435,8437,8441,8443,8451,8455,8457,8463,8607,8609,8611,8619,8625,8638,8645,8647,8655,8656,8658,8677,8681,8683,8697,8807,8814,8818,8819,8821,8825,8830,8834,8837,8849,8851,8862,8867,8873,9159,9163,9166,9167,9169,9176,9179,9182,9191,9313,9463,9481,9484,9488,9493,9500,9502,9504,9506,9510,9512,9666,9667,9671,9674,9676,9682,9683,9685,9689,9693,9706,9837,9865,9868,9870,9876,9880,9882,9886,9888,9896,9901,9904,9905,9908,9912,9918,10061,10070,10072,10076,10078,10081,10082,10085,10089,10091,10093,10100,10103,10107,10110,10112,10114,10117,10118,10121,10123,10125,10127,10222,10279,10281,10286,10287,10304,10312,10314,10474,10479,10484,10492,10494,10495,10499,10501,10502,10510,10521,10524,10532,10535,10542,10659,10662,10670,10678,10691,10694,10695,10710,10714,10716,10722,10857,10879,10892,10905,10912,10915,10917,10919,10986,11062,11082,11092,11217,11231,11234,11237,11246,11248,11252,11255,11259,11263,11264,11392,11401,11404,11406,11414,11421,11429,11577,11583,11585,11587,11588,11591,11613,11615,11616,11620,11636,11639,11640,11731,11735,11738,11744,11747,11750,11752,11758,11771,11775,11776,11778,11780,11782,11783,11785,11787,11790,11793,11795,11796,11799,11908,11925,11935,11938,11942,11944,11948,11954,11955,11958,11960,11974,11976,11983,11985,11988,11990,11991,11992,11995,12001,12003,12006,12012,12115,12118,12125,12137,12142,12145,12150,12151,12152,12155,12156,12159,12163,12164,12165,12168,12172,12181,12183,12189,12191,12202,12210,12212,12226,12231,12234,12235,12334,12347,12348,12350,12351,12355,12361,12366,12367,12369,12370,12372,12373,12374,12379,12380,12383,12386,12391,12393,12395,12404,12415,12417,12526,12532,12546,12555,12560,12566,12568,12573,12579,12581,12584,12587,12589,12592,12604,12609,12712,12715,12721,12727,12730,12733,12736,12738,12742,12743,12746,12752,12755,12757,12767,12768,12774,12776,12780,12782,12793,12795,12811,12924,12927,12928,12931,12933,12937,12939,12944,12950,12952,12956,12958,12959,12962,12965,12969,12973,12975,12991,12997,13000,13009,13010,13018,13141,13146,13148,13149,13153,13161,13164,13168,13174,13181,13184,13335,13338,1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. . . 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+chr19 47518445 47532680 m84039_230401_031619_s3/104336502/ccs 148,280,476,653,788,912,1073,1575,1763,2129,2455,2664,2847,3019,3221,3401,3592,3815,3995,4176,4482,4658,4829,5067,5276,5472,5848,6028,6243,6421,6623,6797,6948,7128,7266,7460,7722,7884,8083,8665,8899,9077,9257,9649,10189,10417,10575,10988,11383,11560,12116,12298,12444,12624,12794,13347,13525,13881,14065, 89,120,89,91,109,109,94,132,130,188,84,116,108,145,86,120,123,130,107,85,110,101,130,120,112,122,115,126,104,95,106,146,179,134,155,142,103,116,110,128,124,117,137,105,141,100,100,96,128,123,103,122,117,134,119,103,112,131,99, 100,237,400,565,744,897,1021,1167,1707,1893,2317,2539,2780,2955,3164,3307,3521,3715,3945,4102,4261,4592,4759,4959,5187,5388,5594,5963,6154,6347,6516,6729,6943,7127,7262,7421,7602,7825,8000,8193,8793,9023,9194,9394,9754,10330,10517,10675,11084,11511,11683,12219,12420,12561,12758,12913,13450,13637,14012, 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,13168,13171,13176,13332,13334,13342,13346,13347,13349,13358,13363,13364,13366,13370,13373,13377,13381,13387,13392,13397,13399,13400,13404,13406,13412,13419,13532,13569,13576,13580,13584,13588,13589,13591,13593,13596,13601,13609,13611,13613,13787,13792,13802,13808,13956,13962,13966,13973,13975,13979,13981,13985,13990,14000,14160,14166,14170,14178,14188,14317,14321,14323,14328,14330,14333,14337,14338,14341,14343,14347,14350,14352,14353,14354,14357,14359,14361,14368,14372,14374,14375,14377,14378,14380,14382,14384,14386,14389,14393,14394,14398,14400,14404,14407,14409,14413,14417,14419,14421,14428,14431,14442,14564,14587,14599,14600,14609,14612,14615,14626,14628,14635,14776,14777,14788,14791,14796,14807,14948,14954,14968,14971,14979,14981,14983,14988,14995,14998,15000,15163,15165,15169,15171,15173,15176,15179,15183,15189,15191,15193,15197,15200,15205,15342,15352,15356,15358,15361,15363,15365,15368,15372,15373,15395,15547,15548,15574,15579,15581,15750,15752,15753,15756,15758,15762,15764,15769,15908,15913,15916,15919,15928,15930,15931,15933,15945,15952,15956,15960,15963,15965,15967,15972,15975,15978,15982,15984,16109,16112,16115,16118,16120,16122,16125,16134,16140,16144,16150,16156,16161,16319,16321,16326,16347,16350,16511,16514,16516,16518,16522,16531,16533,16534,16539,16543,16546,16548,16549,16551,16554,16557,16559,16562,16567,16568,16574,16578,16584,16592,16595,16599,16743,16744,16749,16754,16763,16766,16772,16775,16778,16780,16791,16925,16926,16928,16933,16934,16947,16948,16949,16950,16952,16956,16959,16961,16962,16964,16966,16969,16970,16972,16973,16975,16977,16978,16982,16983,16985,16987,16990,16992,17002,17142,17156,17161,17164,17166,17173,17187,17192,17194,17200,17210,17356,17359,17362,17383,17552,17555,17561,17564,17574,17577,17730,17734,17739,17741,17746,17749,17901,17904,17928,17930,17935,17937,18080,18083,18087,18090,18092,18094,18097,18100,18102,18105,18109,18115,18117,18118,18120,18122,18124,18126,18129,18130,18132,18134,18161,18168,18294,18298,18304,18307,18313,18322,18331,18332,18336,18339,18363,18367,18372,18512,18517,18518,18522,18525,18537,18539,18543,18549,18581,18701,18707,18710,18720,18722,18725,18726,18733,18736,18739,18741,18744,18748,18757,18760,18765,18769,18770,18914,18932,18934,18936,18938,18965,18967,18969,18971,18973,18978,18980,18984,18988,19000,19108,19118,19124,19127,19132,19137,19139,19147,19149,19153,19157,19160,19166,19168,19173,19176,19179,19181,19182,19185,19192,19305,19345,19348,19350,19351,19355,19366,19369, +chr19 47518754 47532290 m84008_230107_003043_s1/9245284/ccs 116,295,490,693,861,1035,1200,1405,1645,1818,2026,2210,2371,2570,2779,2973,3157,3343,3549,3726,4547,4753,4939,5084,5333,5550,5685,5886,6060,6249,6424,6602,6810,6991,7161,7384,7559,7760,7966,8178,8362,8774,8945,9135,9329,9475,9660,9856,10105,10287,10487,10663,10865,11072,11269,11473,11644,11832,12009,12193,12416,12589,12799,13008,13207, 136,129,168,167,147,151,153,140,118,145,143,125,150,159,150,148,132,165,160,792,139,145,144,169,138,126,138,106,143,140,135,157,125,136,161,121,129,138,135,141,318,135,156,176,134,146,187,130,137,143,119,141,117,137,118,139,124,141,152,134,151,140,139,120,108, 46,252,424,658,860,1008,1186,1353,1545,1763,1963,2169,2335,2521,2729,2929,3121,3289,3508,3709,4518,4686,4898,5083,5253,5471,5676,5823,5992,6203,6389,6559,6759,6935,7127,7322,7505,7688,7898,8101,8319,8680,8909,9101,9311,9463,9621,9847,9986,10242,10430,10606,10804,10982,11209,11387,11612,11768,11973,12161,12327,12567,12729,12938,13128,13315, 70,43,66,35,1,27,14,52,100,55,63,41,36,49,50,44,36,54,41,17,29,67,41,1,80,79,9,63,68,46,35,43,51,56,34,62,54,72,68,77,43,94,36,34,18,12,39,9,119,45,57,57,61,90,60,86,32,64,36,32,89,22,70,70,79,75, . . . 45,71,73,76,78,79,86,92,94,100,104,107,109,112,115,252,274,278,282,294,424,445,452,461,473,475,484,487,489,658,669,673,677,680,682,686,692,860,1008,1027,1032,1034,1160,1186,1199,1353,1380,1400,1404,1545,1554,1558,1564,1566,1568,1571,1572,1574,1587,1589,1592,1595,1597,1598,1600,1602,1608,1613,1617,1618,1619,1624,1629,1639,1641,1644,1763,1786,1794,1800,1803,1805,1806,1812,1814,1817,1963,1968,1971,1995,1999,2003,2010,2025,2169,2189,2190,2194,2198,2201,2203,2209,2335,2343,2347,2364,2366,2370,2521,2527,2528,2532,2539,2548,2552,2557,2560,2563,2566,2569,2729,2731,2733,2735,2737,2740,2741,2749,2754,2758,2760,2762,2773,2778,2929,2932,2934,2939,2942,2953,2964,2972,3121,3136,3143,3156,3208,3289,3295,3318,3338,3339,3342,3508,3520,3524,3527,3531,3532,3537,3539,3545,3546,3548,3709,3721,3725,4518,4522,4524,4528,4539,4546,4686,4688,4691,4695,4713,4732,4734,4748,4750,4752,4898,4916,4925,4930,4938,5083,5253,5256,5261,5272,5274,5282,5286,5294,5296,5297,5309,5313,5314,5321,5323,5325,5329,5331,5332,5471,5477,5484,5492,5498,5501,5503,5512,5518,5549,5676,5684,5823,5827,5835,5839,5842,5845,5847,5850,5854,5856,5860,5863,5865,5867,5875,5879,5885,5992,5997,6001,6003,6005,6011,6013,6017,6021,6023,6033,6036,6039,6044,6049,6055,6059,6203,6205,6208,6225,6227,6230,6245,6248,6389,6392,6394,6397,6400,6413,6423,6559,6569,6571,6579,6580,6597,6601,6759,6766,6769,6786,6792,6807,6809,6935,6937,6943,6946,6948,6951,6953,6954,6955,6957,6959,6962,6963,6966,6969,6974,6978,6988,6990,7127,7129,7132,7136,7142,7144,7146,7150,7152,7154,7158,7160,7322,7347,7366,7377,7383,7505,7511,7532,7536,7558,7688,7702,7712,7716,7718,7720,7724,7726,7758,7759,7898,7902,7906,7921,7927,7928,7932,7937,7938,7942,7948,7951,7955,7963,7965,8101,8109,8110,8114,8118,8124,8130,8147,8149,8160,8177,8319,8323,8325,8330,8334,8336,8338,8343,8361,8680,8684,8688,8691,8693,8696,8698,8705,8713,8716,8720,8724,8725,8730,8733,8735,8738,8741,8744,8746,8749,8756,8762,8767,8773,8909,8913,8923,8925,8929,8931,8937,8942,8944,9101,9107,9112,9119,9130,9132,9134,9311,9314,9322,9328,9463,9467,9470,9474,9621,9640,9644,9646,9648,9652,9659,9847,9854,9855,9986,9993,10005,10010,10017,10021,10025,10026,10028,10031,10034,10036,10039,10042,10045,10047,10056,10058,10065,10067,10069,10071,10082,10085,10089,10091,10095,10098,10104,10169,10242,10255,10257,10258,10260,10270,10273,10278,10280,10286,10430,10432,10441,10444,10447,10449,10456,10458,10460,10461,10463,10465,10466,10468,10473,10475,10481,10482,10486,10517,10606,10610,10626,10632,10638,10642,10645,10646,10653,10656,10660,10662,10804,10821,10824,10828,10829,10833,10843,10846,10849,10851,10853,10857,10864,10982,10983,10989,10991,10997,11000,11002,11004,11008,11010,11014,11020,11026,11034,11038,11051,11058,11060,11062,11064,11071,11167,11209,11212,11215,11219,11224,11225,11246,11248,11250,11253,11255,11258,11268,11387,11396,11400,11405,11407,11408,11414,11434,11436,11438,11440,11442,11444,11448,11450,11452,11458,11462,11465,11467,11472,11612,11615,11617,11622,11631,11643,11768,11770,11775,11779,11790,11793,11800,11810,11818,11823,11831,11973,11986,12005,12008,12161,12164,12168,12178,12192,12327,12341,12343,12345,12347,12353,12355,12358,12359,12362,12373,12376,12389,12393,12409,12415,12567,12588,12729,12740,12751,12757,12759,12765,12768,12769,12788,12798,12938,12945,12948,12953,12959,12962,12965,12966,12970,12973,12977,12979,12982,13007,13128,13131,13140,13145,13148,13152,13154,13157,13159,13160,13167,13170,13174,13177,13178,13182,13198,13202,13206,13315,13333,13363,13365,13369,13376,13383,13389,13522, +chr19 47518837 47521124 m84039_230404_003541_s3/117772968/ccs 152,462,703,898,1085,1407,1628,1783,1955, 278,132,194,127,299,169,154,151,152, 151,430,594,897,1025,1384,1576,1782,1934,2107, 1,32,109,1,60,23,52,1,21,1, . . . 1,2,3,5,24,26,151,430,438,441,449,450,461,594,609,613,616,618,621,623,631,633,646,702,897,1025,1029,1051,1069,1077,1084,1384,1393,1398,1400,1406,1576,1579,1580,1584,1587,1590,1593,1597,1599,1611,1625,1627,1782,1934,1942,1952,1954,2107,2261,2265,2282,2284, +chr19 47518978 47534929 m84039_230401_034725_s4/237175162/ccs 88,217,328,512,715,832,965,1047,1161,1249,1370,1531,1794,1872,2043,2244,2408,2542,2678,2813,3042,3142,3483,4023,4133,4510,4807,4932,5240,5489,5788,5927,6129,6259,6382,6542,6644,6934,7025,7142,7297,7502,7634,7899,7993,8126,8407,8502,8659,8844,8961,9148,9250,9429,9670,9992,10295,10439,10663,10746,11047,11160,11340,11497,11802,11930,12070,12323,12566,12767,12931,13416,13628,13785,13878,13983,14064,14175,14332,14420,14558,14676,14807,15017,15147,15458, 108,110,183,202,116,132,76,109,87,120,156,143,77,170,200,158,133,135,134,228,99,293,522,109,303,296,80,307,171,298,138,157,129,122,157,101,217,86,116,154,204,131,167,93,82,280,94,156,168,101,186,101,162,235,275,162,143,209,82,300,112,114,156,262,127,139,252,175,183,163,484,141,101,92,104,80,110,154,87,135,117,130,170,129,308,383, 87,196,327,511,714,831,964,1041,1156,1248,1369,1526,1674,1871,2042,2243,2402,2541,2677,2812,3041,3141,3435,4005,4132,4436,4806,4887,5239,5411,5787,5926,6084,6258,6381,6539,6643,6861,7020,7141,7296,7501,7633,7801,7992,8075,8406,8501,8658,8827,8945,9147,9249,9412,9664,9945,10154,10438,10648,10745,11046,11159,11274,11496,11759,11929,12069,12322,12498,12749,12930,13415,13557,13729,13877,13982,14063,14174,14329,14419,14555,14675,14806,14977,15146,15455,15841, 1,21,1,1,1,1,1,6,5,1,1,5,120,1,1,1,6,1,1,1,1,1,48,18,1,74,1,45,1,78,1,1,45,1,1,3,1,73,5,1,1,1,1,98,1,51,1,1,1,17,16,1,1,17,6,47,141,1,15,1,1,1,66,1,43,1,1,1,68,18,1,1,71,56,1,1,1,1,3,1,3,1,1,40,1,3,1, . . . 4,5,87,116,196,216,327,511,714,831,964,1041,1046,1156,1160,1248,1369,1526,1530,1674,1697,1759,1767,1768,1793,1871,2042,2243,2402,2405,2407,2541,2677,2812,3041,3141,3435,3443,3482,4005,4019,4022,4071,4132,4436,4440,4466,4495,4509,4806,4887,4888,4931,5239,5411,5428,5488,5787,5926,6036,6084,6128,6258,6323,6335,6381,6439,6539,6541,6643,6861,6929,6933,7020,7024,7102,7141,7296,7501,7575,7633,7801,7836,7837,7875,7876,7878,7898,7992,8075,8079,8115,8125,8406,8501,8658,8827,8843,8945,8960,9147,9249,9412,9416,9428,9664,9669,9945,9991,10046,10154,10163,10234,10241,10262,10266,10294,10364,10365,10438,10648,10662,10745,11046,11159,11238,11274,11277,11280,11337,11339,11430,11496,11759,11762,11769,11801,11897,11929,11989,12069,12322,12498,12565,12626,12749,12762,12766,12930,13415,13557,13621,13627,13683,13729,13731,13742,13744,13746,13759,13770,13784,13877,13982,14063,14174,14329,14331,14419,14469,14555,14557,14614,14675,14806,14977,15016,15146,15455,15457,15841,15888,15941,15942,15943,15944,15946,15947, +chr19 47519260 47541371 m84008_230107_003043_s1/164959873/ccs 99,306,479,686,881,1073,1248,1431,1636,1845,2021,2188,2366,2568,2739,2955,3107,3363,3541,3720,4182,4339,4578,4771,4960,5096,5265,5465,5621,5805,6009,6174,6352,6569,6734,6956,7206,7375,7603,7791,8003,8261,8432,8656,8783,8981,9205,9374,9529,9759,10123,10266,10473,10691,10866,10970,11187,11340,11535,11909,12120,12272,12457,12679,12880,13061,13274,13418,13688,13886,14071,14222,14392,14544,14762,14953,15110,15336,15554,15751,15915,16102,16253,16508,16676,16855,17071,17266,17462,17628,17827,18000,18213,18410,18574,18734,19385,19631,19830,19990,20193,20374,20551,20759,21083,21250,21479,21702, 88,112,129,138,143,132,105,111,117,119,108,117,128,120,127,139,143,139,128,391,115,121,121,121,118,143,142,131,105,112,124,136,132,130,168,146,113,152,132,95,94,134,104,97,154,111,108,134,161,283,118,144,128,144,85,142,123,136,306,118,134,148,160,147,116,148,143,165,83,140,133,97,151,164,119,132,148,148,178,128,155,124,199,153,163,170,123,108,106,144,152,130,104,100,144,645,194,142,126,137,121,157,124,94,154,152,114,97, 187,418,608,824,1024,1205,1353,1542,1753,1964,2129,2305,2494,2688,2866,3094,3250,3502,3669,4111,4297,4460,4699,4892,5078,5239,5407,5596,5726,5917,6133,6310,6484,6699,6902,7102,7319,7527,7735,7886,8097,8395,8536,8753,8937,9092,9313,9508,9690,10042,10241,10410,10601,10835,10951,11112,11310,11476,11841,12027,12254,12420,12617,12826,12996,13209,13417,13583,13771,14026,14204,14319,14543,14708,14881,15085,15258,15484,15732,15879,16070,16226,16452,16661,16839,17025,17194,17374,17568,17772,17979,18130,18317,18510,18718,19379,19579,19773,19956,20127,20314,20531,20675,20853,21237,21402,21593,21799, 119,61,78,57,49,43,78,94,92,57,59,61,74,51,89,13,113,39,51,71,42,118,72,68,18,26,58,25,79,92,41,42,85,35,54,104,56,76,56,117,164,37,120,30,44,113,61,21,69,81,25,63,90,31,19,75,30,59,68,93,18,37,62,54,65,65,1,105,115,45,18,73,1,54,72,25,78,70,19,36,32,27,56,15,16,46,72,88,60,55,21,83,93,64,16,6,52,57,34,66,60,20,84,230,13,77,109,95, . . . 37,47,52,53,56,58,68,73,76,78,79,84,89,95,98,187,208,218,233,237,259,265,268,270,274,280,283,288,290,305,418,434,441,446,473,478,608,620,627,630,634,635,642,644,647,648,650,651,656,658,659,660,665,669,671,673,676,679,681,682,684,685,824,826,830,833,834,848,849,851,854,858,861,863,870,873,878,880,1024,1030,1036,1042,1048,1049,1051,1055,1057,1063,1065,1069,1072,1205,1211,1214,1217,1218,1222,1224,1227,1232,1239,1242,1245,1247,1353,1377,1382,1387,1391,1395,1396,1399,1400,1403,1413,1422,1424,1427,1430,1542,1554,1560,1589,1591,1597,1599,1608,1616,1635,1753,1756,1759,1772,1776,1780,1782,1793,1796,1799,1802,1843,1844,1964,1967,1969,1972,1989,1993,1996,1999,2001,2002,2005,2011,2020,2129,2136,2142,2153,2156,2157,2161,2162,2164,2166,2174,2187,2305,2310,2313,2317,2319,2330,2332,2335,2338,2340,2346,2347,2361,2365,2494,2497,2500,2513,2515,2517,2522,2526,2530,2532,2535,2541,2548,2550,2554,2559,2562,2564,2567,2688,2690,2700,2711,2713,2717,2721,2727,2729,2732,2733,2738,2866,2885,2894,2895,2898,2903,2906,2911,2916,2918,2921,2925,2931,2932,2951,2954,3094,3099,3104,3106,3250,3253,3258,3259,3262,3266,3273,3278,3282,3285,3289,3293,3297,3314,3317,3320,3322,3325,3327,3340,3362,3502,3504,3509,3510,3512,3526,3530,3535,3540,3669,3675,3683,3685,3691,3695,3698,3700,3706,3709,3711,3719,4111,4115,4117,4144,4150,4151,4155,4159,4162,4178,4181,4297,4310,4313,4323,4325,4328,4338,4460,4472,4476,4482,4497,4500,4503,4507,4511,4538,4540,4543,4553,4558,4560,4570,4571,4575,4577,4699,4700,4702,4705,4706,4708,4710,4715,4719,4723,4726,4729,4732,4733,4735,4745,4747,4749,4770,4892,4895,4903,4905,4907,4909,4952,4959,5078,5082,5084,5089,5095,5123,5239,5241,5244,5257,5264,5407,5409,5412,5416,5420,5425,5426,5434,5436,5438,5464,5596,5601,5604,5607,5608,5610,5620,5726,5728,5732,5733,5737,5746,5750,5752,5757,5762,5766,5769,5771,5773,5781,5799,5804,5917,5924,5928,5932,5946,5949,5952,5956,5958,5960,5962,5964,5965,5967,5982,5985,5989,5994,5995,5998,6004,6008,6133,6137,6147,6166,6168,6173,6310,6350,6351,6484,6502,6522,6568,6699,6702,6707,6709,6715,6722,6726,6727,6731,6733,6902,6906,6924,6939,6943,6950,6955,7102,7121,7122,7133,7143,7154,7157,7161,7169,7171,7174,7175,7176,7179,7183,7205,7319,7322,7327,7328,7331,7336,7337,7340,7343,7348,7361,7366,7367,7371,7374,7527,7532,7538,7542,7547,7548,7552,7553,7556,7566,7571,7581,7583,7586,7587,7589,7594,7602,7735,7740,7742,7745,7747,7752,7758,7759,7761,7762,7765,7766,7769,7776,7779,7780,7782,7783,7786,7788,7790,7886,7905,7925,7928,7931,7932,7934,7941,7946,7947,7948,7955,7957,7961,7963,7964,7967,7970,7975,7976,7980,7982,7985,7988,8002,8097,8100,8103,8114,8118,8120,8121,8123,8125,8126,8131,8146,8149,8155,8162,8167,8171,8178,8183,8192,8203,8214,8220,8222,8225,8232,8260,8360,8395,8396,8399,8402,8404,8409,8411,8417,8423,8428,8431,8536,8549,8558,8561,8573,8577,8580,8584,8587,8593,8598,8599,8602,8604,8605,8606,8613,8616,8618,8631,8649,8655,8753,8755,8757,8762,8782,8937,8955,8957,8959,8963,8967,8974,8980,9092,9106,9113,9114,9121,9123,9129,9154,9156,9159,9169,9179,9204,9313,9315,9323,9336,9369,9373,9508,9511,9514,9517,9522,9528,9690,9693,9695,9696,9698,9699,9701,9704,9707,9710,9717,9720,9740,9741,9743,9746,9747,9748,9756,9758,10042,10044,10045,10048,10053,10059,10061,10062,10065,10066,10071,10072,10075,10078,10091,10103,10122,10241,10258,10260,10265,10374,10410,10413,10419,10420,10422,10425,10428,10430,10434,10443,10455,10459,10460,10466,10468,10472,10601,10611,10614,10627,10629,10631,10633,10648,10654,10657,10661,10667,10670,10676,10682,10684,10687,10690,10835,10842,10857,10863,10865,10951,10969,11112,11116,11119,11132,11135,11140,11142,11143,11146,11156,11172,11186,11310,11333,11336,11339,11476,11483,11488,11489,11494,11496,11497,11504,11534,11841,11846,11851,11854,11856,11858,11860,11879,11881,11885,11887,11888,11891,11893,11899,11906,11908,12027,12033,12034,12039,12049,12052,12053,12055,12066,12068,12084,12085,12092,12095,12118,12119,12161,12254,12262,12267,12269,12271,12420,12423,12427,12430,12445,12447,12450,12454,12456,12617,12621,12623,12626,12628,12629,12634,12636,12643,12647,12651,12656,12661,12667,12673,12675,12678,12826,12828,12848,12856,12858,12863,12866,12867,12869,12872,12874,12879,12996,12998,13000,13004,13024,13028,13033,13048,13054,13056,13058,13060,13209,13211,13242,13248,13260,13264,13270,13273,13417,13583,13595,13599,13611,13615,13616,13620,13625,13629,13632,13641,13643,13645,13646,13650,13657,13659,13661,13662,13668,13671,13675,13679,13681,13682,13684,13685,13687,13771,13776,13793,13808,13849,13856,13859,13862,13865,13870,13873,13875,13881,13884,13885,14026,14027,14034,14039,14041,14048,14066,14070,14204,14210,14212,14221,14319,14334,14353,14358,14383,14384,14386,14391,14543,14594,14708,14727,14746,14755,14761,14881,14886,14893,14898,14900,14903,14913,14929,14934,14947,14952,15085,15087,15088,15091,15093,15109,15258,15284,15290,15294,15299,15301,15306,15308,15311,15316,15321,15329,15335,15484,15486,15492,15525,15528,15531,15544,15551,15553,15732,15735,15750,15879,15884,15890,15914,15945,16070,16079,16098,16101,1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+chr19 47519556 47545267 m84008_230107_003043_s1/169083681/ccs 1044,1229,1468,1749,2121,2327,2513,3666,4252,4525,4665,4825,5196,5647,6182,6621,7132,7352,7579,7782,7941,8134,8844,9011,9137,9343,9591,9809,9967,10173,10420,10624,10807,10999,11166,11561,12163,12334,12564,12765,12973,13315,13561,13758,13898,14523,15095,16311,16509,16729,16918,17117,17473,17832,18032,18387,18603,18780,19004,19306,19817,20252,20675,21698,22181,22557,22913,23123,23286,23505,23670,24092,24256,24687,24854,25254, 184,201,268,352,135,135,1140,585,272,139,141,272,371,534,438,483,194,213,164,158,167,700,166,125,166,247,161,157,205,212,203,177,191,161,394,547,137,199,183,182,341,205,135,139,624,571,1213,197,214,188,166,355,358,171,323,182,176,223,284,510,434,148,1022,305,375,256,189,162,218,164,367,148,376,163,306,140, 1012,1228,1430,1736,2101,2256,2462,3653,4251,4524,4664,4806,5097,5567,6181,6620,7104,7326,7565,7743,7940,8108,8834,9010,9136,9303,9590,9752,9966,10172,10385,10623,10801,10998,11160,11560,12108,12300,12533,12747,12947,13314,13520,13696,13897,14522,15094,16308,16508,16723,16917,17084,17472,17831,18003,18355,18569,18779,19003,19288,19816,20251,20400,21697,22003,22556,22813,23102,23285,23504,23669,24037,24240,24632,24850,25160,25394, 32,1,38,13,20,71,51,13,1,1,1,19,99,80,1,1,28,26,14,39,1,26,10,1,1,40,1,57,1,1,35,1,6,1,6,1,55,34,31,18,26,1,41,62,1,1,1,3,1,6,1,33,1,1,29,32,34,1,1,18,1,1,275,1,178,1,100,21,1,1,1,55,16,55,4,94,96, . . . 1012,1029,1038,1043,1228,1430,1437,1467,1736,1742,1745,1748,2101,2107,2110,2120,2256,2260,2265,2268,2292,2293,2298,2299,2321,2326,2462,2469,2482,2506,2512,3653,3657,3662,3665,4251,4524,4664,4806,4824,5097,5147,5195,5567,5579,5606,5644,5646,6181,6620,7104,7131,7326,7351,7565,7578,7743,7776,7781,7904,7940,8108,8133,8834,8837,8843,9010,9136,9234,9303,9342,9590,9752,9757,9758,9789,9808,9966,10172,10385,10419,10623,10801,10804,10806,10998,11160,11165,11560,12108,12118,12121,12129,12135,12138,12142,12162,12300,12303,12307,12309,12312,12315,12333,12533,12536,12540,12549,12552,12553,12555,12561,12563,12747,12757,12764,12947,12972,13314,13520,13522,13523,13537,13541,13547,13550,13553,13560,13696,13704,13709,13711,13729,13733,13739,13743,13747,13751,13755,13757,13897,14522,15094,16308,16310,16508,16723,16728,16917,17084,17094,17111,17116,17472,17831,18003,18005,18031,18355,18386,18569,18575,18579,18587,18589,18595,18602,18779,19003,19288,19291,19305,19816,20251,20400,20421,20423,20427,20431,20435,20437,20439,20442,20457,20462,20467,20470,20472,20488,20532,20536,20579,20581,20614,20641,20643,20652,20668,20671,20674,21697,22003,22004,22033,22038,22041,22072,22095,22100,22102,22129,22132,22151,22153,22157,22169,22174,22176,22180,22556,22813,22883,22886,22889,22891,22893,22909,22912,23102,23122,23285,23504,23669,24037,24039,24047,24054,24061,24069,24071,24087,24091,24240,24243,24247,24254,24255,24632,24686,24850,24853,25160,25162,25171,25179,25184,25208,25211,25213,25217,25225,25239,25244,25249,25250,25253,25394,25399,25402,25404,25405,25450,25463,25468,25474,25477,25478,25481,25484,25490, 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38,108,53,80,67,107,240,48,224,21,91,21,36,58,36,13,19,24,84,1,57,55,54,32,34,96,89,24,5,59,46,92,1,93,104,58,117,127,14,41,89,47,25,38,77,64,84,118,122,38,50,53,50,74,75,22, . . . 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From 6383b2815964b880f5ad5fcffe0d12b5dd609c7e Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Tue, 19 May 2026 18:06:44 -0600 Subject: [PATCH 22/24] refactor: rewrite basemod I/O against the MolecularAnnotations spec MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Replace the BaseMods/BaseMod struct pair with parse_mm_ml_into_ma and write_mm_ml, which read and write MM/ML directly against a shared MolecularAnnotations object. Each call's MM group header (e.g. "A+a", "T-a", "N+a") is stored verbatim on Annotation.name so it round-trips through the writer byte-for-byte — including non-standard encodings like N+a that the old path silently normalized to A+a;T-a. --- src/subcommands/ddda_to_m6a.rs | 23 +-- src/subcommands/predict_m6a.rs | 19 +-- src/utils/basemods.rs | 256 ++++++++++++++++----------------- src/utils/ma_io.rs | 6 +- tests/basemods.rs | 246 ++++++++++++++++--------------- 5 files changed, 291 insertions(+), 259 deletions(-) diff --git a/src/subcommands/ddda_to_m6a.rs b/src/subcommands/ddda_to_m6a.rs index 3274d244..8751501a 100644 --- a/src/subcommands/ddda_to_m6a.rs +++ b/src/subcommands/ddda_to_m6a.rs @@ -21,18 +21,21 @@ pub fn ddda_to_m6a_record(record: &mut Record, _opts: &DddaToM6aOptions) { forward_seq = revcomp(&forward_seq); } - // get the bases that will be modified - let mut modified_bases_forward: Vec = vec![]; + // Positions to mark as m6a, paired with the canonical post-Y/R base + // they land on (T for Y, A for R) in molecular orientation. We carry + // the base alongside the position so the write path knows the right + // MM group header without re-indexing the (possibly revcomp'd) seq. + let mut modified_bases_forward: Vec<(u32, u8)> = vec![]; let mut y_count = 0; let mut r_count = 0; let mut new_forward_seq = vec![]; for (idx, bp) in forward_seq.iter().enumerate() { if bp == &b'Y' { - modified_bases_forward.push(idx as u32); + modified_bases_forward.push((idx as u32, b'T')); y_count += 1; new_forward_seq.push(b'T'); } else if bp == &b'R' { - modified_bases_forward.push(idx as u32); + modified_bases_forward.push((idx as u32, b'A')); r_count += 1; new_forward_seq.push(b'A'); } else { @@ -57,9 +60,9 @@ pub fn ddda_to_m6a_record(record: &mut Record, _opts: &DddaToM6aOptions) { // Load existing MM/ML into a MolecularAnnotations, drop any // pre-existing m6a (we're replacing it with the Y/R-derived calls), - // then append the synthesized m6a and write back. write_mm_ml - // reconstructs the canonical group (A+a vs T-a) from the now-replaced - // forward seq. + // then append the synthesized m6a and write back. Each call gets + // its canonical MM group header (A+a or T-a) tagged via + // `canonical_header` so `write_mm_ml` can emit the right groups. let mut annot = MolecularAnnotations::from_record(record); basemods::parse_mm_ml_into_ma(record, &mut annot, 0, 0); annot @@ -67,8 +70,10 @@ pub fn ddda_to_m6a_record(record: &mut Record, _opts: &DddaToM6aOptions) { .retain(|t| t.name != basemods::M6A_TYPE); let qspec = "Q".parse::().expect("Q parses"); let t = annot.add_annotation_type(basemods::M6A_TYPE, qspec); - for pos in modified_bases_forward { - t.add(pos, 1, Strand::Forward, vec![255], None); + for (pos, base) in modified_bases_forward { + let header = basemods::canonical_header(basemods::M6A_TYPE, base) + .expect("ddda_to_m6a only places calls on A/T bases"); + t.add(pos, 1, Strand::Forward, vec![255], Some(header.to_string())); } basemods::write_mm_ml(record, &annot); } diff --git a/src/subcommands/predict_m6a.rs b/src/subcommands/predict_m6a.rs index 27c7a98f..4ebf1fc3 100644 --- a/src/subcommands/predict_m6a.rs +++ b/src/subcommands/predict_m6a.rs @@ -234,29 +234,32 @@ where None => continue, }; // Iterate over A and then T basemods, collecting their forward - // positions + ML qualities into a single sorted m6a list. - let mut m6a_calls: Vec<(u32, u8)> = Vec::new(); - for data in &[a_data, t_data] { + // positions + ML qualities into a single sorted m6a list. Each + // call carries its canonical MM group header — A-base calls + // are "A+a", T-base calls are "T-a" — so `write_mm_ml` can + // emit them under the correct group. + let mut m6a_calls: Vec<(u32, u8, &'static str)> = Vec::new(); + for (data, header) in [(a_data, "A+a"), (t_data, "T-a")] { let cur_predict_en = cur_predict_st + data.count; let cur_predictions = &predictions[cur_predict_st..cur_predict_en]; cur_predict_st += data.count; let (poss, quals) = opts.basemod_from_ml(record, cur_predictions, &data.positions, &data.base_mod); - m6a_calls.extend(poss.into_iter().zip(quals)); + m6a_calls.extend(poss.into_iter().zip(quals).map(|(p, q)| (p, q, header))); } if !m6a_calls.is_empty() { - m6a_calls.sort_by_key(|&(p, _)| p); + m6a_calls.sort_by_key(|&(p, _, _)| p); let qspec = "Q" .parse::() .expect("Q parses"); let t = annot.add_annotation_type(basemods::M6A_TYPE, qspec); - for (pos, qual) in &m6a_calls { + for (pos, qual, header) in &m6a_calls { t.add( *pos, 1, molecular_annotation::Strand::Forward, vec![*qual], - None, + Some(header.to_string()), ); } } @@ -267,7 +270,7 @@ where // Compute nucleosomes + MSPs from the forward m6a positions // and append them to the same MA object we just built up. let modified_bases_forward: Vec = - m6a_calls.iter().map(|&(p, _)| p as i64).collect(); + m6a_calls.iter().map(|&(p, _, _)| p as i64).collect(); nucleosome::add_nucleosomes_to_annotations( record, &mut annot, diff --git a/src/utils/basemods.rs b/src/utils/basemods.rs index f3161130..09c033ff 100644 --- a/src/utils/basemods.rs +++ b/src/utils/basemods.rs @@ -1,22 +1,36 @@ //! MM/ML BAM tag I/O for fiberseq base modifications. //! +//! Scope: m6A (`"a"`) and 5mC (`"m"`) only. MM groups carrying any other +//! mod-type code are logged and skipped on parse — fibertools-rs's typed +//! API only exposes these two canonical fiberseq modifications. Adding a +//! new canonical mod (e.g. 5hmC, `"h"`) is a ~5-line change across +//! [`ma_type_for_mod_code`], [`is_basemod_type`], and +//! [`canonical_header`]. +//! //! Read path: `parse_mm_ml_into_ma` parses a record's MM/ML tags directly -//! into a [`MolecularAnnotations`] as annotation types. No intermediate -//! `BaseMods` struct — the spec object is the sole in-memory -//! representation. +//! into a [`MolecularAnnotations`]. Each call's MM group header (e.g. +//! `"A+a"`, `"T-a"`, `"N+a"`, `"C+m"`) is stored verbatim on +//! [`Annotation::name`], so headers round-trip through `write_mm_ml` +//! byte-for-byte — including non-standard encodings like `N+a` that the +//! old write path silently normalized. //! -//! Mod-type dispatch (exact match on the MM mod_type code): -//! - `"a"` (any group, e.g. `A+a`, `T-a`, `N+a`) → `m6a` type. -//! - `"m"` (any group, e.g. `C+m`, `G+m`) → `cpg` type. -//! - any other code (`C+h`, `T+f`, `C+ac`, ChEBI numeric IDs, etc.) → its -//! own annotation type named verbatim after the MM group header (e.g. -//! `"C+h"`). Calls round-trip through `write_mm_ml` unchanged. +//! Write path: `write_mm_ml` emits MM/ML by reading each annotation's +//! `name` directly. Basemod annotations *must* have `name` set; the +//! parser sets it from the MM tag, and programmatic producers +//! (`predict_m6a`, `ddda_to_m6a`) set it via [`canonical_header`]. A +//! missing `name` on a basemod annotation is a bug and triggers a panic. //! -//! Write path: `write_mm_ml` emits MM/ML from a [`MolecularAnnotations`]. -//! Canonical types (`m6a`, `cpg`) have their groups reconstructed from -//! the forward sequence (`A`→`A+a`, `T`→`T-a`, `C`→`C+m`, `G`→`G+m`). -//! Non-canonical types stored under a valid MM group name are emitted -//! verbatim under that header. +//! MA-tag policy: `ma_io::write_annotations` *strips* `m6a` and `cpg` +//! before MA serialization — MM/ML is the on-disk source of truth, and +//! the MA tag set holds nuc/msp/fire only. This is a policy choice +//! (avoid duplication, single source of truth), not a correctness one. +//! Lifting the strip would expose basemods to MA-native consumers (e.g. +//! the `molecular_annotation` library) at the cost of ~2× disk for +//! basemod data and a "MM/ML wins on read" invariant. The matched +//! invariant on the read side is the idempotency wipe in +//! [`parse_mm_ml_into_ma`]: it discards any basemod-typed annotations +//! present in `annot` before parsing MM/ML, so an MA tag set that +//! wrongly contained basemods doesn't get merged on top of MM/ML. use crate::utils::bio_io::*; use bio::alphabets::dna::revcomp; @@ -31,6 +45,40 @@ use std::collections::BTreeMap; pub const M6A_TYPE: &str = "m6a"; pub const CPG_TYPE: &str = "cpg"; +/// Map an MM mod-type code (the trailing alpha/digits in a group like +/// `A+a`) to a fibertools MA type name. Unknown codes return `None` and +/// the caller skips the group. +fn ma_type_for_mod_code(code: &str) -> Option<&'static str> { + match code { + "a" => Some(M6A_TYPE), + "m" => Some(CPG_TYPE), + _ => None, + } +} + +/// True for annotation types whose on-disk source of truth is MM/ML. +/// Used to gate idempotency wipes (parse), MA-tag emission (ma_io), and +/// MM/ML emission (write). +pub fn is_basemod_type(name: &str) -> bool { + matches!(name, M6A_TYPE | CPG_TYPE) +} + +/// Header for a canonical basemod call landing on `base` (read in +/// forward-strand orientation). Returns `&'static str` for the four +/// possible canonical headers; `None` if the (type, base) pair isn't a +/// canonical fiberseq combination. Used by programmatic producers +/// (`predict_m6a`, `ddda_to_m6a`) to label calls so `write_mm_ml` can +/// emit them under the right MM group. +pub fn canonical_header(type_name: &str, base: u8) -> Option<&'static str> { + match (type_name, base) { + (M6A_TYPE, b'A') => Some("A+a"), + (M6A_TYPE, b'T') => Some("T-a"), + (CPG_TYPE, b'C') => Some("C+m"), + (CPG_TYPE, b'G') => Some("G+m"), + _ => None, + } +} + lazy_static! { // MM:Z:([ACGTUN][-+]([A-Za-z]+|[0-9]+)[.?]?(,[0-9]+)*;)* static ref MM_RE: Regex = @@ -39,30 +87,27 @@ lazy_static! { /// Parse the MM/ML tags of `record` directly into `annot`. Positions are /// stored in molecular (forward) orientation as 1bp annotations with a -/// single `Q` quality score per call. +/// single `Q` quality score per call. Each annotation's `name` carries +/// the verbatim MM group header it was parsed from (e.g. `"A+a"`, +/// `"T-a"`, `"N+a"`, `"C+h"`), so [`write_mm_ml`] round-trips it +/// unchanged. /// /// Per-call filtering: /// - calls with ML quality < `min_ml_score` are dropped. /// - calls within `strip_at_ends` bp of either end of the forward /// sequence are dropped (no-op if `strip_at_ends <= 0`). /// -/// Dispatch by MM mod_type (exact-match): +/// Dispatch by MM mod_type (exact-match) controls the MA type bucket: /// - `"a"` → [`M6A_TYPE`] (collapses `A+a`, `T-a`, `N+a`, etc.) /// - `"m"` → [`CPG_TYPE`] (collapses `C+m`, `G+m`, etc.) /// - any other → annotation type named verbatim after the MM group -/// header (e.g. `"C+h"` for 5hmC, `"C+ac"` for acetyl). [`write_mm_ml`] -/// emits these unchanged. -/// -/// Idempotent: any pre-existing `m6a` / `cpg` / non-canonical basemod -/// types on `annot` are dropped first, so MM/ML always overwrites in- -/// memory state rather than appending. This guards against (a) repeated -/// calls on the same `annot`, and (b) malformed inputs that wrongly -/// emit `m6a` into the MA tag set in addition to MM/ML. +/// header (e.g. `"C+h"` for 5hmC, `"C+ac"` for acetyl). /// -/// For canonical `m6a` / `cpg`, MM's per-group `(canonical_base, -/// strand_sign)` is reconstructed from the forward sequence at write -/// time, so input encodings like `N+a` are normalized to `A+a` / `T-a` -/// on output. +/// Idempotent: any pre-existing basemod-shaped types on `annot` are +/// dropped first (see [`is_basemod_type`]), so MM/ML always overwrites +/// in-memory state rather than appending. This guards against (a) +/// repeated calls on the same `annot`, and (b) malformed inputs that +/// wrongly emit `m6a` into the MA tag set in addition to MM/ML. pub fn parse_mm_ml_into_ma( record: &bam::Record, annot: &mut MolecularAnnotations, @@ -73,9 +118,7 @@ pub fn parse_mm_ml_into_ma( // basemod-shaped type that may already be in `annot` (from a prior // pass, an MA-tag leak in a third-party producer, or repeated calls) // is discarded so we don't silently append on top of stale data. - annot - .annotation_types - .retain(|t| t.name != M6A_TYPE && t.name != CPG_TYPE && !is_valid_mm_header(&t.name)); + annot.annotation_types.retain(|t| !is_basemod_type(&t.name)); let ml_tag = get_u8_tag(record, b"ML"); let Ok(Aux::String(mm_text)) = record.aux(b"MM") else { @@ -92,20 +135,17 @@ pub fn parse_mm_ml_into_ma( let strip = strip_at_ends.max(0) as usize; let upper = seq_len.saturating_sub(strip); - let mut m6a_calls: Vec<(u32, u8)> = Vec::new(); - let mut cpg_calls: Vec<(u32, u8)> = Vec::new(); - // Non-canonical groups: keyed by their MM header string (e.g. "C+h"). - let mut other_calls: BTreeMap> = BTreeMap::new(); + // Per-call accumulator: (ma_type, verbatim_header, pos, qual). The + // header is owned because the regex capture's lifetime ends at the + // next iteration; the ma_type is a static interned name. + let mut calls: Vec<(&'static str, String, u32, u8)> = Vec::new(); let mut num_mods_seen = 0usize; for cap in MM_RE.captures_iter(mm_text) { + // Capture group 2 is the full `base+strand+modtype` prefix — + // exactly the MM group header (e.g. "A+a", "T-a", "C+h", "N+12"). + let header = cap.get(2).map_or("", |m| m.as_str()).to_string(); let mod_base = cap.get(3).map(|m| m.as_str().as_bytes()[0]).unwrap(); - let strand_sign = cap - .get(4) - .map_or("+", |m| m.as_str()) - .chars() - .next() - .unwrap_or('+'); let mod_type_str = cap.get(5).map_or("", |m| m.as_str()).to_string(); let mod_dists_str = cap.get(6).map_or("", |m| m.as_str()); let mod_dists: Vec = mod_dists_str @@ -177,18 +217,18 @@ pub fn parse_mm_ml_into_ma( positions.truncate(resolved); let group_quals = &group_quals[..resolved]; - // Filter + dispatch by mod_type. The canonical fiberseq codes are - // *exactly* "a" (m6A) and "m" (5mC) — any longer alpha mod type - // (`ac` acetyl, `pT` etc.) or ChEBI numeric ID is non-canonical - // and stored under its verbatim MM header so it round-trips - // exactly through write_mm_ml. - let bucket: &mut Vec<(u32, u8)> = match mod_type_str.as_str() { - "a" => &mut m6a_calls, - "m" => &mut cpg_calls, - _ => { - let key = format!("{}{}{}", mod_base as char, strand_sign, mod_type_str); - other_calls.entry(key).or_default() - } + // Canonical "a"/"m" → m6a/cpg; everything else is dropped with a + // warning. The per-call header travels into `Annotation.name` + // so write_mm_ml re-emits it verbatim (preserving A+a vs T-a, + // and non-standard encodings like N+a, on round-trip). + let Some(ma_type) = ma_type_for_mod_code(&mod_type_str) else { + log::warn!( + "MM/ML parser: unsupported mod-type {:?} (group {:?}); skipping {} call(s)", + mod_type_str, + header, + resolved, + ); + continue; }; for (pos, &qual) in positions.iter().copied().zip(group_quals) { if qual < min_ml_score { @@ -198,7 +238,7 @@ pub fn parse_mm_ml_into_ma( if strip > 0 && (p < strip || p >= upper) { continue; } - bucket.push((pos, qual)); + calls.push((ma_type, header.clone(), pos, qual)); } } @@ -210,39 +250,43 @@ pub fn parse_mm_ml_into_ma( ); } - add_calls(annot, M6A_TYPE, &mut m6a_calls); - add_calls(annot, CPG_TYPE, &mut cpg_calls); - for (name, mut calls) in other_calls { - add_calls(annot, &name, &mut calls); + // Group flat call list by MA type so each type's annotations land + // in the correct bucket on the spec object. Within a type, calls + // are sorted by position — even though different MM group headers + // (e.g. A+a and T-a) interleave under m6a, each call's `name` + // keeps its header for the write path. + let mut by_type: BTreeMap<&'static str, Vec<(String, u32, u8)>> = BTreeMap::new(); + for (ma_type, header, pos, qual) in calls { + by_type.entry(ma_type).or_default().push((header, pos, qual)); + } + for (ma_type, mut group) in by_type { + group.sort_by_key(|(_, p, _)| *p); + add_calls(annot, ma_type, &group); } } -fn add_calls(annot: &mut MolecularAnnotations, name: &str, calls: &mut [(u32, u8)]) { +fn add_calls(annot: &mut MolecularAnnotations, name: &str, calls: &[(String, u32, u8)]) { if calls.is_empty() { return; } - calls.sort_by_key(|(p, _)| *p); let qspec = "Q".parse::().expect("Q parses"); let t = annot.add_annotation_type(name, qspec); - for &(pos, qual) in calls.iter() { - t.add(pos, 1, Strand::Forward, vec![qual], None); + for (header, pos, qual) in calls { + t.add(*pos, 1, Strand::Forward, vec![*qual], Some(header.clone())); } } /// Emit MM/ML tags from `annot` onto `record`. Existing `MM` and `ML` /// aux are removed first. /// -/// Sources: -/// - [`M6A_TYPE`] / [`CPG_TYPE`] — canonical fiberseq types. MM groups -/// reconstructed from the forward sequence (`A`→`A+a`, `T`→`T-a`, -/// `C`→`C+m`, `G`→`G+m`). Calls landing on an unexpected base are -/// emitted under that base with `+` strand and a warning. -/// - Any other annotation type whose name is a valid MM group header -/// (e.g. `"C+h"`, `"N+a"`, `"T+12"`) is emitted verbatim under that -/// header. Skip counts are computed against the named base (`N` -/// counts every position). -/// - All other annotation types (`msp`, `nuc`, `fire`, etc.) are -/// skipped — they are not base modifications. +/// Header for each call is read directly from [`Annotation::name`]. +/// Every basemod annotation must carry a header — the parser sets it +/// from the MM tag and programmatic producers set it via +/// [`canonical_header`]. A `None` `name` on a basemod annotation is a +/// caller bug and panics. +/// +/// Non-basemod annotation types (`msp`, `nuc`, `fire`, etc.) are +/// skipped — see [`is_basemod_type`] for the gate. /// /// MM groups are emitted in deterministic (lexicographic header) order. pub fn write_mm_ml(record: &mut bam::Record, annot: &MolecularAnnotations) { @@ -252,56 +296,24 @@ pub fn write_mm_ml(record: &mut bam::Record, annot: &MolecularAnnotations) { record.seq().as_bytes() }; - // header (e.g. "A+a", "C+h") → Vec<(pos, qual)>. BTreeMap gives + // header (e.g. "A+a", "T-a") → Vec<(pos, qual)>. BTreeMap gives // deterministic emission order. let mut groups: BTreeMap> = BTreeMap::new(); - // Canonical types: reconstruct (base, strand) per call from forward seq. - for (type_name, mod_type_char, canonical) in [ - (M6A_TYPE, 'a', &[(b'A', '+'), (b'T', '-')] as &[(u8, char)]), - (CPG_TYPE, 'm', &[(b'C', '+'), (b'G', '+')] as &[(u8, char)]), - ] { - let Some(t) = annot.get_type(type_name) else { - continue; - }; - for a in &t.annotations { - let seq_base = forward_seq.get(a.start as usize).copied().unwrap_or(b'N'); - let (group_base, group_strand) = canonical - .iter() - .find(|&&(b, _)| b == seq_base) - .copied() - .unwrap_or_else(|| { - log::warn!( - "{} call at pos {} on unexpected base {:?}; emitting as {}{}{}", - type_name, - a.start, - seq_base as char, - seq_base as char, - '+', - mod_type_char, - ); - (seq_base, '+') - }); - let header = format!("{}{}{}", group_base as char, group_strand, mod_type_char); - let qual = a.qualities.first().copied().unwrap_or(0); - groups.entry(header).or_default().push((a.start, qual)); - } - } - - // Non-canonical types: name is the MM group header (e.g. "C+h"). - for t in annot.annotation_types.iter() { - if t.name == M6A_TYPE || t.name == CPG_TYPE { - continue; - } - if !is_valid_mm_header(&t.name) { + for t in &annot.annotation_types { + if !is_basemod_type(&t.name) { continue; } for a in &t.annotations { + let header = a.name.clone().unwrap_or_else(|| { + panic!( + "basemod annotation in type {:?} at pos {} has no MM group header; \ + producers must set Annotation.name via canonical_header()", + t.name, a.start, + ) + }); let qual = a.qualities.first().copied().unwrap_or(0); - groups - .entry(t.name.clone()) - .or_default() - .push((a.start, qual)); + groups.entry(header).or_default().push((a.start, qual)); } } @@ -340,15 +352,3 @@ pub fn write_mm_ml(record: &mut bam::Record, annot: &MolecularAnnotations) { .expect("push ML tag"); } -/// True if `name` looks like an MM group header: one canonical base -/// (`ACGTUN`), a strand sign, then a non-empty alphanumeric mod type. -fn is_valid_mm_header(name: &str) -> bool { - let bytes = name.as_bytes(); - if bytes.len() < 3 { - return false; - } - let base_ok = matches!(bytes[0], b'A' | b'C' | b'G' | b'T' | b'U' | b'N'); - let strand_ok = bytes[1] == b'+' || bytes[1] == b'-'; - let mod_ok = bytes[2..].iter().all(|b| b.is_ascii_alphanumeric()); - base_ok && strand_ok && mod_ok -} diff --git a/src/utils/ma_io.rs b/src/utils/ma_io.rs index f623ce1c..d0f6a9ca 100644 --- a/src/utils/ma_io.rs +++ b/src/utils/ma_io.rs @@ -137,8 +137,10 @@ fn read_legacy_nuc_msp(record: &bam::Record) -> Result { /// the MA tag set. pub fn write_annotations(record: &mut bam::Record, annot: &MolecularAnnotations) { // Base modifications (`m6a`, `cpg`) belong in MM/ML — never in the - // MA tag set. Drop them before serialization. See the module docs - // for the on-disk source-of-truth split. + // MA tag set. Drop them before serialization. This is a policy + // choice (single on-disk source of truth), not a correctness one; + // see the basemods module docs for the tradeoff if you want to + // expose basemods in MA tags for downstream MA-native consumers. let mut for_ma = annot.clone(); for_ma.annotation_types.retain(|t| { t.name != crate::utils::basemods::M6A_TYPE && t.name != crate::utils::basemods::CPG_TYPE diff --git a/tests/basemods.rs b/tests/basemods.rs index d633e647..5865d5a9 100644 --- a/tests/basemods.rs +++ b/tests/basemods.rs @@ -1,6 +1,8 @@ use env_logger::{Builder, Target}; -use fibertools_rs::utils::basemods::{parse_mm_ml_into_ma, write_mm_ml, CPG_TYPE, M6A_TYPE}; -use molecular_annotation::MolecularAnnotations; +use fibertools_rs::utils::basemods::{ + canonical_header, parse_mm_ml_into_ma, write_mm_ml, CPG_TYPE, M6A_TYPE, +}; +use molecular_annotation::{MolecularAnnotations, QualitySpec, Strand}; use rust_htslib::bam::record::Aux; use rust_htslib::{bam, bam::Read}; @@ -29,134 +31,47 @@ fn test_mods_round_trip() { } } -/// Non-canonical MM groups (e.g. `C+h`, 5hmC) must survive round-trip -/// through `parse_mm_ml_into_ma` and `write_mm_ml`. The legacy -/// `BaseMods` preserved arbitrary mod types; the new path stores them -/// as annotation types named after the MM group header. +/// Unknown mod-type codes (anything other than `"a"` / `"m"` — +/// including single-char like `C+h` and multi-char like `C+ac`) are +/// dropped on parse with a warning. We don't store them as their own +/// annotation type; fibertools-rs's typed API only covers m6a and cpg. #[test] -fn test_non_canonical_mod_round_trip() { - // Load any record to get a real sequence, then overwrite MM/ML with - // a synthetic non-canonical tag set. +fn test_unknown_modtype_warns_and_skips() { let mut bam = bam::Reader::from_path("tests/data/all.bam").unwrap(); let mut rec = bam.records().next().expect("all.bam has records").unwrap(); - // Find the first three C positions in the forward sequence to place - // hypothetical 5hmC calls on. + // Pick the first C in forward orientation to attach a single C+h + // call to. Then append a real C+m call so we can confirm the unknown + // group doesn't break ML alignment for the canonical one. let fwd = if rec.is_reverse() { bio::alphabets::dna::revcomp(rec.seq().as_bytes()) } else { rec.seq().as_bytes() }; - let c_positions: Vec = fwd + let _first_c = fwd .iter() - .enumerate() - .filter(|(_, &b)| b == b'C' || b == b'c') - .take(3) - .map(|(i, _)| i) - .collect(); - assert!(c_positions.len() >= 3, "need at least 3 C bases"); - - // Build a `C+h,...;` MM tag pointing at those C positions and - // matching ML qualities. - let mut skips: Vec = Vec::with_capacity(3); - let mut c_count = 0usize; - let mut next_target = 0; - for (i, &b) in fwd.iter().enumerate() { - if next_target >= c_positions.len() { - break; - } - if i == c_positions[next_target] { - skips.push(c_count); - c_count = 0; - next_target += 1; - } else if b == b'C' || b == b'c' { - c_count += 1; - } - } - let mm = format!("C+h,{},{},{};", skips[0], skips[1], skips[2]); - let ml: Vec = vec![200, 150, 100]; + .position(|&b| b == b'C') + .expect("seq has a C"); + // C+h,0; then C+m,0; — both attach to the first C in the seq. + let mm = "C+h,0;C+m,0;"; + let ml: Vec = vec![123, 200]; rec.remove_aux(b"MM").ok(); rec.remove_aux(b"ML").ok(); - rec.push_aux(b"MM", Aux::String(&mm)).unwrap(); + rec.push_aux(b"MM", Aux::String(mm)).unwrap(); rec.push_aux(b"ML", Aux::ArrayU8((&ml).into())).unwrap(); - // Parse → write → re-parse, then assert C+h positions and qualities - // round-trip. let mut a = MolecularAnnotations::from_record(&rec); parse_mm_ml_into_ma(&rec, &mut a, 0, 0); - let a_ch = a.get_type("C+h").expect("C+h type present after parse"); - assert_eq!(a_ch.annotations.len(), 3); - - write_mm_ml(&mut rec, &a); - let mut b = MolecularAnnotations::from_record(&rec); - parse_mm_ml_into_ma(&rec, &mut b, 0, 0); - - assert_eq!(a.get_type("C+h"), b.get_type("C+h")); -} - -/// Canonical dispatch is on the exact mod-type code (`"a"` / `"m"`), -/// not the first character. A multi-char alpha mod type like `C+ac` -/// (acetylation) starts with `'a'` but must NOT route into `m6a`; it -/// must be preserved verbatim as a `"C+ac"` annotation type. -#[test] -fn test_multichar_alpha_modtype_not_treated_as_canonical() { - let mut bam = bam::Reader::from_path("tests/data/all.bam").unwrap(); - let mut rec = bam.records().next().expect("all.bam has records").unwrap(); - - let fwd = if rec.is_reverse() { - bio::alphabets::dna::revcomp(rec.seq().as_bytes()) - } else { - rec.seq().as_bytes() - }; - let c_positions: Vec = fwd - .iter() - .enumerate() - .filter(|(_, &b)| b == b'C' || b == b'c') - .take(2) - .map(|(i, _)| i) - .collect(); - assert!(c_positions.len() >= 2); - let mut skips: Vec = Vec::with_capacity(2); - let mut c_count = 0usize; - let mut next_target = 0; - for (i, &b) in fwd.iter().enumerate() { - if next_target >= c_positions.len() { - break; - } - if i == c_positions[next_target] { - skips.push(c_count); - c_count = 0; - next_target += 1; - } else if b == b'C' || b == b'c' { - c_count += 1; - } - } - let mm = format!("C+ac,{},{};", skips[0], skips[1]); - let ml: Vec = vec![180, 220]; - rec.remove_aux(b"MM").ok(); - rec.remove_aux(b"ML").ok(); - rec.push_aux(b"MM", Aux::String(&mm)).unwrap(); - rec.push_aux(b"ML", Aux::ArrayU8((&ml).into())).unwrap(); - - let mut a = MolecularAnnotations::from_record(&rec); - parse_mm_ml_into_ma(&rec, &mut a, 0, 0); - - // Must land in its own type, not in m6a. - assert!( - a.get_type(M6A_TYPE).is_none(), - "C+ac must not be routed to m6a" - ); - let acetyl = a.get_type("C+ac").expect("C+ac type present after parse"); - assert_eq!(acetyl.annotations.len(), 2); - - // And round-trips through write_mm_ml unchanged. - write_mm_ml(&mut rec, &a); - let mut b = MolecularAnnotations::from_record(&rec); - parse_mm_ml_into_ma(&rec, &mut b, 0, 0); - assert_eq!(a.get_type("C+ac"), b.get_type("C+ac")); - assert!(b.get_type(M6A_TYPE).is_none()); + // C+h must be dropped entirely — no "C+h" type, no m6a leakage. + assert!(a.get_type("C+h").is_none(), "C+h must not be stored"); + assert!(a.get_type(M6A_TYPE).is_none(), "C+h must not leak into m6a"); + // C+m still landed under cpg with the correct quality — proving the + // ML offset wasn't desynced by the skipped C+h group. + let cpg = a.get_type(CPG_TYPE).expect("C+m landed under cpg"); + assert_eq!(cpg.annotations.len(), 1); + assert_eq!(cpg.annotations[0].qualities, vec![200]); } /// A malformed MM tag — claiming more `mod_base` positions than the @@ -253,3 +168,110 @@ fn test_parse_mm_ml_idempotent_on_rerun() { "stale m6a must be replaced by MM/ML, not merged" ); } + +/// `N+a` headers must be preserved verbatim through parse→write. Per the +/// SAM spec, `N` matches any base for distance counting; the old write +/// path silently rewrote `N+a` to `A+a;T-a` based on the underlying +/// sequence. The refactor stores each call's MM header on +/// `Annotation.name`, so the literal `N+a` survives. +#[test] +fn test_n_plus_a_preserved_verbatim() { + let mut bam = bam::Reader::from_path("tests/data/all.bam").unwrap(); + let mut rec = bam.records().next().expect("all.bam has records").unwrap(); + + // N+a,0,0,0; marks the first three positions of the forward sequence + // regardless of base. With three zero skips, parse resolves to + // positions [0, 1, 2]. The same encoding round-trips on write + // because the skip-base is N (every base counts). + let mm = "N+a,0,0,0;"; + let ml: Vec = vec![210, 220, 230]; + + rec.remove_aux(b"MM").ok(); + rec.remove_aux(b"ML").ok(); + rec.push_aux(b"MM", Aux::String(mm)).unwrap(); + rec.push_aux(b"ML", Aux::ArrayU8((&ml).into())).unwrap(); + + let mut a = MolecularAnnotations::from_record(&rec); + parse_mm_ml_into_ma(&rec, &mut a, 0, 0); + + let m6a = a.get_type(M6A_TYPE).expect("N+a routes to m6a"); + assert_eq!(m6a.annotations.len(), 3); + // Every annotation should carry the verbatim header `N+a` on its name. + for ann in &m6a.annotations { + assert_eq!(ann.name.as_deref(), Some("N+a")); + } + + write_mm_ml(&mut rec, &a); + let written_mm = match rec.aux(b"MM").unwrap() { + Aux::String(s) => s.to_string(), + _ => panic!("MM tag must be a string"), + }; + assert_eq!( + written_mm, "N+a,0,0,0;", + "N+a must round-trip verbatim, not get normalized to A+a/T-a" + ); + + // And re-parsing yields the same annotation set. + let mut b = MolecularAnnotations::from_record(&rec); + parse_mm_ml_into_ma(&rec, &mut b, 0, 0); + assert_eq!(a.get_type(M6A_TYPE), b.get_type(M6A_TYPE)); +} + +/// Programmatic producers (`predict_m6a`, `ddda_to_m6a`) tag each m6a +/// call with its canonical MM group header via `canonical_header` +/// before adding it to the annotation. This test mirrors that pattern +/// and confirms `write_mm_ml` emits the right groups. +#[test] +fn test_predictor_set_headers_round_trip() { + let mut bam = bam::Reader::from_path("tests/data/all.bam").unwrap(); + let mut rec = bam.records().next().expect("all.bam has records").unwrap(); + + let fwd = if rec.is_reverse() { + bio::alphabets::dna::revcomp(rec.seq().as_bytes()) + } else { + rec.seq().as_bytes() + }; + let first_a = fwd.iter().position(|&b| b == b'A').expect("seq has an A") as u32; + let first_t = fwd.iter().position(|&b| b == b'T').expect("seq has a T") as u32; + + rec.remove_aux(b"MM").ok(); + rec.remove_aux(b"ML").ok(); + let mut annot = MolecularAnnotations::from_record(&rec); + let qspec = "Q".parse::().expect("Q parses"); + let t = annot.add_annotation_type(M6A_TYPE, qspec); + // Each predictor-emitted call carries its canonical header. + let a_header = canonical_header(M6A_TYPE, b'A').unwrap(); + let t_header = canonical_header(M6A_TYPE, b'T').unwrap(); + t.add( + first_a, + 1, + Strand::Forward, + vec![150], + Some(a_header.to_string()), + ); + t.add( + first_t, + 1, + Strand::Forward, + vec![160], + Some(t_header.to_string()), + ); + + write_mm_ml(&mut rec, &annot); + let written_mm = match rec.aux(b"MM").unwrap() { + Aux::String(s) => s.to_string(), + _ => panic!("MM tag must be a string"), + }; + assert!(written_mm.contains("A+a,"), "got: {written_mm}"); + assert!(written_mm.contains("T-a,"), "got: {written_mm}"); + + // Re-parse and confirm positions+qualities survived. + let mut b = MolecularAnnotations::from_record(&rec); + parse_mm_ml_into_ma(&rec, &mut b, 0, 0); + let m6a = b.get_type(M6A_TYPE).expect("m6a present after re-parse"); + let mut positions: Vec = m6a.annotations.iter().map(|a| a.start).collect(); + positions.sort(); + let mut want = vec![first_a, first_t]; + want.sort(); + assert_eq!(positions, want); +} From 716979267a2df75a0186ce55747d5775c5a81e26 Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Wed, 27 May 2026 10:25:04 -0600 Subject: [PATCH 23/24] chore: vendor MA library via workspace, unify rust-htslib at 0.46 Upstream main (PR #109) vendored Molecular-annotation-spec as a workspace member at ./molecular-annotation; switch from the git dependency to a path dependency on the vendored copy. Introduce [workspace.dependencies] pinning rust-htslib at 0.46. Both fibertools-rs and molecular-annotation now consume it via `rust-htslib.workspace = true`. The previous mismatch (root at 0.47, vendored MA also 0.47, upstream root at 0.46) had htslib duplicated in the dep graph with incompatible types across the crate boundary. --- Cargo.lock | 75 ++------------------------------- Cargo.toml | 7 ++- molecular-annotation/Cargo.toml | 4 +- 3 files changed, 10 insertions(+), 76 deletions(-) diff --git a/Cargo.lock b/Cargo.lock index f887b946..4c783ecb 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -341,26 +341,6 @@ dependencies = [ "unty", ] -[[package]] -name = "bindgen" -version = "0.69.5" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "271383c67ccabffb7381723dea0672a673f292304fcb45c01cc648c7a8d58088" -dependencies = [ - "bitflags 2.9.1", - "cexpr", - "clang-sys", - "itertools 0.12.1", - "lazy_static", - "lazycell", - "proc-macro2", - "quote", - "regex", - "rustc-hash", - "shlex", - "syn 2.0.104", -] - [[package]] name = "bio" version = "1.6.0" @@ -1089,15 +1069,6 @@ dependencies = [ "shlex", ] -[[package]] -name = "cexpr" -version = "0.6.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6fac387a98bb7c37292057cffc56d62ecb629900026402633ae9160df93a8766" -dependencies = [ - "nom", -] - [[package]] name = "cfg-expr" version = "0.15.8" @@ -1130,17 +1101,6 @@ dependencies = [ "inout", ] -[[package]] -name = "clang-sys" -version = "1.8.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0b023947811758c97c59bf9d1c188fd619ad4718dcaa767947df1cadb14f39f4" -dependencies = [ - "glob", - "libc", - "libloading", -] - [[package]] name = "clap" version = "4.5.41" @@ -2402,6 +2362,7 @@ dependencies = [ "lazy_static", "linear-map", "log", + "molecular-annotation", "niffler", "noodles", "num", @@ -2410,7 +2371,7 @@ dependencies = [ "rand 0.8.5", "rayon", "regex", - "rust-htslib 0.46.0", + "rust-htslib", "serde", "serde_json", "serde_yaml", @@ -3220,7 +3181,6 @@ version = "2.2.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "e38d7f1c121cd22aa214cb4dadd4277dc5447391eac518b899b29ba6356fbbb2" dependencies = [ - "bindgen", "bzip2-sys", "cc", "curl-sys", @@ -3683,12 +3643,6 @@ version = "1.5.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "bbd2bcb4c963f2ddae06a2efc7e9f3591312473c50c6685e1f298068316e66fe" -[[package]] -name = "lazycell" -version = "1.3.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "830d08ce1d1d941e6b30645f1a0eb5643013d835ce3779a5fc208261dbe10f55" - [[package]] name = "lebe" version = "0.5.2" @@ -4084,13 +4038,12 @@ checksum = "4e519fd9c6131c1c9a4a67f8bdc4f32eb4105b16c1468adea1b8e68c98c85ec4" [[package]] name = "molecular-annotation" version = "0.1.0" -source = "git+https://github.com/fiberseq/Molecular-annotation-spec?branch=main#7e052272a0b4ee45925bd78554c1d244a6761f53" dependencies = [ "bio 2.3.0", "lazy_static", "log", "regex", - "rust-htslib 0.47.1", + "rust-htslib", ] [[package]] @@ -5452,28 +5405,6 @@ dependencies = [ "url", ] -[[package]] -name = "rust-htslib" -version = "0.47.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f62b46e47d8b025589565f0eefe83e8646faf0faf74d17014b1b6ea2c1504930" -dependencies = [ - "bio-types", - "byteorder", - "custom_derive", - "derive-new 0.5.9", - "hts-sys", - "ieee754", - "lazy_static", - "libc", - "libz-sys", - "linear-map", - "newtype_derive", - "regex", - "thiserror 1.0.69", - "url", -] - [[package]] name = "rustc-demangle" version = "0.1.25" diff --git a/Cargo.toml b/Cargo.toml index 0378c8e9..2e177c8e 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -18,6 +18,9 @@ exclude = ["py-ft/", "tests/data/", "Train-FIRE/"] members = ["molecular-annotation"] exclude = ["py-ft", "molecular-annotation/python"] +[workspace.dependencies] +rust-htslib = "0.46" + [[bin]] name = "ft" path = "src/main.rs" @@ -50,7 +53,7 @@ ordered-float = "3.4.0" rayon = "1.10" linear-map = "1.2.0" regex = "1.9.1" -rust-htslib = "0.47" +rust-htslib = { workspace = true } serde = { version = "1.0.104", features = ["derive"], optional = false } @@ -69,7 +72,7 @@ burn = { version = "0.18.0", optional = true, features = [ num = "0.4.3" rand = "0.8.5" noodles = { version = "0.100.0", features = ["fasta", "bed"] } -molecular-annotation = { git = "https://github.com/fiberseq/Molecular-annotation-spec", branch = "main", features = ["htslib"] } +molecular-annotation = { path = "molecular-annotation", features = ["htslib"] } [build-dependencies] burn-import = { version = "0.18.0", default-features = false, features = [ diff --git a/molecular-annotation/Cargo.toml b/molecular-annotation/Cargo.toml index 7644693d..dd4989d2 100644 --- a/molecular-annotation/Cargo.toml +++ b/molecular-annotation/Cargo.toml @@ -13,11 +13,11 @@ separate-lengths = [] # MA contains starts only, lengths in AL array: "1000;msp+ htslib = ["dep:rust-htslib", "dep:log", "dep:regex", "dep:lazy_static", "dep:bio"] [dependencies] -rust-htslib = { version = "0.47", optional = true } +rust-htslib = { workspace = true, optional = true } log = { version = "0.4", optional = true } regex = { version = "1", optional = true } lazy_static = { version = "1", optional = true } bio = { version = "2", optional = true } [dev-dependencies] -rust-htslib = "0.47" +rust-htslib = { workspace = true } From 23c23bd47cc2041fafdf386029ea1ba36b703ea5 Mon Sep 17 00:00:00 2001 From: Cade Mirchandani Date: Wed, 27 May 2026 20:43:55 -0600 Subject: [PATCH 24/24] fix: unify MA tag I/O on the molecular-annotation library The vendored library now owns MM/ML parsing in from_record and emission in to_record. Replace the parallel basemods::{parse_mm_ml_into_ma, write_mm_ml} and the strip-then-to_record path in ma_io::write_annotations with a single codec: read_record / write_record / ensure_basemod_encoding in ma_io. Fixes the write-clobber that zeroed m6a in predict_m6a output (all four m6a_prediction_test cases now pass). Storage type names align with spec mod codes (M6A_TYPE "m6a" -> "a", CPG_TYPE "cpg" -> "m"); display strings in TSV / CLI / filter expressions stay unchanged. ensure_basemod_encoding uses a drain/re-attach pattern because the library's set_encoding panics on non-empty types. All producers (predict_m6a, ddda_to_m6a, strip_basemods, FIRE via serialize_annotations, mock_fire, fibertig) and consumers (FiberseqData, fibertig reader) route through the unified codec. read_annotations / read_ma_tags retained for legacy-fallback tests. tests/basemods.rs removed (round-trip superseded by ma_io::tests; unknown-modtype assertion tested a policy the library no longer enforces). --- src/fiber.rs | 44 +++- src/subcommands/add_nucleosomes.rs | 3 +- src/subcommands/center.rs | 7 +- src/subcommands/ddda_to_m6a.rs | 13 +- src/subcommands/fiber_hmm.rs | 3 +- src/subcommands/mock_fire.rs | 9 +- src/subcommands/predict_m6a.rs | 29 +-- src/subcommands/strip_basemods.rs | 11 +- src/utils/basemods.rs | 346 ++--------------------------- src/utils/fibertig.rs | 5 +- src/utils/ftexpression.rs | 5 +- src/utils/input_bam.rs | 3 +- src/utils/ma_io.rs | 211 ++++++++++++++++-- src/utils/nucleosome.rs | 2 +- tests/basemods.rs | 277 ----------------------- tests/fibertig_test.rs | 2 +- tests/molecular_annotation.rs | 48 +++- 17 files changed, 328 insertions(+), 690 deletions(-) delete mode 100644 tests/basemods.rs diff --git a/src/fiber.rs b/src/fiber.rs index 1e4ac272..588b58c3 100644 --- a/src/fiber.rs +++ b/src/fiber.rs @@ -2,7 +2,7 @@ use super::subcommands::center::CenterPosition; use super::utils::input_bam::FiberFilters; use super::*; use crate::utils::bamannotations::*; -use crate::utils::basemods::{parse_mm_ml_into_ma, CPG_TYPE, M6A_TYPE}; +use crate::utils::basemods::{CPG_TYPE, M6A_TYPE}; use crate::utils::bio_io::*; use crate::utils::ftexpression::apply_filter_fsd; use crate::utils::ma_io::{FIRE_TYPE, MSP_TYPE, NUC_TYPE}; @@ -33,11 +33,38 @@ impl FiberseqData { "." } .to_string(); - let mut annotations = crate::utils::ma_io::read_annotations(&record).unwrap_or_else(|e| { + let mut annotations = crate::utils::ma_io::read_record(&record).unwrap_or_else(|e| { log::warn!("Failed to read annotations: {e}"); MolecularAnnotations::from_record(&record) }); + // Apply read-side basemod filters that parse_mm_ml_into_ma used to do. + // The library now populates m6a/cpg in `annotations` directly; here we + // just prune by min_ml_score and end-strip distance. + if filters.min_ml_score > 0 || filters.strip_starting_basemods > 0 { + let seq_len = record.seq_len(); + let strip = filters.strip_starting_basemods.max(0) as usize; + let upper = seq_len.saturating_sub(strip); + let min_ml = filters.min_ml_score; + for t in annotations.annotation_types.iter_mut() { + if !crate::utils::basemods::is_basemod_type(&t.name) { + continue; + } + t.annotations.retain(|a| { + if a.qualities.first().copied().unwrap_or(0) < min_ml { + return false; + } + if strip > 0 { + let p = a.start as usize; + if p < strip || p >= upper { + return false; + } + } + true + }); + } + } + // get the number of passes let ec = if let Ok(Aux::Float(f)) = record.aux(b"ec") { log::trace!("{f}"); @@ -51,15 +78,6 @@ impl FiberseqData { None => ".".to_string(), }; - // Parse MM/ML directly into the spec object as m6a / cpg types. - // No intermediate BaseMods needed on the read side. - parse_mm_ml_into_ma( - &record, - &mut annotations, - filters.min_ml_score, - filters.strip_starting_basemods, - ); - let mut fsd = FiberseqData { record, annotations, @@ -144,7 +162,9 @@ impl FiberseqData { /// annotations should call this and then hand the record to the /// BAM writer. pub fn serialize_annotations(&mut self) { - crate::utils::ma_io::write_annotations(&mut self.record, &self.annotations); + let mut annot = self.annotations.clone(); + crate::utils::ma_io::ensure_basemod_encoding(&mut annot); + crate::utils::ma_io::write_record(&mut self.record, &annot); } pub fn get_qname(&self) -> String { diff --git a/src/subcommands/add_nucleosomes.rs b/src/subcommands/add_nucleosomes.rs index 013bf455..b91c1755 100644 --- a/src/subcommands/add_nucleosomes.rs +++ b/src/subcommands/add_nucleosomes.rs @@ -1,5 +1,6 @@ use crate::cli::AddNucleosomeOptions; use crate::fiber::FiberseqData; +use crate::utils::basemods::M6A_TYPE; use crate::utils::nucleosome::*; use crate::*; use rayon::iter::ParallelIterator; @@ -23,7 +24,7 @@ pub fn add_nucleosomes_to_bam(nuc_opts: &mut AddNucleosomeOptions) { // m6a positions in molecular (forward) orientation let m6a: Vec = fd .annotations - .get_forward_coords("m6a") + .get_forward_coords(M6A_TYPE) .map(|v| v.into_iter().map(|(s, _)| s as i64).collect()) .unwrap_or_default(); let record = fd.record.clone(); diff --git a/src/subcommands/center.rs b/src/subcommands/center.rs index dd392ce5..fd5d11e2 100644 --- a/src/subcommands/center.rs +++ b/src/subcommands/center.rs @@ -1,6 +1,7 @@ use crate::cli::CenterOptions; use crate::fiber::FiberseqData; use crate::utils::bamannotations::primary_qual; +use crate::utils::basemods::{CPG_TYPE, M6A_TYPE}; use crate::utils::bio_io; use crate::*; use bio::alphabets::dna::revcomp; @@ -114,7 +115,7 @@ impl CenteredFiberData { .fiber .annotations .project_query(self.mol_offset, flip) - .filter(|p| p.type_name == "m6a") + .filter(|p| p.type_name == M6A_TYPE) .map(|p| p.start) .collect(); let msp_boundaries: Vec = self @@ -264,8 +265,8 @@ impl CenteredFiberData { Vec>, Vec, ) { - let (m6a, _, m6a_qual) = self.centered_for_type("m6a"); - let (cpg, _, cpg_qual) = self.centered_for_type("cpg"); + let (m6a, _, m6a_qual) = self.centered_for_type(M6A_TYPE); + let (cpg, _, cpg_qual) = self.centered_for_type(CPG_TYPE); let (nuc_st, nuc_en, _) = self.centered_for_type("nuc"); let (msp_st, msp_en, _) = self.centered_for_type("msp"); let (fire_st, fire_en, fire_qual) = self.centered_for_type("fire"); diff --git a/src/subcommands/ddda_to_m6a.rs b/src/subcommands/ddda_to_m6a.rs index 8751501a..d48c1d57 100644 --- a/src/subcommands/ddda_to_m6a.rs +++ b/src/subcommands/ddda_to_m6a.rs @@ -1,5 +1,6 @@ use crate::cli::DddaToM6aOptions; use crate::utils::basemods; +use crate::utils::ma_io; use crate::*; use anyhow::Error; use bio::alphabets::dna::revcomp; @@ -62,9 +63,12 @@ pub fn ddda_to_m6a_record(record: &mut Record, _opts: &DddaToM6aOptions) { // pre-existing m6a (we're replacing it with the Y/R-derived calls), // then append the synthesized m6a and write back. Each call gets // its canonical MM group header (A+a or T-a) tagged via - // `canonical_header` so `write_mm_ml` can emit the right groups. - let mut annot = MolecularAnnotations::from_record(record); - basemods::parse_mm_ml_into_ma(record, &mut annot, 0, 0); + // `canonical_header` so the library's MM/ML serializer emits the + // right groups. + let mut annot = ma_io::read_record(record).unwrap_or_else(|e| { + log::warn!("read_record failed for {:?}: {e}", String::from_utf8_lossy(record.qname())); + MolecularAnnotations::from_record(record) + }); annot .annotation_types .retain(|t| t.name != basemods::M6A_TYPE); @@ -75,7 +79,8 @@ pub fn ddda_to_m6a_record(record: &mut Record, _opts: &DddaToM6aOptions) { .expect("ddda_to_m6a only places calls on A/T bases"); t.add(pos, 1, Strand::Forward, vec![255], Some(header.to_string())); } - basemods::write_mm_ml(record, &annot); + ma_io::ensure_basemod_encoding(&mut annot); + ma_io::write_record(record, &annot); } pub fn ddda_to_m6a(opts: &mut DddaToM6aOptions) -> Result<(), Error> { diff --git a/src/subcommands/fiber_hmm.rs b/src/subcommands/fiber_hmm.rs index e06c306f..1a6b39cb 100644 --- a/src/subcommands/fiber_hmm.rs +++ b/src/subcommands/fiber_hmm.rs @@ -1,4 +1,5 @@ use crate::cli::FiberHmmOptions; +use crate::utils::basemods::M6A_TYPE; use crate::*; use anyhow::Error; use bio::alphabets::dna::revcomp; @@ -10,7 +11,7 @@ pub fn run_fiber_hmm(opts: &mut FiberHmmOptions) -> Result<(), Error> { // m6a positions on the forward (molecular) strand let _m6a: Vec = fiber .annotations - .get_forward_coords("m6a") + .get_forward_coords(M6A_TYPE) .map(|v| v.into_iter().map(|(s, _)| s).collect()) .unwrap_or_default(); // forward strand sequence diff --git a/src/subcommands/mock_fire.rs b/src/subcommands/mock_fire.rs index f386cece..7e64a0f3 100644 --- a/src/subcommands/mock_fire.rs +++ b/src/subcommands/mock_fire.rs @@ -124,13 +124,14 @@ fn create_mock_fire_record( // Build MA-spec annotations and emit. Mock FIRE only produces MSPs with // the FIRE precision (Q-scaled) quality; no nucleosomes are populated. - // Direct `ma_io::write_annotations` (rather than the - // `FiberseqData::serialize_annotations` path used elsewhere) is intentional - // here — we're synthesizing a record from BED, so there's no + // Direct `ensure_basemod_encoding` + `ma_io::write_record` (rather than + // the `FiberseqData::serialize_annotations` path used elsewhere) is + // intentional here — we're synthesizing a record from BED, so there's no // `FiberseqData` to round-trip through. let mut annot = MolecularAnnotations::from_record(&record); ma_io::add_fire_annotations(&mut annot, &starts, &lengths, &quals); - ma_io::write_annotations(&mut record, &annot); + ma_io::ensure_basemod_encoding(&mut annot); + ma_io::write_record(&mut record, &annot); Ok(record) } diff --git a/src/subcommands/predict_m6a.rs b/src/subcommands/predict_m6a.rs index 4ebf1fc3..8c086a9b 100644 --- a/src/subcommands/predict_m6a.rs +++ b/src/subcommands/predict_m6a.rs @@ -1,6 +1,7 @@ use crate::cli::PredictM6AOptions; use crate::utils::basemods; use crate::utils::bio_io; +use crate::utils::ma_io; use crate::utils::nucleosome; use crate::*; use bio::alphabets::dna::revcomp; @@ -219,11 +220,14 @@ where assert_eq!(data.len(), records.len()); let mut cur_predict_st = 0; for (option_data, record) in data.iter().zip(records) { - // Load existing MM/ML into a MolecularAnnotations, then drop any - // pre-existing m6a calls — we're about to replace them with the - // model's predictions. CpG / other annotation types are preserved. - let mut annot = molecular_annotation::MolecularAnnotations::from_record(record); - basemods::parse_mm_ml_into_ma(record, &mut annot, 0, 0); + // Load existing annotations (MA tags + MM/ML via library, with + // legacy ns/nl/as/al fallback), then drop any pre-existing m6a + // calls — we're about to replace them with the model's predictions. + // CpG / other annotation types are preserved. + let mut annot = ma_io::read_record(record).unwrap_or_else(|e| { + log::warn!("read_record failed for {:?}: {e}", String::from_utf8_lossy(record.qname())); + molecular_annotation::MolecularAnnotations::from_record(record) + }); annot .annotation_types .retain(|t| t.name != basemods::M6A_TYPE); @@ -236,8 +240,8 @@ where // Iterate over A and then T basemods, collecting their forward // positions + ML qualities into a single sorted m6a list. Each // call carries its canonical MM group header — A-base calls - // are "A+a", T-base calls are "T-a" — so `write_mm_ml` can - // emit them under the correct group. + // are "A+a", T-base calls are "T-a" — so the library's MM/ML + // serializer emits them under the correct group. let mut m6a_calls: Vec<(u32, u8, &'static str)> = Vec::new(); for (data, header) in [(a_data, "A+a"), (t_data, "T-a")] { let cur_predict_en = cur_predict_st + data.count; @@ -264,9 +268,6 @@ where } } - // write the ml and mm tags - basemods::write_mm_ml(record, &annot); - // Compute nucleosomes + MSPs from the forward m6a positions // and append them to the same MA object we just built up. let modified_bases_forward: Vec = @@ -278,10 +279,10 @@ where &opts.nuc_opts, ); - // Single MA write — m6a went out via MM/ML above; nuc/msp - // (and any pre-existing annotation types we preserved) go - // out here. - crate::utils::ma_io::write_annotations(record, &annot); + // Tag basemod types as MM/ML-encoded so to_record emits them as + // MM/ML rather than the MA tag set; nuc/msp/fire stay Encoding::Ma. + ma_io::ensure_basemod_encoding(&mut annot); + ma_io::write_record(record, &annot); // clear the existing data if !opts.keep { diff --git a/src/subcommands/strip_basemods.rs b/src/subcommands/strip_basemods.rs index d2e24607..f355bed4 100644 --- a/src/subcommands/strip_basemods.rs +++ b/src/subcommands/strip_basemods.rs @@ -1,8 +1,8 @@ use crate::cli::StripBasemodsOptions; use crate::utils::bamannotations::primary_qual; -use crate::utils::basemods; use crate::utils::basemods::{CPG_TYPE, M6A_TYPE}; use crate::utils::bio_io::BamChunk; +use crate::utils::ma_io; use bio::alphabets::dna::revcomp; use molecular_annotation::MolecularAnnotations; use rayon::iter::ParallelIterator; @@ -26,8 +26,10 @@ pub fn strip_base_mods(opts: &mut StripBasemodsOptions) { let records: Vec<&mut Record> = chunk .par_iter_mut() .map(|record| { - let mut annot = MolecularAnnotations::from_record(record); - basemods::parse_mm_ml_into_ma(record, &mut annot, 0, 0); + let mut annot = ma_io::read_record(record).unwrap_or_else(|e| { + log::warn!("read_record failed for {:?}: {e}", String::from_utf8_lossy(record.qname())); + MolecularAnnotations::from_record(record) + }); // Drop whole annotation types. if filter_mod == "5mC" || filter_mod == "CpG" { @@ -76,7 +78,8 @@ pub fn strip_base_mods(opts: &mut StripBasemodsOptions) { }); } - basemods::write_mm_ml(record, &annot); + ma_io::ensure_basemod_encoding(&mut annot); + ma_io::write_record(record, &annot); record }) .collect(); diff --git a/src/utils/basemods.rs b/src/utils/basemods.rs index 09c033ff..4ce6dc22 100644 --- a/src/utils/basemods.rs +++ b/src/utils/basemods.rs @@ -1,64 +1,19 @@ -//! MM/ML BAM tag I/O for fiberseq base modifications. +//! Type-name constants and header helpers for fiberseq base modifications. //! -//! Scope: m6A (`"a"`) and 5mC (`"m"`) only. MM groups carrying any other -//! mod-type code are logged and skipped on parse — fibertools-rs's typed -//! API only exposes these two canonical fiberseq modifications. Adding a -//! new canonical mod (e.g. 5hmC, `"h"`) is a ~5-line change across -//! [`ma_type_for_mod_code`], [`is_basemod_type`], and -//! [`canonical_header`]. +//! Storage type names are spec MM mod codes (`"a"` for m6A, `"m"` for 5mC); +//! display labels in TSV output and CLI aliases use the fibertools-friendly +//! names (`"m6a"`, `"5mC"`). //! -//! Read path: `parse_mm_ml_into_ma` parses a record's MM/ML tags directly -//! into a [`MolecularAnnotations`]. Each call's MM group header (e.g. -//! `"A+a"`, `"T-a"`, `"N+a"`, `"C+m"`) is stored verbatim on -//! [`Annotation::name`], so headers round-trip through `write_mm_ml` -//! byte-for-byte — including non-standard encodings like `N+a` that the -//! old write path silently normalized. -//! -//! Write path: `write_mm_ml` emits MM/ML by reading each annotation's -//! `name` directly. Basemod annotations *must* have `name` set; the -//! parser sets it from the MM tag, and programmatic producers -//! (`predict_m6a`, `ddda_to_m6a`) set it via [`canonical_header`]. A -//! missing `name` on a basemod annotation is a bug and triggers a panic. -//! -//! MA-tag policy: `ma_io::write_annotations` *strips* `m6a` and `cpg` -//! before MA serialization — MM/ML is the on-disk source of truth, and -//! the MA tag set holds nuc/msp/fire only. This is a policy choice -//! (avoid duplication, single source of truth), not a correctness one. -//! Lifting the strip would expose basemods to MA-native consumers (e.g. -//! the `molecular_annotation` library) at the cost of ~2× disk for -//! basemod data and a "MM/ML wins on read" invariant. The matched -//! invariant on the read side is the idempotency wipe in -//! [`parse_mm_ml_into_ma`]: it discards any basemod-typed annotations -//! present in `annot` before parsing MM/ML, so an MA tag set that -//! wrongly contained basemods doesn't get merged on top of MM/ML. - -use crate::utils::bio_io::*; -use bio::alphabets::dna::revcomp; -use lazy_static::lazy_static; -use molecular_annotation::{MolecularAnnotations, QualitySpec, Strand}; -use regex::Regex; -use rust_htslib::bam; -use rust_htslib::bam::record::Aux; -use std::collections::BTreeMap; +//! BAM tag I/O is owned by `utils::ma_io`; this module is purely a +//! constants + header-formatting helper module. -/// Annotation type names emitted by `parse_mm_ml_into_ma`. -pub const M6A_TYPE: &str = "m6a"; -pub const CPG_TYPE: &str = "cpg"; - -/// Map an MM mod-type code (the trailing alpha/digits in a group like -/// `A+a`) to a fibertools MA type name. Unknown codes return `None` and -/// the caller skips the group. -fn ma_type_for_mod_code(code: &str) -> Option<&'static str> { - match code { - "a" => Some(M6A_TYPE), - "m" => Some(CPG_TYPE), - _ => None, - } -} +/// Annotation type name for m6A calls (spec MM mod code). +pub const M6A_TYPE: &str = "a"; +/// Annotation type name for 5mC calls (spec MM mod code). +pub const CPG_TYPE: &str = "m"; /// True for annotation types whose on-disk source of truth is MM/ML. -/// Used to gate idempotency wipes (parse), MA-tag emission (ma_io), and -/// MM/ML emission (write). +/// Used to gate MA-tag emission (ma_io) and MM/ML encoding flips. pub fn is_basemod_type(name: &str) -> bool { matches!(name, M6A_TYPE | CPG_TYPE) } @@ -67,8 +22,9 @@ pub fn is_basemod_type(name: &str) -> bool { /// forward-strand orientation). Returns `&'static str` for the four /// possible canonical headers; `None` if the (type, base) pair isn't a /// canonical fiberseq combination. Used by programmatic producers -/// (`predict_m6a`, `ddda_to_m6a`) to label calls so `write_mm_ml` can -/// emit them under the right MM group. +/// (`predict_m6a`, `ddda_to_m6a`) to label calls with the right MM +/// group header so the library's MM/ML serializer emits them under the +/// correct group. pub fn canonical_header(type_name: &str, base: u8) -> Option<&'static str> { match (type_name, base) { (M6A_TYPE, b'A') => Some("A+a"), @@ -78,277 +34,3 @@ pub fn canonical_header(type_name: &str, base: u8) -> Option<&'static str> { _ => None, } } - -lazy_static! { - // MM:Z:([ACGTUN][-+]([A-Za-z]+|[0-9]+)[.?]?(,[0-9]+)*;)* - static ref MM_RE: Regex = - Regex::new(r"((([ACGTUN])([-+])([A-Za-z]+|[0-9]+))[.?]?((,[0-9]+)*;)*)").unwrap(); -} - -/// Parse the MM/ML tags of `record` directly into `annot`. Positions are -/// stored in molecular (forward) orientation as 1bp annotations with a -/// single `Q` quality score per call. Each annotation's `name` carries -/// the verbatim MM group header it was parsed from (e.g. `"A+a"`, -/// `"T-a"`, `"N+a"`, `"C+h"`), so [`write_mm_ml`] round-trips it -/// unchanged. -/// -/// Per-call filtering: -/// - calls with ML quality < `min_ml_score` are dropped. -/// - calls within `strip_at_ends` bp of either end of the forward -/// sequence are dropped (no-op if `strip_at_ends <= 0`). -/// -/// Dispatch by MM mod_type (exact-match) controls the MA type bucket: -/// - `"a"` → [`M6A_TYPE`] (collapses `A+a`, `T-a`, `N+a`, etc.) -/// - `"m"` → [`CPG_TYPE`] (collapses `C+m`, `G+m`, etc.) -/// - any other → annotation type named verbatim after the MM group -/// header (e.g. `"C+h"` for 5hmC, `"C+ac"` for acetyl). -/// -/// Idempotent: any pre-existing basemod-shaped types on `annot` are -/// dropped first (see [`is_basemod_type`]), so MM/ML always overwrites -/// in-memory state rather than appending. This guards against (a) -/// repeated calls on the same `annot`, and (b) malformed inputs that -/// wrongly emit `m6a` into the MA tag set in addition to MM/ML. -pub fn parse_mm_ml_into_ma( - record: &bam::Record, - annot: &mut MolecularAnnotations, - min_ml_score: u8, - strip_at_ends: i64, -) { - // MM/ML is the on-disk source of truth for base modifications; any - // basemod-shaped type that may already be in `annot` (from a prior - // pass, an MA-tag leak in a third-party producer, or repeated calls) - // is discarded so we don't silently append on top of stale data. - annot.annotation_types.retain(|t| !is_basemod_type(&t.name)); - - let ml_tag = get_u8_tag(record, b"ML"); - let Ok(Aux::String(mm_text)) = record.aux(b"MM") else { - log::trace!("No MM tag found"); - return; - }; - - let forward_bases = if record.is_reverse() { - convert_seq_uppercase(revcomp(record.seq().as_bytes())) - } else { - convert_seq_uppercase(record.seq().as_bytes()) - }; - let seq_len = forward_bases.len(); - let strip = strip_at_ends.max(0) as usize; - let upper = seq_len.saturating_sub(strip); - - // Per-call accumulator: (ma_type, verbatim_header, pos, qual). The - // header is owned because the regex capture's lifetime ends at the - // next iteration; the ma_type is a static interned name. - let mut calls: Vec<(&'static str, String, u32, u8)> = Vec::new(); - let mut num_mods_seen = 0usize; - - for cap in MM_RE.captures_iter(mm_text) { - // Capture group 2 is the full `base+strand+modtype` prefix — - // exactly the MM group header (e.g. "A+a", "T-a", "C+h", "N+12"). - let header = cap.get(2).map_or("", |m| m.as_str()).to_string(); - let mod_base = cap.get(3).map(|m| m.as_str().as_bytes()[0]).unwrap(); - let mod_type_str = cap.get(5).map_or("", |m| m.as_str()).to_string(); - let mod_dists_str = cap.get(6).map_or("", |m| m.as_str()); - let mod_dists: Vec = mod_dists_str - .trim_end_matches(';') - .split(',') - .map(|s| s.trim()) - .filter(|s| !s.is_empty()) - .map(|s| s.parse().unwrap()) - .collect(); - - if mod_dists.is_empty() { - continue; - } - - // Resolve positions in forward sequence via the MM distance - // encoding: each value is "how many of `mod_base` to skip - // before the next modified base." - let mut positions: Vec = vec![0; mod_dists.len()]; - let mut cur_mod_idx = 0; - let mut dist_from_last_mod_base = 0i64; - for (cur_seq_idx, cur_base) in forward_bases.iter().enumerate() { - if cur_mod_idx >= mod_dists.len() { - break; - } - if (*cur_base == mod_base || mod_base == b'N') - && dist_from_last_mod_base == mod_dists[cur_mod_idx] - { - positions[cur_mod_idx] = cur_seq_idx as u32; - dist_from_last_mod_base = 0; - cur_mod_idx += 1; - } else if *cur_base == mod_base { - dist_from_last_mod_base += 1; - } - } - let resolved = cur_mod_idx; - if resolved != mod_dists.len() { - // MM tag claims more `mod_base` positions than the forward - // sequence actually has. Warn and emit only the calls we - // could resolve — the alternative was to panic the whole - // worker. ML offsets must still advance by the on-disk - // slot count (`mod_dists.len()`) so the next group reads - // from the correct ML section. - log::warn!( - "MM/ML parser: {} (reverse={}) — MM group ended {} positions short of the forward sequence; truncating", - String::from_utf8_lossy(record.qname()), - record.is_reverse(), - mod_dists.len() - resolved, - ); - } - - // Pair this group's calls with ML qualities. The on-disk ML - // section for this group has `mod_dists.len()` entries even if - // we could only resolve `resolved` of them. - let group_end = num_mods_seen + mod_dists.len(); - let group_quals: Vec = if group_end > ml_tag.len() { - let needed = group_end - ml_tag.len(); - let mut existing = ml_tag[num_mods_seen..].to_vec(); - existing.extend(std::iter::repeat_n(0, needed)); - log::warn!( - "ML tag is too short for the number of modifications found in the MM tag. Assuming an ML value of 0 after the first {group_end} modifications." - ); - existing - } else { - ml_tag[num_mods_seen..group_end].to_vec() - }; - num_mods_seen = group_end; - // Drop ML qualities whose position couldn't be resolved, so the - // dispatch zip below pairs only the surviving calls. - positions.truncate(resolved); - let group_quals = &group_quals[..resolved]; - - // Canonical "a"/"m" → m6a/cpg; everything else is dropped with a - // warning. The per-call header travels into `Annotation.name` - // so write_mm_ml re-emits it verbatim (preserving A+a vs T-a, - // and non-standard encodings like N+a, on round-trip). - let Some(ma_type) = ma_type_for_mod_code(&mod_type_str) else { - log::warn!( - "MM/ML parser: unsupported mod-type {:?} (group {:?}); skipping {} call(s)", - mod_type_str, - header, - resolved, - ); - continue; - }; - for (pos, &qual) in positions.iter().copied().zip(group_quals) { - if qual < min_ml_score { - continue; - } - let p = pos as usize; - if strip > 0 && (p < strip || p >= upper) { - continue; - } - calls.push((ma_type, header.clone(), pos, qual)); - } - } - - if ml_tag.len() != num_mods_seen { - log::warn!( - "ML tag ({}) different number than MM tag ({}).", - ml_tag.len(), - num_mods_seen, - ); - } - - // Group flat call list by MA type so each type's annotations land - // in the correct bucket on the spec object. Within a type, calls - // are sorted by position — even though different MM group headers - // (e.g. A+a and T-a) interleave under m6a, each call's `name` - // keeps its header for the write path. - let mut by_type: BTreeMap<&'static str, Vec<(String, u32, u8)>> = BTreeMap::new(); - for (ma_type, header, pos, qual) in calls { - by_type.entry(ma_type).or_default().push((header, pos, qual)); - } - for (ma_type, mut group) in by_type { - group.sort_by_key(|(_, p, _)| *p); - add_calls(annot, ma_type, &group); - } -} - -fn add_calls(annot: &mut MolecularAnnotations, name: &str, calls: &[(String, u32, u8)]) { - if calls.is_empty() { - return; - } - let qspec = "Q".parse::().expect("Q parses"); - let t = annot.add_annotation_type(name, qspec); - for (header, pos, qual) in calls { - t.add(*pos, 1, Strand::Forward, vec![*qual], Some(header.clone())); - } -} - -/// Emit MM/ML tags from `annot` onto `record`. Existing `MM` and `ML` -/// aux are removed first. -/// -/// Header for each call is read directly from [`Annotation::name`]. -/// Every basemod annotation must carry a header — the parser sets it -/// from the MM tag and programmatic producers set it via -/// [`canonical_header`]. A `None` `name` on a basemod annotation is a -/// caller bug and panics. -/// -/// Non-basemod annotation types (`msp`, `nuc`, `fire`, etc.) are -/// skipped — see [`is_basemod_type`] for the gate. -/// -/// MM groups are emitted in deterministic (lexicographic header) order. -pub fn write_mm_ml(record: &mut bam::Record, annot: &MolecularAnnotations) { - let forward_seq = if record.is_reverse() { - revcomp(record.seq().as_bytes()) - } else { - record.seq().as_bytes() - }; - - // header (e.g. "A+a", "T-a") → Vec<(pos, qual)>. BTreeMap gives - // deterministic emission order. - let mut groups: BTreeMap> = BTreeMap::new(); - - for t in &annot.annotation_types { - if !is_basemod_type(&t.name) { - continue; - } - for a in &t.annotations { - let header = a.name.clone().unwrap_or_else(|| { - panic!( - "basemod annotation in type {:?} at pos {} has no MM group header; \ - producers must set Annotation.name via canonical_header()", - t.name, a.start, - ) - }); - let qual = a.qualities.first().copied().unwrap_or(0); - groups.entry(header).or_default().push((a.start, qual)); - } - } - - let mut mm_tag = String::new(); - let mut ml_tag: Vec = Vec::new(); - for (header, mut calls) in groups { - calls.sort_by_key(|(p, _)| *p); - ml_tag.extend(calls.iter().map(|&(_, q)| q)); - mm_tag.push_str(&header); - // First byte of the header is the skip base (`N` counts everything). - let skip_base = header.as_bytes()[0]; - let mut last_pos = 0usize; - for (pos, _) in &calls { - let p = *pos as usize; - let in_between = if last_pos < p { - forward_seq[last_pos..p] - .iter() - .filter(|&&b| skip_base == b'N' || b == skip_base) - .count() - } else { - 0 - }; - last_pos = p + 1; - mm_tag.push_str(&format!(",{in_between}")); - } - mm_tag.push(';'); - } - - record.remove_aux(b"MM").ok(); - record.remove_aux(b"ML").ok(); - record - .push_aux(b"MM", Aux::String(&mm_tag)) - .expect("push MM tag"); - record - .push_aux(b"ML", Aux::ArrayU8((&ml_tag).into())) - .expect("push ML tag"); -} - diff --git a/src/utils/fibertig.rs b/src/utils/fibertig.rs index cf6fdd94..c362d322 100644 --- a/src/utils/fibertig.rs +++ b/src/utils/fibertig.rs @@ -349,7 +349,8 @@ impl FiberTig { } } - crate::utils::ma_io::write_annotations(&mut record, annotations); + crate::utils::ma_io::ensure_basemod_encoding(annotations); + crate::utils::ma_io::write_record(&mut record, annotations); records.push(record); } @@ -587,7 +588,7 @@ impl FiberTig { if record.tid() < 0 { continue; } - let annot = crate::utils::ma_io::read_annotations(&record)?; + let annot = crate::utils::ma_io::read_record(&record)?; if annot.get_type(FIBERTIG_TYPE).is_none() { continue; } diff --git a/src/utils/ftexpression.rs b/src/utils/ftexpression.rs index 7872b6b9..f5fa6c3f 100644 --- a/src/utils/ftexpression.rs +++ b/src/utils/ftexpression.rs @@ -1,4 +1,5 @@ use crate::fiber::FiberseqData; +use crate::utils::basemods::{CPG_TYPE, M6A_TYPE}; use crate::utils::input_bam::FiberFilters; #[derive(Debug)] @@ -144,8 +145,8 @@ pub fn apply_filter_fsd(fsd: &mut FiberseqData, filt: &FiberFilters) -> Result<( let type_name = match parser.feat_name.as_str() { "msp" => "msp", "nuc" => "nuc", - "m6a" => "m6a", - "5mC" => "cpg", + "m6a" => M6A_TYPE, + "5mC" => CPG_TYPE, other => anyhow::bail!("Unknown feature name: {}", other), }; match parser.fn_name.as_str() { diff --git a/src/utils/input_bam.rs b/src/utils/input_bam.rs index 4e384a2a..a27ec634 100644 --- a/src/utils/input_bam.rs +++ b/src/utils/input_bam.rs @@ -321,6 +321,7 @@ impl std::default::Default for InputBam { mod tests { use super::*; use crate::fiber::FiberseqData; + use crate::utils::basemods::M6A_TYPE; use molecular_annotation::{MolecularAnnotations, QualitySpec, Strand}; /// Build a minimal `FiberseqData` shaped only for `passes_fire_filter`. @@ -337,7 +338,7 @@ mod tests { } } if m6a_count > 0 { - let t = annotations.add_annotation_type("m6a", "Q".parse().expect("Q parses")); + let t = annotations.add_annotation_type(M6A_TYPE, "Q".parse().expect("Q parses")); for i in 0..m6a_count { t.add(i as u32, 1, Strand::Forward, vec![0], None); } diff --git a/src/utils/ma_io.rs b/src/utils/ma_io.rs index d0f6a9ca..8dfd2847 100644 --- a/src/utils/ma_io.rs +++ b/src/utils/ma_io.rs @@ -15,12 +15,12 @@ //! - `fire` (no strand, `Q` linear precision 0–255) //! //! `m6a` and `cpg` types may appear *in memory* on a [`MolecularAnnotations`] -//! populated by [`crate::utils::basemods::parse_mm_ml_into_ma`], but are -//! NEVER read or written here: their on-disk source of truth is `MM`/`ML`. -//! The writer below strips them before emission as a safety net. +//! populated by the library's MM/ML parser. Their on-disk source of truth +//! is `MM`/`ML`; [`ensure_basemod_encoding`] flags those types so the +//! library serializes them into MM/ML rather than the MA tag set. use anyhow::{bail, Result}; -use molecular_annotation::{MolecularAnnotations, QualitySpec, Strand}; +use molecular_annotation::{Encoding, MolecularAnnotations, QualitySpec, SkipFlag, Strand}; use rust_htslib::bam::{self, record::Aux}; /// Annotation type names used by fibertools-rs. @@ -32,6 +32,83 @@ pub const FIRE_TYPE: &str = "fire"; /// MA tag is present. These are never emitted; we only ingest them. pub const LEGACY_READ_TAGS: &[&[u8]] = &[b"ns", b"nl", b"as", b"al", b"aq"]; +/// Reads annotations from a BAM record's tags. +/// +/// Delegates to the library's combined MA-spec + MM/ML parser. If the +/// library returns an empty annotation set and the record carries legacy +/// `ns`/`nl`/`as`/`al`/`aq` tags, falls back to `read_legacy_nuc_msp`. +/// Tolerant of malformed MM/ML — the library handles those internally +/// without panicking. +pub fn read_record(record: &bam::Record) -> Result { + let mut annot = MolecularAnnotations::from_record(record); + // If MA tag is absent, also ingest legacy nuc/msp tags. The library + // already populates basemod types (m6a/cpg) from MM/ML, so we merge + // legacy-derived nuc/msp into whatever the library produced rather + // than gating on `annotation_types.is_empty()` (which would skip the + // legacy fallback whenever MM/ML is present). + let has_ma = matches!(record.aux(b"MA"), Ok(Aux::String(_))); + if !has_ma { + let has_legacy_nuc = matches!(record.aux(b"ns"), Ok(_)); + let has_legacy_msp = matches!(record.aux(b"as"), Ok(_)); + if has_legacy_nuc || has_legacy_msp { + let legacy = read_legacy_nuc_msp(record)?; + for t in legacy.annotation_types.into_iter() { + if annot.get_type(&t.name).is_some() { + continue; + } + let new_t = annot.add_annotation_type(&t.name, t.quality_spec.clone()); + for a in t.annotations.into_iter() { + new_t.add(a.start, a.length, a.strand, a.qualities, a.name); + } + } + } + } + Ok(annot) +} + +/// Writes annotations to a BAM record's tags via the library's `to_record`. +/// +/// Each `AnnotationType`'s `Encoding` controls which tag set it lands in: +/// `Encoding::MmMl` types go to MM/ML, `Encoding::Ma` types go to MA/AQ/AN. +/// Producers must call [`ensure_basemod_encoding`] before this if they +/// constructed basemod types via `add_annotation_type` (which defaults to +/// `Encoding::Ma`). +pub fn write_record(record: &mut bam::Record, annot: &MolecularAnnotations) { + annot.to_record(record); +} + +/// Sets `Encoding::MmMl { skip_flag: SkipFlag::Implicit }` on any basemod +/// annotation types (`M6A_TYPE`, `CPG_TYPE`) present in `annot`. +/// +/// Idempotent. Call unconditionally before [`write_record`] to guarantee +/// m6a / cpg land in MM/ML rather than the MA tag set. +/// +/// Implementation note: the library's `AnnotationType::set_encoding` +/// panics on non-empty types (encoding is meant to be locked in at +/// construction). We work around that by draining the annotations, +/// flipping `set_encoding` on the empty shell, and re-attaching the +/// annotations afterwards. Preserves order, qualities, and per-call +/// names. If the library ever relaxes set_encoding to allow flipping +/// on populated types, the drain/re-attach can be replaced with a +/// straight call. +pub fn ensure_basemod_encoding(annot: &mut MolecularAnnotations) { + let target = Encoding::MmMl { + skip_flag: SkipFlag::Implicit, + }; + for t in annot.annotation_types.iter_mut() { + if !crate::utils::basemods::is_basemod_type(&t.name) { + continue; + } + if t.encoding == target { + continue; // idempotent fast path + } + let drained: Vec = + std::mem::take(&mut t.annotations); + t.set_encoding(target); + t.annotations = drained; + } +} + /// Read annotations from a BAM record. /// /// Prefers spec MA tags; falls back to legacy `ns`/`nl`/`as`/`al`/`aq`. Always @@ -130,24 +207,6 @@ fn read_legacy_nuc_msp(record: &bam::Record) -> Result { Ok(annot) } -/// Write annotations to a BAM record. -/// -/// Emits MA-spec tags only. Base modifications (`m6a`, `cpg`) are stripped -/// before serialization — their on-disk source of truth is `MM`/`ML`, not -/// the MA tag set. -pub fn write_annotations(record: &mut bam::Record, annot: &MolecularAnnotations) { - // Base modifications (`m6a`, `cpg`) belong in MM/ML — never in the - // MA tag set. Drop them before serialization. This is a policy - // choice (single on-disk source of truth), not a correctness one; - // see the basemods module docs for the tradeoff if you want to - // expose basemods in MA tags for downstream MA-native consumers. - let mut for_ma = annot.clone(); - for_ma.annotation_types.retain(|t| { - t.name != crate::utils::basemods::M6A_TYPE && t.name != crate::utils::basemods::CPG_TYPE - }); - for_ma.to_record(record); -} - /// Convenience for callers that still operate on raw `i64` arrays of /// nucleosome and MSP coordinates. Returns /// `(nuc_starts, nuc_lengths, msp_starts, msp_lengths, msp_qual)` derived @@ -159,7 +218,7 @@ pub fn write_annotations(record: &mut bam::Record, annot: &MolecularAnnotations) pub fn extract_nuc_msp_arrays( record: &bam::Record, ) -> Result<(Vec, Vec, Vec, Vec, Vec)> { - let annot = read_annotations(record)?; + let annot = read_record(record)?; let (nuc_starts, nuc_lengths) = annot .get_type(NUC_TYPE) .map(|t| { @@ -285,7 +344,7 @@ pub fn build_nuc_msp_annotations( /// Returns `(starts, lengths, precisions)`. All three are empty if the record /// has no `fire` MA type. pub fn extract_fire_arrays(record: &bam::Record) -> Result<(Vec, Vec, Vec)> { - let annot = read_annotations(record)?; + let annot = read_record(record)?; Ok(annot .get_type(FIRE_TYPE) .map(|t| { @@ -315,3 +374,107 @@ fn u8_array(record: &bam::Record, tag: &[u8]) -> Option> { _ => None, } } + +#[cfg(test)] +mod tests { + use super::*; + use molecular_annotation::{MolecularAnnotations, QualitySpec, Strand}; + use rust_htslib::bam::record::Aux; + + /// Build a synthetic record with the given forward sequence. Aligned-blocks + /// metadata is not needed for these I/O tests because we only exercise + /// tag-level round-trips, not coordinate liftovers. + fn synth_record(seq: &[u8]) -> bam::Record { + let mut record = bam::Record::new(); + let qual = vec![60u8; seq.len()]; + // unmapped record, no cigar — sufficient for tag round-trip + record.set(b"test_read", None, seq, &qual); + record + } + + #[test] + fn read_write_record_roundtrips_basemod_and_msp() { + use crate::utils::basemods::{canonical_header, M6A_TYPE}; + + // 10bp sequence with A's at positions 0, 4, 8 + let mut record = synth_record(b"ATCGATCGAT"); + + // Build annotations: one m6a call at position 0 (A+a header), + // one msp annotation 5..8 with quality 200. + let mut annot = MolecularAnnotations::from_record(&record); + let qspec_q = "Q".parse::().expect("Q parses"); + + let m6a_type = annot.add_annotation_type(M6A_TYPE, qspec_q.clone()); + let header = canonical_header(M6A_TYPE, b'A').unwrap().to_string(); + m6a_type.add(0, 1, Strand::Forward, vec![240], Some(header)); + + let msp_type = annot.add_annotation_type(MSP_TYPE, qspec_q); + msp_type.add(5, 3, Strand::Unknown, vec![100], None); + + // Producer contract: tag basemod types with Encoding::MmMl before write. + ensure_basemod_encoding(&mut annot); + + write_record(&mut record, &annot); + + // Round-trip: read back and assert. After Phase 1's constant flip, + // M6A_TYPE == "a" — same name the library uses internally, so no + // translation is required at this boundary. + let back = read_record(&record).expect("read_record"); + + let m6a = back + .annotation_types + .iter() + .find(|t| t.name == M6A_TYPE) + .expect("m6a type present after round-trip"); + assert_eq!(m6a.annotations.len(), 1); + assert_eq!(m6a.annotations[0].start, 0); + assert_eq!(m6a.annotations[0].qualities, vec![240]); + + let msp = back + .annotation_types + .iter() + .find(|t| t.name == MSP_TYPE) + .expect("msp type present after round-trip"); + assert_eq!(msp.annotations.len(), 1); + assert_eq!(msp.annotations[0].start, 5); + assert_eq!(msp.annotations[0].length, 3); + } + + #[test] + fn read_record_falls_back_to_legacy_ns_as() { + use rust_htslib::bam::record::Aux; + + let mut record = synth_record(b"ATCGATCGAT"); + + // Push legacy `ns`/`nl` (one nuc 2..4) and `as`/`al` (one msp 6..9). + // No MA tag, no MM/ML. + let ns: Vec = vec![2]; + let nl: Vec = vec![2]; + let as_starts: Vec = vec![6]; + let al: Vec = vec![3]; + record.push_aux(b"ns", Aux::ArrayU32((&ns).into())).unwrap(); + record.push_aux(b"nl", Aux::ArrayU32((&nl).into())).unwrap(); + record.push_aux(b"as", Aux::ArrayU32((&as_starts).into())).unwrap(); + record.push_aux(b"al", Aux::ArrayU32((&al).into())).unwrap(); + + let annot = read_record(&record).expect("read_record"); + + let nuc = annot + .annotation_types + .iter() + .find(|t| t.name == NUC_TYPE) + .expect("nuc populated from legacy ns/nl"); + assert_eq!(nuc.annotations.len(), 1); + assert_eq!(nuc.annotations[0].start, 2); + assert_eq!(nuc.annotations[0].length, 2); + + let msp = annot + .annotation_types + .iter() + .find(|t| t.name == MSP_TYPE) + .expect("msp populated from legacy as/al"); + assert_eq!(msp.annotations.len(), 1); + assert_eq!(msp.annotations[0].start, 6); + assert_eq!(msp.annotations[0].length, 3); + } +} diff --git a/src/utils/nucleosome.rs b/src/utils/nucleosome.rs index 8f50a011..700e561a 100644 --- a/src/utils/nucleosome.rs +++ b/src/utils/nucleosome.rs @@ -187,7 +187,7 @@ pub fn filter_for_end( /// Compute nucleosomes + MSPs from `m6a` calls and append them to /// `annot` in place. Writing the MA tags onto the record is the /// caller's responsibility (typically via [`FiberseqData::serialize_annotations`] -/// or [`ma_io::write_annotations`]). +/// or [`ma_io::ensure_basemod_encoding`] + [`ma_io::write_record`]). pub fn add_nucleosomes_to_annotations( record: &bam::Record, annot: &mut MolecularAnnotations, diff --git a/tests/basemods.rs b/tests/basemods.rs deleted file mode 100644 index 5865d5a9..00000000 --- a/tests/basemods.rs +++ /dev/null @@ -1,277 +0,0 @@ -use env_logger::{Builder, Target}; -use fibertools_rs::utils::basemods::{ - canonical_header, parse_mm_ml_into_ma, write_mm_ml, CPG_TYPE, M6A_TYPE, -}; -use molecular_annotation::{MolecularAnnotations, QualitySpec, Strand}; -use rust_htslib::bam::record::Aux; -use rust_htslib::{bam, bam::Read}; - -#[test] -/// Round-trip MM/ML through the new MolecularAnnotations-based parser -/// and writer: load MM/ML into a MolecularAnnotations, write it back to -/// the record, re-parse, and assert the m6a/cpg annotation types are -/// equal. Positions and ML qualities round-trip exactly; the MM tag's -/// per-group encoding is normalized to canonical fiberseq form on -/// output (see basemods.rs module docs for the canonicalization table). -fn test_mods_round_trip() { - let _ = Builder::new() - .target(Target::Stderr) - .filter(None, log::LevelFilter::Debug) - .try_init(); - let mut bam = bam::Reader::from_path("tests/data/all.bam").unwrap(); - for rec in bam.records() { - let mut rec = rec.unwrap(); - let mut a = MolecularAnnotations::from_record(&rec); - parse_mm_ml_into_ma(&rec, &mut a, 0, 0); - write_mm_ml(&mut rec, &a); - let mut b = MolecularAnnotations::from_record(&rec); - parse_mm_ml_into_ma(&rec, &mut b, 0, 0); - assert_eq!(a.get_type(M6A_TYPE), b.get_type(M6A_TYPE)); - assert_eq!(a.get_type(CPG_TYPE), b.get_type(CPG_TYPE)); - } -} - -/// Unknown mod-type codes (anything other than `"a"` / `"m"` — -/// including single-char like `C+h` and multi-char like `C+ac`) are -/// dropped on parse with a warning. We don't store them as their own -/// annotation type; fibertools-rs's typed API only covers m6a and cpg. -#[test] -fn test_unknown_modtype_warns_and_skips() { - let mut bam = bam::Reader::from_path("tests/data/all.bam").unwrap(); - let mut rec = bam.records().next().expect("all.bam has records").unwrap(); - - // Pick the first C in forward orientation to attach a single C+h - // call to. Then append a real C+m call so we can confirm the unknown - // group doesn't break ML alignment for the canonical one. - let fwd = if rec.is_reverse() { - bio::alphabets::dna::revcomp(rec.seq().as_bytes()) - } else { - rec.seq().as_bytes() - }; - let _first_c = fwd - .iter() - .position(|&b| b == b'C') - .expect("seq has a C"); - - // C+h,0; then C+m,0; — both attach to the first C in the seq. - let mm = "C+h,0;C+m,0;"; - let ml: Vec = vec![123, 200]; - rec.remove_aux(b"MM").ok(); - rec.remove_aux(b"ML").ok(); - rec.push_aux(b"MM", Aux::String(mm)).unwrap(); - rec.push_aux(b"ML", Aux::ArrayU8((&ml).into())).unwrap(); - - let mut a = MolecularAnnotations::from_record(&rec); - parse_mm_ml_into_ma(&rec, &mut a, 0, 0); - - // C+h must be dropped entirely — no "C+h" type, no m6a leakage. - assert!(a.get_type("C+h").is_none(), "C+h must not be stored"); - assert!(a.get_type(M6A_TYPE).is_none(), "C+h must not leak into m6a"); - // C+m still landed under cpg with the correct quality — proving the - // ML offset wasn't desynced by the skipped C+h group. - let cpg = a.get_type(CPG_TYPE).expect("C+m landed under cpg"); - assert_eq!(cpg.annotations.len(), 1); - assert_eq!(cpg.annotations[0].qualities, vec![200]); -} - -/// A malformed MM tag — claiming more `mod_base` positions than the -/// forward sequence actually contains — must warn and truncate, not -/// panic. The next group's ML qualities must still align with its -/// positions (ML offsets are based on on-disk slot count, not resolved -/// count). -#[test] -fn test_malformed_mm_truncates_without_panic() { - let mut bam = bam::Reader::from_path("tests/data/all.bam").unwrap(); - let mut rec = bam.records().next().expect("all.bam has records").unwrap(); - - let fwd = if rec.is_reverse() { - bio::alphabets::dna::revcomp(rec.seq().as_bytes()) - } else { - rec.seq().as_bytes() - }; - let total_a = fwd.iter().filter(|&&b| b == b'A' || b == b'a').count(); - let total_c = fwd.iter().filter(|&&b| b == b'C' || b == b'c').count(); - assert!(total_a >= 2 && total_c >= 1); - - // First group `A+a` claims `total_a + 2` positions — two more than - // the sequence has, forcing the resolver to truncate. Second group - // `C+m` claims one legitimate C. The ML tag has the on-disk slot - // count for both groups; if ML offsets advance correctly, the - // C+m quality is the LAST byte. - let bogus_a_count = total_a + 2; - let mut mm = String::from("A+a"); - for _ in 0..bogus_a_count { - mm.push_str(",0"); - } - mm.push(';'); - mm.push_str("C+m,0;"); - - let mut ml: Vec = vec![100; bogus_a_count]; - ml.push(222); // sentinel for the C+m call - - rec.remove_aux(b"MM").ok(); - rec.remove_aux(b"ML").ok(); - rec.push_aux(b"MM", Aux::String(&mm)).unwrap(); - rec.push_aux(b"ML", Aux::ArrayU8((&ml).into())).unwrap(); - - let mut a = MolecularAnnotations::from_record(&rec); - // Must not panic. - parse_mm_ml_into_ma(&rec, &mut a, 0, 0); - - // The resolved m6a count equals the number of A bases in the - // sequence (truncated from the claimed bogus count). - let m6a = a.get_type(M6A_TYPE).expect("m6a present"); - assert_eq!(m6a.annotations.len(), total_a); - // And the C+m quality survived intact — proving the ML offset - // didn't get shifted by the truncated A+a section. - let cpg = a.get_type(CPG_TYPE).expect("cpg present"); - assert_eq!(cpg.annotations.len(), 1); - assert_eq!(cpg.annotations[0].qualities, vec![222]); -} - -/// `parse_mm_ml_into_ma` is idempotent: calling it twice on the same -/// `annot` (or once on an `annot` that already has a stale `m6a` type -/// from elsewhere) must overwrite, not append. -#[test] -fn test_parse_mm_ml_idempotent_on_rerun() { - let mut bam = bam::Reader::from_path("tests/data/all.bam").unwrap(); - let rec = bam - .records() - .filter_map(|r| r.ok()) - .find(|r| matches!(r.aux(b"MM"), Ok(Aux::String(_)))) - .expect("all.bam has at least one record with MM"); - - let mut once = MolecularAnnotations::from_record(&rec); - parse_mm_ml_into_ma(&rec, &mut once, 0, 0); - let once_m6a = once.get_type(M6A_TYPE).cloned(); - let once_cpg = once.get_type(CPG_TYPE).cloned(); - - // Second pass on the same annot must produce the same counts. - parse_mm_ml_into_ma(&rec, &mut once, 0, 0); - assert_eq!(once.get_type(M6A_TYPE).cloned(), once_m6a); - assert_eq!(once.get_type(CPG_TYPE).cloned(), once_cpg); - - // Pre-seeded stale m6a (as if leaked into the MA tag set by a bad - // producer) must be discarded, not merged. - let mut seeded = MolecularAnnotations::from_record(&rec); - let qspec = "Q" - .parse::() - .expect("Q parses"); - seeded - .add_annotation_type(M6A_TYPE, qspec) - .add(0, 1, molecular_annotation::Strand::Forward, vec![123], None) - .add(1, 1, molecular_annotation::Strand::Forward, vec![45], None); - parse_mm_ml_into_ma(&rec, &mut seeded, 0, 0); - assert_eq!( - seeded.get_type(M6A_TYPE).cloned(), - once_m6a, - "stale m6a must be replaced by MM/ML, not merged" - ); -} - -/// `N+a` headers must be preserved verbatim through parse→write. Per the -/// SAM spec, `N` matches any base for distance counting; the old write -/// path silently rewrote `N+a` to `A+a;T-a` based on the underlying -/// sequence. The refactor stores each call's MM header on -/// `Annotation.name`, so the literal `N+a` survives. -#[test] -fn test_n_plus_a_preserved_verbatim() { - let mut bam = bam::Reader::from_path("tests/data/all.bam").unwrap(); - let mut rec = bam.records().next().expect("all.bam has records").unwrap(); - - // N+a,0,0,0; marks the first three positions of the forward sequence - // regardless of base. With three zero skips, parse resolves to - // positions [0, 1, 2]. The same encoding round-trips on write - // because the skip-base is N (every base counts). - let mm = "N+a,0,0,0;"; - let ml: Vec = vec![210, 220, 230]; - - rec.remove_aux(b"MM").ok(); - rec.remove_aux(b"ML").ok(); - rec.push_aux(b"MM", Aux::String(mm)).unwrap(); - rec.push_aux(b"ML", Aux::ArrayU8((&ml).into())).unwrap(); - - let mut a = MolecularAnnotations::from_record(&rec); - parse_mm_ml_into_ma(&rec, &mut a, 0, 0); - - let m6a = a.get_type(M6A_TYPE).expect("N+a routes to m6a"); - assert_eq!(m6a.annotations.len(), 3); - // Every annotation should carry the verbatim header `N+a` on its name. - for ann in &m6a.annotations { - assert_eq!(ann.name.as_deref(), Some("N+a")); - } - - write_mm_ml(&mut rec, &a); - let written_mm = match rec.aux(b"MM").unwrap() { - Aux::String(s) => s.to_string(), - _ => panic!("MM tag must be a string"), - }; - assert_eq!( - written_mm, "N+a,0,0,0;", - "N+a must round-trip verbatim, not get normalized to A+a/T-a" - ); - - // And re-parsing yields the same annotation set. - let mut b = MolecularAnnotations::from_record(&rec); - parse_mm_ml_into_ma(&rec, &mut b, 0, 0); - assert_eq!(a.get_type(M6A_TYPE), b.get_type(M6A_TYPE)); -} - -/// Programmatic producers (`predict_m6a`, `ddda_to_m6a`) tag each m6a -/// call with its canonical MM group header via `canonical_header` -/// before adding it to the annotation. This test mirrors that pattern -/// and confirms `write_mm_ml` emits the right groups. -#[test] -fn test_predictor_set_headers_round_trip() { - let mut bam = bam::Reader::from_path("tests/data/all.bam").unwrap(); - let mut rec = bam.records().next().expect("all.bam has records").unwrap(); - - let fwd = if rec.is_reverse() { - bio::alphabets::dna::revcomp(rec.seq().as_bytes()) - } else { - rec.seq().as_bytes() - }; - let first_a = fwd.iter().position(|&b| b == b'A').expect("seq has an A") as u32; - let first_t = fwd.iter().position(|&b| b == b'T').expect("seq has a T") as u32; - - rec.remove_aux(b"MM").ok(); - rec.remove_aux(b"ML").ok(); - let mut annot = MolecularAnnotations::from_record(&rec); - let qspec = "Q".parse::().expect("Q parses"); - let t = annot.add_annotation_type(M6A_TYPE, qspec); - // Each predictor-emitted call carries its canonical header. - let a_header = canonical_header(M6A_TYPE, b'A').unwrap(); - let t_header = canonical_header(M6A_TYPE, b'T').unwrap(); - t.add( - first_a, - 1, - Strand::Forward, - vec![150], - Some(a_header.to_string()), - ); - t.add( - first_t, - 1, - Strand::Forward, - vec![160], - Some(t_header.to_string()), - ); - - write_mm_ml(&mut rec, &annot); - let written_mm = match rec.aux(b"MM").unwrap() { - Aux::String(s) => s.to_string(), - _ => panic!("MM tag must be a string"), - }; - assert!(written_mm.contains("A+a,"), "got: {written_mm}"); - assert!(written_mm.contains("T-a,"), "got: {written_mm}"); - - // Re-parse and confirm positions+qualities survived. - let mut b = MolecularAnnotations::from_record(&rec); - parse_mm_ml_into_ma(&rec, &mut b, 0, 0); - let m6a = b.get_type(M6A_TYPE).expect("m6a present after re-parse"); - let mut positions: Vec = m6a.annotations.iter().map(|a| a.start).collect(); - positions.sort(); - let mut want = vec![first_a, first_t]; - want.sort(); - assert_eq!(positions, want); -} diff --git a/tests/fibertig_test.rs b/tests/fibertig_test.rs index 98f7c81b..bfbd811c 100644 --- a/tests/fibertig_test.rs +++ b/tests/fibertig_test.rs @@ -544,7 +544,7 @@ fn build_tagged_record( t.add(*s, *l, Strand::Forward, vec![], name); } } - ma_io::write_annotations(&mut record, &annot); + ma_io::write_record(&mut record, &annot); record } diff --git a/tests/molecular_annotation.rs b/tests/molecular_annotation.rs index 1a33173f..8b73afe2 100644 --- a/tests/molecular_annotation.rs +++ b/tests/molecular_annotation.rs @@ -12,7 +12,9 @@ use std::path::PathBuf; -use fibertools_rs::utils::ma_io::{read_annotations, write_annotations, MSP_TYPE, NUC_TYPE}; +use fibertools_rs::utils::ma_io::{ + read_annotations, read_record, write_record, MSP_TYPE, NUC_TYPE, +}; use molecular_annotation::{MolecularAnnotations, QualitySpec, Strand}; use rust_htslib::bam::record::Aux; use rust_htslib::bam::{self, Read}; @@ -86,13 +88,31 @@ fn legacy_read_matches_raw_tags() { fn ma_write_then_read_roundtrips() { for fixture in FIXTURES { for record in read_records(fixture) { - let original = read_annotations(&record).unwrap(); + // Use the unified codec (read_record + write_record). The legacy + // pair (read_annotations + write_annotations) cannot round-trip + // MM/ML basemod annotations through MA-only emission; the unified + // codec handles both tag sets via the library's from_record / + // to_record. + let original = read_record(&record).unwrap(); let mut converted = record.clone(); - write_annotations(&mut converted, &original); - - let round = read_annotations(&converted).unwrap(); + write_record(&mut converted, &original); + + let round = read_record(&converted).unwrap(); + + // Compare annotation types as a name-keyed set, not as a Vec — + // the library's to_record / from_record pair doesn't guarantee + // a stable type ordering across the round-trip (MM/ML-derived + // types and MA-tag-derived types interleave differently on the + // read side depending on which tags exist on the record). + // Per-type content equality is what we actually want to verify. + let sort_by_name = |types: &[molecular_annotation::AnnotationType]| { + let mut sorted: Vec<_> = types.iter().cloned().collect(); + sorted.sort_by(|a, b| a.name.cmp(&b.name)); + sorted + }; assert_eq!( - round.annotation_types, original.annotation_types, + sort_by_name(&round.annotation_types), + sort_by_name(&original.annotation_types), "{fixture}: MA round-trip" ); } @@ -162,8 +182,22 @@ fn reverse_strand_keeps_molecular_coords() { #[test] fn missing_annotations_yield_empty_container() { let mut blank = read_records("nuc_example.bam").into_iter().next().unwrap(); + // Strip every annotation source — including MM/ML, which the vendored + // library's from_record now parses into m6a/cpg basemod annotations. + // Pre-library-upgrade this test stripped only MA + legacy ns/nl/as/al; + // MM/ML wasn't read by from_record then, so leaving it in was a no-op. for tag in [ - b"MA", b"AL", b"AQ", b"AN", b"ns", b"nl", b"as", b"al", b"aq", + b"MA" as &[u8], + b"AL", + b"AQ", + b"AN", + b"ns", + b"nl", + b"as", + b"al", + b"aq", + b"MM", + b"ML", ] { blank.remove_aux(tag).ok(); }