feat!: use MolecularAnnotation spec and library#107

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cademirch wants to merge 24 commits into

fiberseq:mainfrom

cademirch:molecular-annotation

Commits on May 27, 2026

fix: adapt ma_io to per-annotation strand and renamed MA record API
cademirch
committed
docs: refresh ma_io module overview
cademirch
committed
feat: ma_io fire+P builder and extractor
cademirch
committed
feat: integrate MA spec into all subcommands
cademirch
committed
fix: faithful range lengths at indel boundaries
cademirch
committed
refactor: derive FiberseqData accessors from MolecularAnnotations
cademirch
committed
chore: update ma library dep
cademirch
committed
refactor: factor out primary_qual; debug-assert single-quality types
cademirch
committed
refactor: move centering onto MA spec project_query/project_reference
cademirch
committed
refactor: migrate fibertig BED ↔ BAM pipeline onto MA spec
cademirch
committed
refactor: collapse BaseMods onto MolecularAnnotations
cademirch
committed
chore: delete bamlift, migrate coord tests to spec liftover
cademirch
committed
refactor: centralize MA I/O on FiberseqData
cademirch
committed
refactor: emit fibertig annotations as MA-spec tags, drop fs/fl/fa
cademirch
committed
fix: read FIRE precision from `fire` type, not msp.qual()
cademirch
committed
fix: clear stale annotations before re-adding on producer re-runs
cademirch
committed
fix: tighten MM/ML basemod dispatch and idempotency
cademirch
committed
fix: recover from malformed MM tags without panicking
cademirch
committed
fix: correct FIRE quality spec; use strand::unknown for nuc/msp/fire
cademirch
committed
refactor: drop legacy tag emission across all writers
cademirch
committed
refactor: treat MSP and FIRE as independent annotation types
cademirch
committed
refactor: rewrite basemod I/O against the MolecularAnnotations spec
cademirch
committed
chore: vendor MA library via workspace, unify rust-htslib at 0.46
cademirch
committed

Commits on May 28, 2026

fix: unify MA tag I/O on the molecular-annotation library
cademirch
committed

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feat!: use MolecularAnnotation spec and library#107

feat!: use MolecularAnnotation spec and library#107
cademirch wants to merge 24 commits into
fiberseq:mainfrom
cademirch:molecular-annotation

Commits on May 27, 2026

fix: adapt ma_io to per-annotation strand and renamed MA record API

docs: refresh ma_io module overview

feat: ma_io fire+P builder and extractor

feat: integrate MA spec into all subcommands

fix: faithful range lengths at indel boundaries

refactor: derive FiberseqData accessors from MolecularAnnotations

chore: update ma library dep

refactor: factor out primary_qual; debug-assert single-quality types

refactor: move centering onto MA spec project_query/project_reference

refactor: migrate fibertig BED ↔ BAM pipeline onto MA spec

refactor: collapse BaseMods onto MolecularAnnotations

chore: delete bamlift, migrate coord tests to spec liftover

refactor: centralize MA I/O on FiberseqData

refactor: emit fibertig annotations as MA-spec tags, drop fs/fl/fa

fix: read FIRE precision from `fire` type, not msp.qual()

fix: clear stale annotations before re-adding on producer re-runs

fix: tighten MM/ML basemod dispatch and idempotency

fix: recover from malformed MM tags without panicking

fix: correct FIRE quality spec; use strand::unknown for nuc/msp/fire

refactor: drop legacy tag emission across all writers

refactor: treat MSP and FIRE as independent annotation types

refactor: rewrite basemod I/O against the MolecularAnnotations spec

chore: vendor MA library via workspace, unify rust-htslib at 0.46

Commits on May 28, 2026

fix: unify MA tag I/O on the molecular-annotation library