From 4f76809d7756f6e15bf0261ed6e5434ee06ce52f Mon Sep 17 00:00:00 2001
From: kojix2 <2xijok@gmail.com>
Date: Sat, 25 Jan 2025 15:34:05 +0900
Subject: [PATCH 1/3] Add value_name for resolution argument

---
 d4tools/src/plot/cli.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/d4tools/src/plot/cli.yml b/d4tools/src/plot/cli.yml
index 76d9097..27727ed 100644
--- a/d4tools/src/plot/cli.yml
+++ b/d4tools/src/plot/cli.yml
@@ -14,6 +14,7 @@ args:
         short: R
         long: resolution
         help: Specify the resolution of the output image
+        value_name: widthxheight
     - region:
         required: true
         short: r

From 5281dc9a5154ddc38d1e7265ccaa527c9e2bd5f5 Mon Sep 17 00:00:00 2001
From: kojix2 <2xijok@gmail.com>
Date: Sat, 25 Jan 2025 16:36:49 +0900
Subject: [PATCH 2/3] Add options for binning data

---
 d4tools/src/plot/cli.yml | 12 +++++++++++-
 d4tools/src/plot/mod.rs  | 35 ++++++++++++++++++++++++++++++++++-
 2 files changed, 45 insertions(+), 2 deletions(-)

diff --git a/d4tools/src/plot/cli.yml b/d4tools/src/plot/cli.yml
index 27727ed..0e23328 100644
--- a/d4tools/src/plot/cli.yml
+++ b/d4tools/src/plot/cli.yml
@@ -20,4 +20,14 @@ args:
         short: r
         long: region
         help: Regions to be plotted
-        value_name: chr[:start[-end]]
\ No newline at end of file
+        value_name: chr[:start[-end]]
+    - nbins:
+        short: n
+        long: nbins
+        help: Number of bins for data downsampling
+        value_name: n
+    - bin-width:
+        short: w
+        long: bin-width
+        help: Width of each bin in base pairs
+        value_name: width
diff --git a/d4tools/src/plot/mod.rs b/d4tools/src/plot/mod.rs
index 7918bfa..52c0f69 100644
--- a/d4tools/src/plot/mod.rs
+++ b/d4tools/src/plot/mod.rs
@@ -86,7 +86,40 @@ pub fn entry_point(args: Vec<String>) -> Result<(), Box<dyn std::error::Error>>
         })
         .unwrap();
 
-    let data = downsample_data(input, &chr, (left, right), 256)?;
+    let range_length = right as u64 - left as u64 + 1;
+
+    let nbins = matches.value_of("nbins").map(|v| v.parse::<u64>().unwrap());
+    let bin_width = matches
+        .value_of("bin-width")
+        .map(|v| v.parse::<u64>().unwrap());
+
+    let nbins = match (nbins, bin_width) {
+        (Some(n), None) => n,
+        (None, Some(width)) => {
+            if width == 0 {
+                panic!("Invalid bin-width: cannot be zero");
+            }
+            (range_length / width).max(1)
+        }
+        (Some(n), Some(width)) => {
+            if width == 0 {
+                panic!("Invalid bin-width: cannot be zero");
+            }
+            let calculated_nbins = (range_length / width).max(1);
+            if n != calculated_nbins {
+                panic!(
+                    "Conflicting options: --nbins ({}) and --bin-width ({}) do not match.",
+                    n, width
+                );
+            }
+            n
+        }
+        (None, None) => 256,
+    };
+
+    let nbins = nbins as usize;
+
+    let data = downsample_data(input, &chr, (left, right), nbins)?;
 
     let pos_range = plotters::data::fitting_range(data.iter().map(|x| &x.0));
     let mut data_range = plotters::data::fitting_range(data.iter().map(|x| &x.1));

From a2755df9bff98babcfa3ae4a9985a1cbe3d7a961 Mon Sep 17 00:00:00 2001
From: kojix2 <2xijok@gmail.com>
Date: Thu, 11 Jun 2026 00:19:33 +0900
Subject: [PATCH 3/3] Fix plot bin calculation edge cases

Assisted-by: Codex 5.5
---
 d4tools/src/plot/mod.rs | 35 +++++++++++++++++++++++++++++++----
 1 file changed, 31 insertions(+), 4 deletions(-)

diff --git a/d4tools/src/plot/mod.rs b/d4tools/src/plot/mod.rs
index 52c0f69..a8535b5 100644
--- a/d4tools/src/plot/mod.rs
+++ b/d4tools/src/plot/mod.rs
@@ -54,6 +54,25 @@ fn downsample_data(
         .collect())
 }
 
+fn actual_range_length(
+    path: &str,
+    chr: &str,
+    mut range: (u32, u32),
+) -> Result<u64, Box<dyn std::error::Error>> {
+    let input: d4::D4TrackReader = d4::D4TrackReader::open(path)?;
+    let target = input
+        .header()
+        .chrom_list()
+        .iter()
+        .find(|this| this.name == chr)
+        .unwrap();
+
+    range.0 = range.0.min(target.size as u32);
+    range.1 = range.1.max(range.0).min(target.size as u32);
+
+    Ok(range.1 as u64 - range.0 as u64 + 1)
+}
+
 pub fn entry_point(args: Vec<String>) -> Result<(), Box<dyn std::error::Error>> {
     let yaml = load_yaml!("cli.yml");
     let matches = App::from_yaml(yaml)
@@ -86,7 +105,7 @@ pub fn entry_point(args: Vec<String>) -> Result<(), Box<dyn std::error::Error>>
         })
         .unwrap();
 
-    let range_length = right as u64 - left as u64 + 1;
+    let range_length = actual_range_length(input, &chr, (left, right))?;
 
     let nbins = matches.value_of("nbins").map(|v| v.parse::<u64>().unwrap());
     let bin_width = matches
@@ -94,18 +113,26 @@ pub fn entry_point(args: Vec<String>) -> Result<(), Box<dyn std::error::Error>>
         .map(|v| v.parse::<u64>().unwrap());
 
     let nbins = match (nbins, bin_width) {
-        (Some(n), None) => n,
+        (Some(n), None) => {
+            if n == 0 {
+                panic!("Invalid nbins: cannot be zero");
+            }
+            n
+        }
         (None, Some(width)) => {
             if width == 0 {
                 panic!("Invalid bin-width: cannot be zero");
             }
-            (range_length / width).max(1)
+            (range_length - 1) / width + 1
         }
         (Some(n), Some(width)) => {
+            if n == 0 {
+                panic!("Invalid nbins: cannot be zero");
+            }
             if width == 0 {
                 panic!("Invalid bin-width: cannot be zero");
             }
-            let calculated_nbins = (range_length / width).max(1);
+            let calculated_nbins = (range_length - 1) / width + 1;
             if n != calculated_nbins {
                 panic!(
                     "Conflicting options: --nbins ({}) and --bin-width ({}) do not match.",