fix: ft call-peaks --haps fills the H1/H2 columns

src/cli/call_peaks_opts.rs

@@ -34,10 +34,6 @@ pub struct CallPeaksOptions {
     /// Include nucleosome and MSP coverage in pileup (default: only FIRE coverage)
     #[clap(long)]
     pub include_nuc_msp: bool,
-
-    /// Include haplotype-specific calls
-    #[clap(long)]
-    pub haps: bool,
 }
 
 /// The knobs of the shared peak caller. Flattened into `CallPeaksOptions` for the
@@ -81,6 +77,10 @@ pub struct PeakCallingParams {
     /// Minimum FIRE coverage required to calculate a score (default: 4)
     #[clap(long, default_value = "4", hide = true)]
     pub min_fire_coverage: i32,
+
+    /// Include haplotype-specific calls
+    #[clap(long)]
+    pub haps: bool,
 }
 
 /// Local-max window and merge geometry: meaningful for any element source, so

src/subcommands/call_peaks/peaks.rs

@@ -637,7 +637,7 @@ pub fn call_peaks_for_chrom(
             track_fire_elements: true, // Enable FIRE element tracking for peak calling
         },
         rolling_max: Some(params.merge.window_size),
-        haps: false,
+        haps: params.haps,
         per_base: false,
         keep_zeros: false,
         min_fire_coverage: Some(params.min_fire_coverage),

src/subcommands/pileup.rs

@@ -699,19 +699,25 @@ impl<'a> FiberseqPileup<'a> {
             &None,
         );
         let (hap1_data, hap2_data) = if pileup_opts.haps {
+            // Only all_data's FIRE elements are ever read (peak boundaries in
+            // call-peaks), so do not pay for them on the haplotype tracks.
+            let hap_opts = FireTrackOptions {
+                track_fire_elements: false,
+                ..fire_track_opts.clone()
+            };
             (
                 Some(FireTrack::new(
                     chrom.to_string(),
                     chrom_start,
                     chrom_end,
-                    fire_track_opts.clone(),
+                    hap_opts.clone(),
                     &None,
                 )),
                 Some(FireTrack::new(
                     chrom.to_string(),
                     chrom_start,
                     chrom_end,
-                    fire_track_opts.clone(),
+                    hap_opts,
                     &None,
                 )),
             )

src/subcommands/union_peaks.rs

@@ -254,6 +254,7 @@ pub fn run_union_peaks(opts: &UnionPeaksOptions) -> Result<()> {
         max_fdr: 1.0,
         min_fire_frac: Some(0.0),
         min_fire_frac_filter: 0.0,
+        haps: false, // BED intervals carry no HP tag
     };
 
     let mut writer = bio_io::writer(&opts.out)?;

tests/regression/call_peaks.rs

@@ -12,3 +12,22 @@ fn call_peaks_ctcf_snapshot() {
     ]);
     insta::assert_snapshot!(out);
 }
+
+/// `--haps` must fill the H1/H2 columns from HP tags (issue #140: the flag was
+/// parsed but never reached the pileup, so every haplotype column was zero).
+#[test]
+fn call_peaks_haps_fills_haplotype_columns() {
+    let out = run(&[
+        "call-peaks",
+        fixture("NAPA.bam").to_str().unwrap(),
+        "--haps",
+        "--min-fire-frac",
+        "0.5",
+    ]);
+    let peak = out.lines().find(|l| !l.starts_with('#')).expect("one peak");
+    let cols: Vec<&str> = peak.split('\t').collect();
+    // coverage, coverage_H1, coverage_H2
+    assert_eq!(cols[5], "95");
+    assert_eq!(cols[10], "45");
+    assert_eq!(cols[15], "14");
+}