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fix(correct): rejects BAM carries the input header verbatim (#332 contract) #397

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Merged
nh13 merged 1 commit into from
Jun 15, 2026
Merged

fix(correct): rejects BAM carries the input header verbatim (#332 contract) #397

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15 changes: 9 additions & 6 deletions src/lib/pipeline/chains/builder.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -1209,9 +1209,11 @@ impl<'a> ChainBuilder<'a> {
/// presence + numeric ranges). Loads UMI sequences and encodes them into
/// [`EncodedUmiSet`] up front.
///
/// The `rejects_header` is the primary output header stamped as `SO:unsorted`
/// via [`header_as_unsorted`] — matching the Phase 2 behaviour in
/// `build_correct_chain`.
/// The `rejects_header` is the **input header verbatim** (PR #332 contract:
/// rejects are raw-input records, so they carry the input's `@HD` sort
/// fields + RG/PG — not the consensus/output header). For `correct`,
/// `self.header` is the input header (correct preserves input order and does
/// not replace `self.header` with a consensus header), so it is used as-is.
///
/// Registers a [`CorrectFinalizeHook`] for: per-thread accumulator reduce →
/// `finalize_metrics` → summary + warn banners → `--min-corrected` ratio
Expand All @@ -1226,7 +1228,6 @@ impl<'a> ChainBuilder<'a> {
/// implemented).
///
/// [`EncodedUmiSet`]: crate::commands::correct::EncodedUmiSet
/// [`header_as_unsorted`]: crate::sam::header_as_unsorted
/// [`DecompressedBlock`]: crate::pipeline::steps::types::DecompressedBlock
/// [`CorrectFinalizeHook`]: crate::pipeline::chains::commands::correct::CorrectFinalizeHook
#[allow(clippy::too_many_lines)]
Expand All @@ -1241,7 +1242,7 @@ impl<'a> ChainBuilder<'a> {
};
use crate::pipeline::steps::group::queryname::GroupByQueryname;
use crate::pipeline::steps::serialize::SerializeBamRecords;
use crate::sam::{SamTag, header_as_unsorted};
use crate::sam::SamTag;
use log::info;

// `Intermediate` is used when correct feeds into align-and-merge
Expand Down Expand Up @@ -1335,7 +1336,9 @@ impl<'a> ChainBuilder<'a> {
let rejects_path = correct_opts.rejects_path.as_ref().ok_or_else(|| {
anyhow!("rejects_path unexpectedly None (build_for dispatch bug)")
})?;
let rejects_header = header_as_unsorted(&self.header);
// PR #332 contract: rejects carry the INPUT header verbatim (raw-input
// records, input order). For correct, `self.header` IS the input header.
let rejects_header = self.header.clone();
let rejects_write =
WriteBgzfFile::new(rejects_path, &rejects_header, self.tuning.compression_level)
.map_err(|e| anyhow!("WriteBgzfFile (rejects): {e}"))?;
Expand Down
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