From e2fc88fe75a842f7a5da9aa71379df557f69cb46 Mon Sep 17 00:00:00 2001
From: Nils Homer <nilshomer@gmail.com>
Date: Wed, 10 Jun 2026 22:16:33 -0700
Subject: [PATCH] fix(correct): rejects BAM carries the input header verbatim
 (#332 contract)
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`fgumi correct --rejects` stamped the rejects BAM with header_as_unsorted(self.header),
stripping the input's @HD GO/SS sort fields and forcing SO:unsorted. Per the PR #332
rejects contract, rejects are raw-input records (input order, already via correct's
fan-out branch) and must carry the INPUT header verbatim. For correct, self.header IS
the input header (correct preserves input order and does not swap in a consensus
header), so use it as-is for the rejects writer.

Fixes test_bgzf_eof::{test_correct_rejects_has_bgzf_eof,
test_correct_single_threaded_rejects_has_bgzf_eof}. The simplex/duplex/codec rejects
paths still use header_as_unsorted via their mutex side-channel; correcting those
requires the full fan-out migration (input header + input order together, since a
header-only change would mislabel the mutex-order records) — tracked separately.
---
 src/lib/pipeline/chains/builder.rs | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/src/lib/pipeline/chains/builder.rs b/src/lib/pipeline/chains/builder.rs
index bdb718013..1f186842d 100644
--- a/src/lib/pipeline/chains/builder.rs
+++ b/src/lib/pipeline/chains/builder.rs
@@ -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
@@ -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)]
@@ -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
@@ -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}"))?;