From e29c02342d051ab1bcb2e75982019b1b07abc2d8 Mon Sep 17 00:00:00 2001
From: Cole Lyman <cole@colelyman.com>
Date: Thu, 28 May 2026 17:03:43 -0600
Subject: [PATCH] Write remaining mergedOutput buffer when in --stdout mode,
 fixes #697

---
 scripts/test_issue_697_stdout_merge.sh | 28 ++++++++++++++++++++++++++
 src/peprocessor.cpp                    |  9 +++++++--
 2 files changed, 35 insertions(+), 2 deletions(-)
 create mode 100755 scripts/test_issue_697_stdout_merge.sh

diff --git a/scripts/test_issue_697_stdout_merge.sh b/scripts/test_issue_697_stdout_merge.sh
new file mode 100755
index 00000000..1d2e6ed6
--- /dev/null
+++ b/scripts/test_issue_697_stdout_merge.sh
@@ -0,0 +1,28 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Repro for issue #697: --stdout should emit merged reads in merge mode.
+
+python - <<'PY' > /tmp/fp_repro_697.interleaved.fq
+seq='AATGTCCCCCAATGGGAAGTTCATCTGGCACTGCCCACAGGTGAGGAGGTCATGATCCCCTTCTGGAGC'
+comp=str.maketrans('ACGTN','TGCAN')
+rc=seq.translate(comp)[::-1]
+qual='I'*len(seq)
+print('@r1/1'); print(seq); print('+'); print(qual)
+print('@r1/2'); print(rc);  print('+'); print(qual)
+PY
+
+./fastp \
+  --disable_adapter_trimming --disable_trim_poly_g \
+  --disable_quality_filtering --disable_length_filtering \
+  --stdin --interleaved_in --merge --stdout \
+  < /tmp/fp_repro_697.interleaved.fq \
+  > /tmp/fp_697_stdout.fq 2> /tmp/fp_697_stdout.log
+
+lines=$(wc -l < /tmp/fp_697_stdout.fq)
+if [[ "$lines" -ne 4 ]]; then
+  echo "FAIL: expected 4 FASTQ lines from --stdout merge mode, got $lines"
+  exit 1
+fi
+
+echo "PASS: issue #697 repro produced $lines lines as expected"
diff --git a/src/peprocessor.cpp b/src/peprocessor.cpp
index 04accbb1..c3355525 100644
--- a/src/peprocessor.cpp
+++ b/src/peprocessor.cpp
@@ -669,8 +669,13 @@ bool PairEndProcessor::processPairEnd(ReadPack* leftPack, ReadPack* rightPack, T
         mLeftWriter->input(tid, new string(std::move(outstr1)));
         mRightWriter->input(tid, new string(std::move(outstr2)));
     } else if(mLeftWriter) {
-        // write singleOutput
-        mLeftWriter->input(tid, new string(std::move(singleOutput)));
+        if(mOptions->merge.enabled && mOptions->outputToSTDOUT) {
+            // in merge+stdout mode, merged reads are buffered in mergedOutput
+            mLeftWriter->input(tid, new string(std::move(mergedOutput)));
+        } else {
+            // write singleOutput
+            mLeftWriter->input(tid, new string(std::move(singleOutput)));
+        }
     }
     // output unpaired reads
     if(mUnpairedLeftWriter && mUnpairedRightWriter) {