Return a nonzero exit status for detected paired-end read-count mismatches - #719
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thierrygosselin wants to merge 2 commits into
Open
thierrygosselin wants to merge 2 commits into
thierrygosselin wants to merge 2 commits into
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Replace the warning-and-stop behaviour at the existing paired-pack count check with an explicit error and nonzero exit status. Include both input filenames in the error message instead of silently discarding unmatched reads. This addresses detected count mismatches in separate paired-end files. It does not add identifier validation or change interleaved input handling.
Test both shorter-mate directions around pack boundaries and with inputs exceeding 40,000 reads, using one and four threads. Require a nonzero exit status and an explicit count-mismatch diagnostic. Verify that equal inputs and intentional reads_to_process limits continue to succeed. All 20 cases pass with the fix. Unmodified Conda fastp 1.3.6 returns success for all 12 unequal-input cases.
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Summary
When paired input packs contain different numbers of reads, fastp currently warns, discards unmatched reads, and can finish with exit status 0.
This PR changes the existing mismatch check to fail explicitly and identify both input files.
Changes
error_exit()when paired-pack counts differ.Regression tests
Added synthetic tests covering:
--reads_to_processlimits.Run with:
On macOS ARM64, all 20 cases pass with the patch. Unmodified Conda fastp 1.3.6 returns success for all 12 unequal-input cases.
Relationship to #694
Related to #694: this addresses failure reporting when a count mismatch is detected. I did not reproduce the historical hang in these tests, so this PR does not claim to resolve every deadlock scenario described there.
Scope
This patch concerns the existing count check for separate paired-end files. It does not validate read identifiers, change interleaved input handling, or scan beyond an intentional processing limit.
Linux execution has not been tested.