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Exit instead of hanging when the output can't be written - #33
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When a write failed (output pipe closed, disk full) with input still left to read, the reader thread stayed blocked on the full read-ahead queue and the thread scope waited for it forever. The queue is now dropped once the writer stops, so the reader exits, and workers skip reads still queued. Present since v0.1.0. Output is unchanged. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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If bonefish couldn't write its output (downstream `samtools sort` killed, disk full, piped into `head`) and there were still reads left to read, it hung at 0% CPU instead of exiting. The reader thread stayed blocked on the full read-ahead queue, and the thread scope waited for it forever. This has been present since v0.1.0. Alignments are never affected, but a failed pipeline step holds its node until the job's time limit.
Fix:
bonefish now exits within a few seconds with exit code 1 and the error ("Broken pipe", "No space left on device").
Tests:
🤖 Generated with Claude Code