Fix OutputFileWriter crash when produce_fastq=false and only BAM outp…#268
Merged
Conversation
…ut requested The no-files guard in OutputFileWriter.__init__ was raising ValueError whenever file_handles was empty, but in BAM-only mode the top-level OFW intentionally has no open file handle (pysam manages the merged BAM directly). Guard now exempts the case where a BAM output path is set. Adds unit tests for BAM-only and VCF-only OFW construction, and integration tests for all three produce_fastq=false output combinations through the full runner, which would have caught this regression. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Collaborator
Author
|
Found a small bug during integration tests. Fixed and tests written by Claude to help prevent this kind of error. |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
…ut requested
The no-files guard in OutputFileWriter.init was raising ValueError whenever file_handles was empty, but in BAM-only mode the top-level OFW intentionally has no open file handle (pysam manages the merged BAM directly). Guard now exempts the case where a BAM output path is set.
Adds unit tests for BAM-only and VCF-only OFW construction, and integration tests for all three produce_fastq=false output combinations through the full runner, which would have caught this regression.