Adding logic to check if files exist before appending them after mult… #98
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Pull Request Overview
This PR fixes issues related to multiprocessing output files by adding checks to ensure that each chunk file exists before attempting to read and append its contents.
- Added file existence checks for text chunk files before copying their contents.
- Added file existence checks for BAM chunk files before merging them.
Comments suppressed due to low confidence (1)
src/summarize_alignment.py:801
- Consider logging a warning or error if the expected first text chunk does not exist, as this might indicate an underlying issue in file generation.
if os.path.exists(first_chunk):
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| outpath_bam = output_prefix + ".tagged.bam" | ||
| bam_reader = pysam.AlignmentFile(first_bam_chunk, "rb", check_sq=False) |
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Since a file existence check is performed later for 'first_bam_chunk', consider checking os.path.exists(first_bam_chunk) prior to initializing bam_reader to avoid potential file open errors.
Suggested change
| outpath_bam = output_prefix + ".tagged.bam" | |
| bam_reader = pysam.AlignmentFile(first_bam_chunk, "rb", check_sq=False) | |
| outpath_bam = output_prefix + ".tagged.bam" | |
| if not os.path.exists(first_bam_chunk): | |
| logging.error("The file %s does not exist. Cannot proceed.", first_bam_chunk) | |
| raise FileNotFoundError(f"The file {first_bam_chunk} does not exist.") |
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Fixing multiprocessing output files issues