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When 0 reads remain after decontamination, an invalid gzip file is created #24

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bede opened this issue Jul 23, 2023 · 1 comment
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When 0 reads remain after decontamination, an invalid gzip file is created #24

bede opened this issue Jul 23, 2023 · 1 comment
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bug Something isn't working
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bede commented Jul 23, 2023 •
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Samtools considers an empty SAM/BAM file invalid, irritatingly. Workaround is to create empty but valid gzip file e.g.:

with gzip.open('empty.fastq.gz', 'wb') as f:
    pass
@bede bede added this to the 1.0.0 milestone Dec 23, 2023
@bede bede mentioned this issue Dec 23, 2023
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@bede bede added the bug Something isn't working label Dec 23, 2023
bede added a commit that referenced this issue Jan 13, 2024
@bede
Fixes issue where empty output FASTQs were invalid gzip files (#24)
0b5ad56
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bede commented Jan 13, 2024

Fixed in 0b5ad56

@bede bede closed this as completed Jan 13, 2024
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