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Revisit SE/PE auto-detection as Samtools adds lots of @PG lines #384

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FelixKrueger opened this issue Oct 16, 2020 · 1 comment
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Revisit SE/PE auto-detection as Samtools adds lots of @PG lines #384

FelixKrueger opened this issue Oct 16, 2020 · 1 comment
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New versions of Samtools seem to add lots of lines starting with @PQ, and this seems to screw up the single-end/paired-end auto detection of deduplicate_bismark and bismark_methylation_extractor.

In the methylation course we have seen PE files being processed as SE.
@FelixKrueger FelixKrueger self-assigned this Oct 16, 2020
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FelixKrueger commented Oct 30, 2020 •
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Changed the auto-detect behaviour in deduplicate_bismark here: 390f02d

@FelixKrueger FelixKrueger mentioned this issue Jan 25, 2021
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