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[FIX] Missing SQ header in BAM output #2515

Merged
merged 1 commit into from
Apr 12, 2024
Merged

[FIX] Missing SQ header in BAM output #2515

merged 1 commit into from
Apr 12, 2024

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eseiler
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@eseiler eseiler commented Apr 9, 2024 •
edited

The BAM output is missing the @SQ headers derived from the context.

According to the SAM spec, the header should contain the references.

When rewriting a seqan2 BAM with samtools view -hb, the @SQ lines are silently regenerated (from the l_name, name, and l_ref data fields in the list of reference information in the BAM file).

@eseiler eseiler marked this pull request as ready for review April 9, 2024 16:40
smehringer
smehringer requested changes Apr 11, 2024
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include/seqan/bam_io/write_bam.h Outdated Show resolved Hide resolved
@eseiler eseiler requested a review from smehringer April 11, 2024 13:42
@eseiler eseiler merged commit db5e0ce into seqan:main Apr 12, 2024
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@eseiler eseiler deleted the fix/bam branch April 12, 2024 08:54
@eseiler eseiler mentioned this pull request Apr 18, 2024
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@smehringer smehringer smehringer approved these changes

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@eseiler @smehringer