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Modify SAM spec document to better represent restrictions in the SEQ field

Open Psy-Fer opened this issue 1 year ago • 4 comments

Currently, the sam spec document (https://samtools.github.io/hts-specs/SAMv1.pdf) has the following for the mandatory SEQ field

10 SEQ String *|[A-Za-z=.]+ segment SEQuence

image

This doesn't really match up with the IUPAC base restriction within the BAM spec, and so anything that is not IUPAC is converted to N.

This isn't clear in the document.

I propose this should be updated to avoid confusion.

Cheers, James

Psy-Fer avatar Oct 31 '24 03:10 Psy-Fer