Nils Homer

Why not solve it in pysam so everyone can benefit? https://github.com/pysam-developers/pysam/issues/1153

That makes sense. My only hesitancy is that the interface is tied to a specific samtools version, so we’d have to pin the version and revisit the available options each...

@tfenne here's a little tool that may help for now: https://gist.github.com/nh13/79609e2f9d638e98e4db1a1b4a949b5e

@mschubert would you be willing to share some of your data, or one FASTQ record that should have been matched to a sample along with the expected barcode?

Thank-you @mschubert for the clear report!

@msto bump

I think @tfenne was advocating for new files in this PR not to be added to util, not that you would also refactor the existing util directory. Can you please...

I would suggest `platform` as well, given it's the synonym for `vendor` that's used in the SAM spec. @msto does that work?

Do you mean when testing locally? I see we have codecov: https://github.com/fulcrumgenomics/fgpyo/blob/04c1a9c7d2cffefb327f960b8186e88bc1da56a6/.github/workflows/pythonpackage.yml#L87-L90

Do we need a codecov subscription beyond https://github.com/fulcrumgenomics/fgpyo/issues/130#issuecomment-2227067094?