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pachterlab / splitcode

Flexible and efficient parsing, interpreting and editing of sequencing reads
https://pachterlab.github.io/splitcode/
BSD 2-Clause "Simplified" License
39 stars 2 forks source link

feature request: support unmapped BAMs as input #17

Open znorgaard opened 3 months ago

znorgaard commented 3 months ago

For some workflows, you may already have unmapped BAMs when you're ready to use splitcode and it would be helpful if you weren't required to convert them back to FASTQs.

As a specific example, PacBio HiFi data comes off instrument demultiplexed as unmapped BAMs. To do additional tag based extraction or demultiplexing with splitcode you currently need to convert to FASTQ.

Yenaled commented 3 months ago

Thanks -- I do think it'd be very useful as a feature (I mostly just hate writing the code to read/write BAM files which is why I haven't implemented it haha). Labeling this as an enhancement.