feature request: include sequences about bamread HOT 7 CLOSED

Do you know the relevant functions in pysam? I’ll look into it. Thanks for the suggestion.

from bamread.

I haven't looked at your code but if you are using AlignedSegment, then query_sequence should give it to you https://pysam.readthedocs.io/en/latest/api.html#pysam.AlignedSegment.query_sequence

from bamread.

I'll look into it. Will probably have lots of time Monday 👍

from bamread.

Noticed that this was just a one line change, so I just submitted a PR now #4

from bamread.

Here is some code that needs changing too: https://github.com/pyranges/bamread/blob/master/bamread/src/bamread.pyx

I'll do it, but do you have an example bam I could use?

from bamread.

I don't think anything else needs changing. I've been using the branch with my PR to read in sequences without any other changes. Here's an example BAM, in case it's helpful: https://github.com/openvax/varlens/blob/master/test/data/rna_chr17_41244936.bam

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Looking at this now. I've had lots to do - sorry for being tardy!

from bamread.