feature request: include sequences

[timodonnell]

Thanks for a great library. It would be very helpful as a general purpose tool if bamread.read_bam_full had the ability to include the query sequences.

[endrebak]

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

[timodonnell]

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

[endrebak]

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

[timodonnell]

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

[endrebak]

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?

[timodonnell]

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

[endrebak]

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