Mate pair positions using pysam

Question

[QVINTVS_FABIVS_MAXIMVS]

I can do this for the read in pysam

pos = read.positions
# returns a list of positions

I want to do this for the mate. There is no .mpositions but there is a .mpos

Thanks!

[horticulturesh]

Hello,

It seems that .mpos is deprecated by .next_reference_start now, but I still have a problem using it. If the mate read of a read exists and it is aligned to a position of the chrom, .next_reference_start returns a region of aligned mate reads or just the start?

Thanks a lot,
Fredsamhaak

[John]

Please make a new question horticulturesh, you've "answered" a few other questions with your own questions, which is not how this is supposed to work :P Write a new question, give as much code/data as you can, and you will get an answer :)