Does this library work with SAM files?

Question

Does this library work with SAM files?

nellore opened this issue 6 years ago · comments

I seem to be running into the error at https://github.com/brentp/hts-nim/blob/master/src/hts/bam.nim#L242 when I try to open a SAM file. Am I doing something silly, or is SAM not supported yet?

Thanks!
A

Brent Pedersen · Answer 1 · Fri Apr 20 2018 04:54:50 GMT+0800 (China Standard Time)

thanks for reporting this. I hadn't noticed this but I just pushed a fix.
please let me know if you have any more issues or questions.

abhinav · Answer 2 · Fri Apr 20 2018 06:25:58 GMT+0800 (China Standard Time)

Thanks for getting on this so fast! I don't think the issue is resolved yet; I don't get any records when I try to iterate over a SAM. So the new test in bamtest.nim doesn't iterate over any records and necessarily succeeds, at least on my Macbook.

Brent Pedersen · Answer 3 · Fri Apr 20 2018 07:11:22 GMT+0800 (China Standard Time)

well, that was sloppy of me. It actually iterates now. thanks for persisting.

abhinav · Answer 4 · Sat Apr 21 2018 05:33:39 GMT+0800 (China Standard Time)

Woooorks! Thanks so much for this slice of awesome.

A

Brent Pedersen · Answer 5 · Sat Apr 21 2018 09:15:04 GMT+0800 (China Standard Time)

sure. let me know if you hit any other issues. there are definitely parts that have not been exercised.