MD tag

[JakeHagen]

Hi
I might be missing it, but is there anyway to access the information stored in the MD tag?

[xunjieli]

The following snippet should do it. Let me know if you have more question.

#!/usr/bin/env python3.7
from nucleus.io import sam
sam_path = "test.sam"
with sam.SamReader(sam_path, parse_aux_fields=True) as reader:
  for read in reader:
    for tag in read.info:
       if tag == 'MD':
          print(read.info[tag].values[0].string_value)

[JakeHagen]

ok great. I was missing the parse_aux_fields=True. Thank you