Some questions about the alignment length calculation

[samuell]

Hi,

I'm trying to understand the alignment length calculation in get_align_len().

Based on the definition of CIGAR_OPS_ALL:

CIGAR_OPS_ALL = [0, 1, 2, 4]

... together with the definition of these integer values in the PySam docs I get that get_align_len() counts all:

• Matches
• Insertions
• Deletions
• Softclips

Based on this I've go two questions:

1. What is the main motivation for not using pysam.AlignedSegment.query_alignment_length directly?
2. I notice that the query_alignment_length does not count deletions, which I understandmight be one reason why you did not want it?
3. I'm still a little confused as to why you are not including mismatches in your calculation, which is something that is done in query_alignment_length?

Sorry for my if I have missed some explanation of these implementation details somewhere!

Also to be clear, I'm probably just ignorant of how the calculation should be done, so mostly asking to understand this better!

[samuell]

I'm still a little confused as to why you are not including mismatches in your calculation, which is something that is done in query_alignment_length?

Ah, regarding 3. above, I have now learned that apparently the original standard of the CIGAR format is used here, where explicit mismatches are not included. So that explains that.

Still curious about questions 1 and 2, if you have the time though :)