Failed to display bam alignment details if the CIGAR has "H" or "S"

[songtaogui]

Hi, @lidaof

I was trying to display bam file using WashU browser v48.5.3, however, some of my bam records could not be correctly parsed:

The cigar of this alignment is "4S173M1I184M22D413M"

I have noticed that the "incorrect records" all have soft or hard mask CIGARs (S or H). And in the bam parse script, it seems that the "H" and "S" cigars are not considered.

Is this the reason of incorrect parsing? and how could I display bam with masked records using WashU browser?

Thank you

Best wishes,

SongtaoGui

[lidaof]

Hi @songtaogui, yes, you are correct. I will see what I can do to improve the bam track. Thanks for reporting this issue.

[lidaof]

Hi @xzhuo i guess this has been fixed in your recent PR?

[xzhuo]

The "H" and "S" in the CIGAR string should have been fixed. But there are other issues with the bam track, including the "D" string is still there.

[lidaof]

Thanks! Looks like we would keep this issue open :)