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dwinter / accuMUlate

code for calling mutatons from MA lines
MIT License
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Deletions being reported as SNPs #34

Closed reedacartwright closed 7 years ago

reedacartwright commented 7 years ago

In the following situation accuMUlate reports deletions as SNPs (tview-like output):

TAC
.*.
.*.
,*,
,*,

This is reported as an A>C SNP instead of a deletion. I suspect that CIGAR parsing is failing (these lines have hard clipping as well).

dwinter commented 7 years ago

Hmmm, that seems like a problem. I can look at it next week, in the meantime can you or @arcova send an example location I can use to test this?

arcova commented 7 years ago

@dwinter- sorry to be slow to respond. i've had crappy internet over the weekend. do you just want a .bam or .sam file with info on just that single example site?

dwinter commented 7 years ago

Hey @arcova , I think I've worked this out.

Probably easier if I push the fixed code (once I've added some tests etc) and get you to compile it and run it on your end to check if it actually works on the real data