pezmaster31/bamtools — Issue #30: pileup engine
Author: earonesty
Created: 2012-01-20 20:03:23+00:00
State: open

Not an "Issue"....

i modified the pileup engine to be a "multiple bam" pileup engine (uses a priority queue, it's cute), but then i ran into an issue where i wanted to get the "quality score" for each base in the pileup, and the PositionInAlignment is good for getting the AlignedBase ... but not the QualityString.

Essentially, I'm creating a "PositionInQuery" class member.

I *think* all I have to do is Subtract any "Deletions" from the "PositionInAlignment" as I pass them to get PositionInQuery... but I'm wondering if I'm working too hard for nothing.

Is that all?