Skip to content
This repository

Error with soft-clip at beginning of reference #42

jtb opened this Issue October 09, 2012 · 1 comment

2 participants

Justin Erik Garrison
jtb commented October 09, 2012

I have a read at position 0 and cigar 1S100M. So the soft-clip base is actually at -1. In the soft clip condition in AlleleParser.cpp (around line 1627), the third argument in makeallele becomes the largest unsigned int and causes a substring function to fail. I wouldn't think a soft-clip base should be counted towards the allele at a position.

Erik Garrison
ekg commented January 06, 2013

This sounds right. I'm working on a solution.

Erik Garrison ekg closed this issue from a commit January 06, 2013
Erik Garrison improve scaling of probabilities, resolve #42
When using --allele-balance-priors, --binomial-obs-priors, scale
probabilities according to the number of possible observation

Resolve #42 by preventing use of soft-clipped sequence at the beginning
of the reference.
Erik Garrison ekg closed this in f3e5186 January 06, 2013
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Something went wrong with that request. Please try again.