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Error with soft-clip at beginning of reference #42

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jtb opened this Issue October 09, 2012 · 1 comment

2 participants

Justin Erik Garrison
Justin
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
Owner
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
permutations.

Resolve #42 by preventing use of soft-clipped sequence at the beginning
of the reference.
f3e5186
Erik Garrison ekg closed this in f3e5186 January 06, 2013
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