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Error with soft-clip at beginning of reference #42

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jtb opened this Issue Oct 9, 2012 · 1 comment

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jtb commented Oct 9, 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.

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ekg commented Jan 6, 2013

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

@ekg ekg closed this in f3e5186 Jan 6, 2013

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