Mark DePristo 34bdf20132 Bugfix for bad AD values in UG/HC ... -- In the case where we have multiple potential alternative alleles *and* we weren't calling all of them (so that n potential values < n called) we could end up trimming the alleles down which would result in the mismatch between the PerReadAlleleLikelihoodMap alleles and the VariantContext trimmed alleles. -- Fixed by doing two things (1) moving the trimming code after the annotation call and (2) updating AD annotation to check that the alleles in the VariantContext and the PerReadAlleleLikelihoodMap are concordant, which will stop us from degenerating in the future. -- delivers [#50897077]		2013-06-05 17:48:41 -04:00
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gatk/walkers	Bugfix for bad AD values in UG/HC	2013-06-05 17:48:41 -04:00
utils	New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points.	2013-05-13 09:36:39 -04:00