Eric Banks b4749757f8 Fixes for SLOD: 1) didn't work properly for multi-allelics (randomly chose an allele, possibly one that wasn't genotyped in the full context); 2) in cases when there were more alt alleles than the max allowed and the user is calculating SB, we would recompute the best alt alleles(s); 3) for some reason, we were recomputing the LOD for the full context when we'd already done that. Given that this passes integration tests on my end, this should be the last commit before the release.		2012-03-12 01:07:07 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Fixes for SLOD: 1) didn't work properly for multi-allelics (randomly chose an allele, possibly one that wasn't genotyped in the full context); 2) in cases when there were more alt alleles than the max allowed and the user is calculating SB, we would recompute the best alt alleles(s); 3) for some reason, we were recomputing the LOD for the full context when we'd already done that. Given that this passes integration tests on my end, this should be the last commit before the release.	2012-03-12 01:07:07 -04:00
test	CalibrateGenotypeLikelihoods now emits the position of the variant for debugging	2012-03-09 16:00:07 -05:00