Guillermo del Angel a807205fc3 a) Minor optimization to softMax() computation to avoid redundant operations, results in about 5-10% increase in speed in indel calling. ... b) Added (but left commented out since it may affect integration tests and to isolate commits) fix to per-sample DP reporting, so that deletions are included in count. c) Bug fix to avoid having non-reference genotypes assigned to samples with PL=0,0,0. Correct behavior should be to no-call these samples, and to ignore these samples when computing AC distribution since their likelihoods are not informative.		2011-09-09 18:00:23 -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	a) Minor optimization to softMax() computation to avoid redundant operations, results in about 5-10% increase in speed in indel calling.	2011-09-09 18:00:23 -04:00
test	CompOverlap no longer keeps track of the number of comp sites since it wasn't (and cannot) keeping track of them correctly.	2011-09-09 09:45:24 -04:00