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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R	Bugfix for singleton runs. Now with histograms where possible	2011-09-06 16:54:01 -04:00
c	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	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
packages	Added edu.mit.broad.picard to Queue packaged jar.	2011-07-23 14:40:29 -04:00
perl	Moving these supported perl scripts to public	2011-07-01 17:26:25 -04:00
scala	Merged bug fix from Stable into Unstable	2011-09-09 01:34:55 -04:00
testdata	GZIP VCF for testing	2011-08-19 09:05:39 -04:00