Mark DePristo f838815343 Updating MD5s for confidence ref site estimation in IndependentAllelesDiploidExactAFCalc ... -- Included logic to only add priors for alleles with sufficient evidence to be called polymorphic. If no alleles are poly make sure to add priors of first allele		2012-10-23 06:47:53 -04:00
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datasources	ExperimentalReadShardBalancerUnitTest was being skipped; fixed	2012-09-22 01:56:39 -04:00
downsampling	Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)"	2012-09-10 15:52:39 -04:00
executive	…
filters	Updated and more thorough version of the BadCigar read filter	2012-08-17 17:05:27 -04:00
iterators	Experimental, downsampler-friendly read shard balancer	2012-09-21 22:17:58 -04:00
refdata	Part I of GSA-462: Consistent RODBinding access across Ref and Read trackers	2012-08-30 10:15:10 -04:00
report	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
samples	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
traversals	Retiring TraverseReads and TraverseLoci after testing confirms nano scheduler version in single threaded version is fine	2012-10-22 16:55:06 -04:00
walkers	Updating MD5s for confidence ref site estimation in IndependentAllelesDiploidExactAFCalc	2012-10-23 06:47:53 -04:00
CommandLineGATKUnitTest.java	Adding Unit Tests to cover the exception catching for Picard errors: because we are using String matching, we want to ensure that we know if/when the exception text changes underneath us.	2012-07-18 21:48:58 -04:00
EngineFeaturesIntegrationTest.java	Proper error handling in NanoScheduler	2012-09-19 17:03:13 -04:00
GenomeAnalysisEngineUnitTest.java	Removed the "Walker" suffix from all walkers that had it.	2012-07-20 17:27:11 -04:00
WalkerManagerUnitTest.java	Fixing walker unit test with the new naming convention	2012-07-20 17:50:29 -04:00