Mark DePristo ccac77d888 Bugfix for incorrect allele counting in IndelSummary ... -- Previous version would count all alt alleles as present in a sample, even if only 1 were present, because of the way VariantEval subsetted VCs -- Updated code for subsetting VCs by sample to be clearer about how it handles rederiving alleles -- Update a few pieces of code to get previous correct behavior -- Updated a few MD5s as now ref calls at sites in dbSNP are counted as having a comp sites, and therefore show up in known sites when Novelty strat is on (which I think is correct) -- Walkers that used old subsetting function with true are now using clearer version that does rederive alleles by default		2012-08-01 15:45:12 -04:00
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datasources	Add removeProgramRecords argument	2012-08-01 15:33:05 -04:00
downsampling	Make downsampler classes themselves generic (instead of just the Downsampler interface)	2012-06-13 16:43:39 -04:00
executive	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
filters	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
iterators	Officially removing all code associated with extended events. Note that I still have a longer term project on my plate to refactor the ReadBackedPileup, but that's a much larger effort.	2012-06-15 15:55:03 -04:00
refdata	RMDTrackBuilderUnitTest now uses private/testdata file to avoid filesystem race conditions	2012-07-25 22:05:04 -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	Removed the "Walker" suffix from all walkers that had it.	2012-07-20 17:27:11 -04:00
walkers	Bugfix for incorrect allele counting in IndelSummary	2012-08-01 15:45:12 -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	Sorting out HMS error handling (fingers crossed)	2012-07-25 23:13:12 -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