Mark DePristo 9121b98167 CombineVariants outputs the first non-MISSING qual, not the maximum ... -- When merging multiple VCF records at a site, the combined VCF record has the QUAL of the first VCF record with a non-MISSING QUAL value. The previous behavior was to take the max QUAL, which resulted in sometime strange downstream confusion.		2012-08-19 10:29:38 -04:00
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datasources	Adding support of X and = CIGAR operators to the GATK	2012-08-10 14:54:07 -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	Updated and more thorough version of the BadCigar read filter	2012-08-17 17:05:27 -04:00
iterators	Adding support of X and = CIGAR operators to the GATK	2012-08-10 14:54:07 -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	CombineVariants outputs the first non-MISSING qual, not the maximum	2012-08-19 10:29:38 -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