Guillermo del Angel f4b409fa0d CombineVariants bug fix: when merging records with disparate alleles we were leaving AC,AF fields intact. This had as a consequence that we could end up with a record with 3 alt alleles but only 2 values in AC,AF fields. Now, if alleles in combined vc are different from original, and if AC,AF fields can't be recomputed from genotypes, we remove attributes from vc map since they'll be invalid anyway. Integration test md5 changed since there were several badly merged records in result		2011-10-21 14:07:20 -04:00
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arguments	Removed -B support. Now explodes with error if -B provided.	2011-08-16 16:13:47 -04:00
datasources	SampleDataSource -> SampleDB	2011-10-03 09:33:30 -07:00
executive	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
filters	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
iterators	Fixing test bugs for WindowMaker that required empty sample list	2011-09-30 14:18:27 -04:00
refdata	Fix for dynamic type determination for bgzip files	2011-09-21 15:39:19 -04:00
report	GATKReport v0.2:	2011-08-03 00:24:47 -04:00
samples	Fixed bad expected value in PedReaderUnitTest	2011-10-06 08:16:47 -07:00
traversals	BugFix for unit test	2011-09-07 14:54:10 -04:00
walkers	CombineVariants bug fix: when merging records with disparate alleles we were leaving AC,AF fields intact. This had as a consequence that we could end up with a record with 3 alt alleles but only 2 values in AC,AF fields. Now, if alleles in combined vc are different from original, and if AC,AF fields can't be recomputed from genotypes, we remove attributes from vc map since they'll be invalid anyway. Integration test md5 changed since there were several badly merged records in result	2011-10-21 14:07:20 -04:00
EngineFeaturesIntegrationTest.java	Thanks to Mark for agreeing to transition from 'variants' back to 'variant'. I think I got them all but I've been jumping all around the code, so there might be a straggler or two.	2011-08-09 12:04:55 -04:00
GenomeAnalysisEngineUnitTest.java	Fixing broken paths to the testdata directory throughout the codebase.	2011-06-29 17:36:47 -04:00
WalkerManagerUnitTest.java	Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant.	2011-08-10 12:20:18 -04:00