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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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Eric Banks a2597e7f00 This commit incorporates several different changes that each pretty much break all the VCF-based integration tests, so I bunched them all together. We now officially emit VCF4.1 files (woo hoo), which means that the VCF headers are now all different (header version is 4.1 plus counts for some of the annotations are 'A' or 'G'). Also, I've added a Read Filter for reads with MQ=255 ('unavailable' in the SAM spec) and have applied this to the UG and the RMS MQ annotation. 2011-07-12 14:11:53 -04:00
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arguments Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
datasources Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
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 Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
refdata Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
report Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
traversals Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
walkers This commit incorporates several different changes that each pretty much break all the VCF-based integration tests, so I bunched them all together. We now officially emit VCF4.1 files (woo hoo), which means that the VCF headers are now all different (header version is 4.1 plus counts for some of the annotations are 'A' or 'G'). Also, I've added a Read Filter for reads with MQ=255 ('unavailable' in the SAM spec) and have applied this to the UG and the RMS MQ annotation. 2011-07-12 14:11:53 -04:00
GenomeAnalysisEngineUnitTest.java Fixing broken paths to the testdata directory throughout the codebase. 2011-06-29 17:36:47 -04:00
WalkerManagerUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00