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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Mark DePristo 03741fb640 Merge branch 'master' into rodRefactor 
Conflicts:
	public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
	public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
	public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
	public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
 		2011-08-02 14:21:58 -04:00
..
annotator Merge branch 'master' into rodRefactor 2011-08-02 14:21:58 -04:00
beagle 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
coverage Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
diffengine Revert "Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable" 2011-07-19 18:38:53 -04:00
fasta Merge branch 'master' into rodRefactor 2011-08-02 14:21:58 -04:00
filters 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
genotyper Merge branch 'master' into rodRefactor 2011-08-02 14:21:58 -04:00
indels Updating tools to use the RodBinding<T> syntax 2011-08-02 14:05:51 -04:00
phasing Updated MD5 for PhaseByTransmissionIntegrationTest 2011-07-26 17:52:25 -04:00
qc Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
recalibration Updating tools to use the RodBinding<T> syntax 2011-08-02 14:05:51 -04:00
validation When using the BWA bindings, you have to explicitly call close() to get the 2011-07-21 12:13:29 -04:00
varianteval Merge branch 'master' into rodRefactor 2011-08-02 14:21:58 -04:00
variantrecalibration Walker test system refactoring. All MD5DB related functions are now in MD5DB.java. 2011-07-18 10:46:01 -04:00
variantutils Merge branch 'master' into rodRefactor 2011-08-02 14:21:58 -04:00
BAQIntegrationTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ClipReadsWalkersIntegrationTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
PileupWalkerIntegrationTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
PrintReadsIntegrationTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
PrintReadsWalkerUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00