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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Christopher Hartl 5d706c9e92 Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 
Removing PSP and CSM

Conflicts:

	public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java
	public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
 		2011-07-19 20:25:33 -04:00
..
annotator 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
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 Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -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 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
indels Updated to reflect dbsnp conversion fix 2011-06-30 11:55:56 -04:00
phasing Corrected typo in MergeAndMatchHaplotypes integration test 2011-07-17 22:50:54 -04:00
qc Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
recalibration Adding MappingQualityUnavailableReadFilter to the SNP and indel CountCovariates 2011-07-12 15:39:07 -04:00
validation BWA bindings and tests moved to public (was required for ValidationAmplicons) 2011-07-19 20:11:31 -04:00
varianteval Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -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 Revert "Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable" 2011-07-19 18:38:53 -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