Kiran V Garimella ac9c66138d Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable		2011-07-18 00:20:33 -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	Oops, forgot to update unit test	2011-07-14 14:00:19 -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
sequenom	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
varianteval	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
variantrecalibration	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
variantutils	Uncommenting a stray commented test.	2011-07-17 15:38:33 -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