Mark DePristo 51b0dd01c3 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable		2011-07-18 10:47:29 -04:00
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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	Removed the SpecificDifference class. Now Difference classes always have the option to remember specific master and test values. This means that all summarized differences carry with them specific examples of their differences. Consequently, now even summarized differences give at least one example of the specific difference, even when the count of the difference is > 1. Unit tests updated. Added DiffObjects integrationtest. VCFDiffableReader now specifically reads the first line of the VCF file to capture the version number.	2011-07-18 10:42:35 -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	Walker test system refactoring. All MD5DB related functions are now in MD5DB.java.	2011-07-18 10:46:01 -04:00
variantutils	Walker test system refactoring. All MD5DB related functions are now in MD5DB.java.	2011-07-18 10:46:01 -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