Eric Banks bb0e3a26fc Added integration test for VCF writing. Also, bug fix for writing the GT-free records.		2011-07-13 14:57:21 -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	Difference is now the general form -- used to be SummarizedDifference. The old Difference class is now a subclass of Difference that includes pointers to specific the master and test DiffElements.	2011-07-12 15:20:28 -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	Fixing integration tests I broke yesterday; removing batch merging test since we don't support that anymore.	2011-07-13 10:01:23 -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	Added integration test for VCF writing. Also, bug fix for writing the GT-free records.	2011-07-13 14:57:21 -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