Eric Banks f10588420c Fixing path to dbSNP file as the other one was replaced		2011-08-04 12:36:24 -04:00
..
annotator	Removing the Genomic Annotator and its supporting classes	2011-07-25 15:10:25 -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	GATKReport v0.2:	2011-08-03 00:24:47 -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	The Unified Genotyper now does NOT emit SLOD/SB by default; to compute SB use --computeSLOD	2011-08-02 10:14:21 -04:00
indels	Fixing path to dbSNP file as the other one was replaced	2011-08-04 12:36:24 -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	Fixing path to dbSNP file as the other one was replaced	2011-08-04 12:36:24 -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	GATKReport v0.2:	2011-08-03 00:24:47 -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	Adding integration test for left alignment of indels	2011-08-03 12:19:44 -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