Eric Banks c2ebe58712 Merge remote-tracking branch 'Laurent/master'		2011-11-16 09:34:47 -05:00
..
CNV	Updating md5 because the file changed	2011-09-23 07:33:20 -04:00
annotator	SnpEff 2.0.4 support	2011-11-15 18:36:22 -05:00
beagle	Intermediate (but necessary) fix for Beagle walkers: if a marker is absent in the Beagle output files, but present in the input vcf, there's no reason why it should be omitted in the output vcf. Rather, the vc is written as is from the input vcf	2011-09-13 16:57:37 -04:00
coverage	Updating MD5s	2011-10-04 15:54:45 -07:00
diffengine	DiffObjects no longer prints out the file name in the status so MD5 are stable	2011-10-10 15:10:57 -04:00
fasta	More updates to be consistent with the new rod syntax.	2011-08-09 10:11:37 -04:00
filters	Thanks to Mark for agreeing to transition from 'variants' back to 'variant'. I think I got them all but I've been jumping all around the code, so there might be a straggler or two.	2011-08-09 12:04:55 -04:00
genotyper	Updating UG integration tests (needed updating only because the -mbq default is different from the old -mmq one).	2011-11-02 21:13:44 -04:00
indels	Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative.	2011-10-27 23:55:11 -04:00
phasing	Merge branch 'PhaseByTransmission'	2011-11-14 11:31:28 +01:00
qc	Removing a public -> private dependency from the test suite.	2011-10-13 21:32:52 -04:00
recalibration	Update MD5s for SOLiD recalibration	2011-10-13 18:01:51 -04:00
validation	Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative.	2011-10-27 23:55:11 -04:00
varianteval	SnpEff 2.0.4 support	2011-11-15 18:36:22 -05:00
variantrecalibration	Changing the VQSR command line syntax back to the parsed tags approach. This cleans up the code and makes sure we won't be parsing the same rod file multiple times. I've tried to update the appropriate qscripts.	2011-09-12 12:17:43 -04:00
variantutils	Bug fix in SelectVariants when using a discordance track but no sample specifications. Added integration test to test this.	2011-11-07 15:25:16 -05:00
BAQIntegrationTest.java	merge master	2011-10-25 16:08:39 -04:00
ClipReadsWalkersIntegrationTest.java	Updating MD5s for updated BAM with read groups	2011-10-06 12:15:48 -07:00
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	GATKSAMRecord refactor	2011-11-03 15:43:26 -04:00