Mark DePristo e73406b9b5 CountReadsInActiveRegions now emits a detailed GATK report ... -- This report details which intervals are coming in and how many reads they contain -- Added integration test to verify that the intervals aren't changing, before heading into the ART refactor		2012-03-14 17:26:37 -04:00
..
CNV	Updating md5 because the file changed	2011-09-23 07:33:20 -04:00
activeregionqc	CountReadsInActiveRegions now emits a detailed GATK report	2012-03-14 17:26:37 -04:00
annotator	Updating integration tests now that standard annotations support multiple alleles	2012-02-27 11:32:26 -05:00
beagle	Minor tweaks to T2D-related qscripts. Replacing old md5s from the BeagleIntegrationTest. All differences boiled down either to the accounting of genotypes changed (./. --> 0/0 is no longer a "changed" genotype, and original genotypes that were ./. are represented as OG=. rather than OG=./. .)	2012-01-23 08:25:34 -05:00
bqsr	Unit tests for the context covariate	2012-03-01 17:56:45 -05:00
coverage	DoC now properly handles reference N bases + misc. additional cleanups	2012-02-25 11:32:50 -05:00
diagnostics	GATKReport v1.0	2012-03-12 23:09:19 -04:00
diffengine	GATKReport v1.0	2012-03-12 23:09:19 -04:00
fasta	Removing the legacy -L "interval1;interval2" syntax	2011-11-21 13:18:53 -05:00
filters	Again, fixing the add call when we really mean replace	2011-11-21 19:15:56 -05:00
genotyper	Adding integration test to cover errors from my previous commit (GENOTYPE_GIVEN_ALLELE bugs reported by Sara Pulit and Chris Hartl)	2012-03-13 12:43:40 -04:00
indels	Rename *PerformanceTest test classes to *LargeScaleTest	2011-12-22 10:38:49 -05:00
phasing	Merge with master	2011-11-19 09:56:06 -05:00
qc	First version of VariantContextBuilder	2011-11-18 11:06:15 -05:00
recalibration	Patching special case in the adaptor clipping	2012-01-11 17:47:44 -05:00
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	Updating md5s because MultiallelicSummary is now standard	2012-03-13 16:31:13 -04:00
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	GATKReport v1.0	2012-03-12 23:09:19 -04:00
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	Updated integration tests for the new adaptor clipping fix.	2011-12-30 18:47:14 -05:00
PrintReadsIntegrationTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
PrintReadsUnitTest.java	Better location for the downsampling of reads in PrintReads	2012-01-14 14:06:09 -05:00