Eric Banks ddaf51a50f Updated one integration test for indels		2012-01-25 19:18:51 -05:00
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CNV	Updating md5 because the file changed	2011-09-23 07:33:20 -04:00
annotator	Allow appending with the dbSNP ID even if a (different) ID is already present for the variant rod.	2012-01-25 11:35:54 -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
coverage	Patching special case in the adaptor clipping	2012-01-11 17:47:44 -05:00
diffengine	Right aligning GATKReport numeric columns and updated MD5s in tests.	2011-12-05 23:22:15 -05:00
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	Updated one integration test for indels	2012-01-25 19:18:51 -05:00
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	Bug fix for VariantSummary	2012-01-05 21:51:06 -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: if there are multiple records at a given position, it turns out that SelectVariants would drop all variants that follow after one that fails filters (instead of dropping just the failing one). Added an integration test to cover this case.	2011-12-19 10:04:33 -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	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