Eric Banks 07c3bd32b3 Bug fix: merge NO_VARIATION records with those of another type. The sad part is that this WAS covered by integration tests but someone updated the MD5s without actually paying attention...		2012-03-21 12:42:13 -04:00
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CNV	Updating md5 because the file changed	2011-09-23 07:33:20 -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	Improved, public version of ErrorRateByCycle	2012-03-07 13:10:08 -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	Rewriting a few of the indel integration tests for multi-allelics. The old tests were running b37 calls against a b36 reference, so the calls were all ref. The new tests are run against the pilot1 data and then those calls are fed back into the the same bam to test genotype given alleles, with a sprinkling of bi- and tri-allelics.	2012-03-16 14:21:27 -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	Bugfix for VariantEval	2012-03-06 16:56:59 -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: merge NO_VARIATION records with those of another type. The sad part is that this WAS covered by integration tests but someone updated the MD5s without actually paying attention...	2012-03-21 12:42:13 -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