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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Guillermo del Angel 782453235a Updated VariantEvalIntegrationTest since there's a new column separating nMixed and nComplex in CountVariants 
Misc updates to WholeGenomeIndelCalling.scala
Bug fix in VariantEval (may be temporary, need more investigation): if -disc option is used in sites-only vcf's then a null pointer exception is produced, caused by recent introduction of -xl_sf options.
 		2011-08-20 12:24:22 -04:00
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CNV Fixed bug that required symbolic alleles to be padded with reference base and added integration test to test parsing and output of symbolic alleles 2011-08-12 12:23:44 -04:00
annotator Improved descriptions for the SnpEff annotations in the VCF header 2011-08-17 16:09:10 -04:00
beagle 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
coverage Moving more tools over to the new rod system 2011-08-10 13:42:35 -04:00
diffengine GATKReport v0.2: 2011-08-03 00:24:47 -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 Fixing syntax of BQSR and UG performance tests. 2011-08-11 17:04:09 -04:00
indels Moving more tools over to the new rod system 2011-08-10 13:42:35 -04:00
phasing Update to new RodBinding system 2011-08-11 17:54:16 -04:00
qc 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
recalibration Fixing syntax of BQSR and UG performance tests. 2011-08-11 17:04:09 -04:00
validation Continuing progress towards RodBinding 1.0 2011-08-03 17:19:28 -04:00
varianteval Updated VariantEvalIntegrationTest since there's a new column separating nMixed and nComplex in CountVariants 2011-08-20 12:24:22 -04:00
variantrecalibration Updating VQSR for new RodBinding syntax. Cleaning up indel specific parts of VQSR. 2011-08-10 10:20:37 -04:00
variantutils Dynamic typing of vcf.gz files 2011-08-19 09:05:11 -04:00
BAQIntegrationTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ClipReadsWalkersIntegrationTest.java Swapped argument order but not MD5 order 2011-08-19 16:55:56 -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