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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Mark DePristo b08d63a6b8 Documentation and code cleanup for ClipReads, CallableLoci, and VariantsToTable 
-- Swapped -o [summary] and -ob [bam] for more standard -o [bam] and -os [summary] arguments.
-- @Advanced arguments
 		2011-08-19 15:06:37 -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 Implementation in VE was confusing 'variant' status vs. 'polymorphic' status. This led to issues because we now match types of eval and comp; specifically, subsetting a VC to a monomorphic sample can't change the 'variant' status of the VC (it's still a variant site or otherwise we'll never match the comps, which breaks GenotypeConcordance). CountVariants really got this wrong. Fixed. VE now passes all integration tests. 2011-08-12 02:22:44 -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 Documentation and code cleanup for ClipReads, CallableLoci, and VariantsToTable 2011-08-19 15:06:37 -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