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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
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Ami Levy-Moonshine b4447cdca2 In cases where one uses VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE we used to verify that the samples names are unique in VariantContextUtils.simpleMerge for each VCs. It couse to a bug that was reported on the forum (when a VCs had 2 VC from the same sample). 
Now we will check it only in CombineVariants.init using the headers. A new function was added to SamplesUtils with unitTests in CVunitTest.java.
 		2013-01-25 15:49:51 -05:00
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annotator Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
beagle Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
bqsr Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
compression/reducereads Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
diagnostics Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
diffengine Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
fasta Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
filters Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
genotyper Optimized the Allele Biased Downsampling: now it doesn't re-sort the pileup but just removes reads from the original one. 2013-01-18 11:17:31 -05:00
haplotypecaller Updating HC md5s for new cutting algorithm and default band pass filter parameters 2013-01-25 11:07:29 -05:00
indels Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
phasing Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
validation Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
varianteval Since GenotypeConcordance is now a standalone walker, remove the old GenotypeConcordance evaluation module and the associated integration tests. 2013-01-23 14:47:23 -05:00
variantrecalibration Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
variantutils In cases where one uses VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE we used to verify that the samples names are unique in VariantContextUtils.simpleMerge for each VCs. It couse to a bug that was reported on the forum (when a VCs had 2 VC from the same sample). 2013-01-25 15:49:51 -05:00