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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Mark DePristo dede3a30e9 Improvements to the validation report of VariantEval 
-- If eval has genotypes and comp has genotypes, then subset the genotypes of comp down to the samples being evaluated when considering TP, FP, FN, TN status.  This is important in the case where you want to use this to assess, for example, the quality of calls on NA12878 but you have a CEU trio comp VCF.  The previous version was counting sites polymorphic in mom against the calls in NA12878.
-- Added testdata VCF and integrationtests to ensure this behavior continues in the future
-- TODO: actually run integration tests when I have an internet connection
 		2012-07-18 16:07:47 -04:00
..
CNV BCF2 with support symbolic alleles 2012-06-30 11:22:48 -04:00
annotator Updating many MD5s to reflect correct fixed headers 2012-06-26 15:28:34 -04:00
beagle Fixing remaining integration test errors. Adding missing ex2.bcf 2012-06-30 16:23:11 -04:00
bqsr Refactored/renamed the nested integer array; cleaned up code a bit. 2012-07-03 00:12:33 -04:00
coverage DoC now properly handles reference N bases + misc. additional cleanups 2012-02-25 11:32:50 -05:00
diagnostics Fixing remaining integration test errors. Adding missing ex2.bcf 2012-06-30 16:23:11 -04:00
diffengine Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
fasta Removing the legacy -L "interval1;interval2" syntax 2011-11-21 13:18:53 -05:00
filters BCF2 with support symbolic alleles 2012-06-30 11:22:48 -04:00
genotyper Bug fix in MLEAC calculation for when the exact model says the greedy AC of the alternate allele is zero. 2012-06-22 12:38:48 -04:00
indels Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
phasing - Multi-allelic sites are now correctly ignored - Reporting of mendelian violations enhanced - Corrected TP overflow by caping it to Bye.MAX_VALUE 2012-07-17 15:21:10 -04:00
qc First version of VariantContextBuilder 2011-11-18 11:06:15 -05:00
validation Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
varianteval Improvements to the validation report of VariantEval 2012-07-18 16:07:47 -04:00
variantrecalibration In ApplyRecalibration marking filter as PASS instead of '.' when the site passes by calling .passFilters(). 2012-07-13 15:40:56 -04:00
variantutils Bug fix when specifying a JEXL expression for a field that doesn't exist: we should treat the whole expression as false, but we were rethrowing the JEXL exception in this case. Added integration test to cover this in SelectVariants 2012-07-10 13:59:00 -04:00
BAQIntegrationTest.java merge master 2011-10-25 16:08:39 -04:00
ClipReadsWalkersIntegrationTest.java Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
FlagStatIntegrationTest.java Adding integration test for Flag Stat 2012-04-10 22:40:38 -04:00
PileupWalkerIntegrationTest.java Had some free time, so I unplugged extended events from the walkers. Now they exist only in LocusIteratorByState, but ReadProperties.generateExtendedEvents() always returns false so that block is never actually executed anymore. I don't want to touch LIBS because I think David is in there right now. 2012-04-02 14:27:36 -04:00
PrintReadsIntegrationTest.java Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
PrintReadsUnitTest.java Better location for the downsampling of reads in PrintReads 2012-01-14 14:06:09 -05:00