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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Mark DePristo 385a3c630f Added check in VariantContext.validate to ensure that getEnd() == END value when present 
-- Fixed bug in VariantDataManager that this validation mode was intended to detect going forward
-- Still no VariantRecalibrationWalkersIntegrationTest for indels with BCF2 but that's because LowQual is missing from test VCF
 		2012-06-30 11:22:48 -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 Updating many MD5s to reflect correct fixed headers 2012-06-26 15:28:34 -04:00
bqsr NestedHashMap-based implementation of BQSRv2 along with a few minor optimizations. Not a huge runtime upgrade over the long bitset approach, but it allows us to implement further optimizations going forward. Integration test change because the original version had a bug in the quantized qual table creation. 2012-06-27 16:55:49 -04:00
coverage DoC now properly handles reference N bases + misc. additional cleanups 2012-02-25 11:32:50 -05:00
diagnostics Enabling symbolic alleles in BCF2 2012-06-30 11:22:48 -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 Updating many MD5s to reflect correct fixed headers 2012-06-26 15:28:34 -04:00
qc First version of VariantContextBuilder 2011-11-18 11:06:15 -05:00
recalibration Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
validation Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
varianteval Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
variantrecalibration Added check in VariantContext.validate to ensure that getEnd() == END value when present 2012-06-30 11:22:48 -04:00
variantutils Update integration tests to reflect new FT header line standard and new DiagnoseTargets field names 2012-06-28 10:06:06 -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