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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Mark DePristo 5f5885ec78 Updating many MD5s to reflect correct fixed headers 
-- Previous bugfix ensures that header fixing is always on in the GATK by default, even after integration tests that failed and when through the VCFDiffableReader.  Updating md5s to reflect this.
 		2012-06-26 15:28:34 -04:00
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CNV Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -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 Ryan confirmed that we don't need separate arguments to control the context size for insertions and deletions, which allows us to cut down the expensive context calculations. 2012-06-15 09:28:56 -04:00
coverage DoC now properly handles reference N bases + misc. additional cleanups 2012-02-25 11:32:50 -05:00
diagnostics Added integration Tests for DiagnoseTargets 2012-06-25 17:02:46 -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 Updating many MD5s to reflect correct fixed headers 2012-06-26 15:28:34 -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 Updating many MD5s to reflect correct fixed headers 2012-06-26 15:28:34 -04:00
variantutils Updating many MD5s to reflect correct fixed headers 2012-06-26 15:28:34 -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