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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Mark DePristo 734756d6b2 Final fixes before BCF2 mark III push 
-- Added MLEAC and MLEAF format lines to PoolCallerWalker
-- VariantFiltrationWalker now throws an error when JEXL variables cannot be found (XXX < 0.5) but passes through (albeit with a disgusting warning) when a variable is found but its value is a bad type (AF < 0.5) where AF == [0.04,0.00] at multi-allelic variation
-- Allow values to pass assertEquals in VariantContextTestProvider when one file contains X=[null, null] and the other has X missing
 		2012-06-21 15:17:22 -04:00
..
CNV Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
annotator Final fixes before BCF2 mark III push 2012-06-21 15:17:22 -04:00
beagle Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -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 DiagnoseTargets with working Q1,Median,Q3 2012-05-29 10:16:45 -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 Final fixes before BCF2 mark III push 2012-06-21 15:17:22 -04:00
genotyper Final fixes before BCF2 mark III push 2012-06-21 15:17:22 -04:00
indels Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
phasing Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -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 Final fixes before BCF2 mark III push 2012-06-21 15:17:22 -04:00
variantutils Final fixes before BCF2 mark III push 2012-06-21 15:17:22 -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