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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Mark DePristo c1ac0e2760 BCF2 cleanup 
-- allowMissingVCFHeaders is now part of -U argument.  If you want specifically unsafe VCF processing you need -U LENIENT_VCF_PROCESSING.  Updated lots of files to use this
-- LENIENT_VCF_PROCESSING disables on the fly VCF header cleanup.  This is now implemented via a member variable, not a class variable, which I believe was changing the GATK behavior during integration tests, causing some files to fail that pass when run as a single test because the header reading behavior was changing depending on previous failures.
 		2012-06-26 15:28:33 -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 BCF2 cleanup 2012-06-26 15:28:33 -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 Final fixes before BCF2 mark III push 2012-06-21 15:17:22 -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 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 BCF2 cleanup 2012-06-26 15:28:33 -04:00
variantutils BCF2 cleanup 2012-06-26 15:28:33 -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