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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Mark DePristo c0a31b2e5b CombineVariants parallel integration tests 
-- All tests but one (using old bad VCF3 input) run unmodified with parallel code.
-- Disabled UNSAFE_VCF_PROCESSING for all but that test, which changes md5s because the output files have fixed headers
-- Minor optimizations to simpleMerge
 		2012-08-15 21:13:16 -04:00
..
CNV BCF2 with support symbolic alleles 2012-06-30 11:22:48 -04:00
annotator FisherStrand now uses RankSumTest isUsableBase to decide if a read should be included in testing 2012-07-18 16:07:47 -04:00
beagle Fixing remaining integration test errors. Adding missing ex2.bcf 2012-06-30 16:23:11 -04:00
bqsr Cleanup BQSR classes 2012-07-31 08:11:03 -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 Several more walkers have been brought up to use the new Allele representation. 2012-07-27 02:14:25 -04:00
filters Integration test to ensure VariantFiltration makes . -> PASS/FAIL like VQSR 2012-07-25 08:56:39 -04:00
genotyper The UnifiedGenotyper now makes use of base insertion and base deletion quality scores if they exist in the reads. 2012-08-07 13:58:22 -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 Allele refactoring checkpoint #3: all integration tests except for PoolCaller are passing now. Fixed a couple of bugs from old code that popped up during md5 difference review. Added VariantContextUtils.requiresPaddingBase() method for tools that create alleles to use for determining whether or not to add the ref padding base. One of the HaplotypeCaller tests wasn't passing because of RankSumTest differences, so I added a TODO for Ryan to look into this. 2012-07-27 15:48:40 -04:00
varianteval In AlleleCount stratification, check to make sure the AC (or MLEAC) is valid (i.e. not higher than number of chromosomes) and throw a User Error if it isn't. Added a test for bad AC. 2012-08-14 15:02:30 -04:00
variantrecalibration Bugfixes for BCF with VQSR 2012-08-07 17:22:39 -04:00
variantutils CombineVariants parallel integration tests 2012-08-15 21:13:16 -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 Removed the "Walker" suffix from all walkers that had it. 2012-07-20 17:27:11 -04:00