Mark DePristo 9121b98167 CombineVariants outputs the first non-MISSING qual, not the maximum ... -- When merging multiple VCF records at a site, the combined VCF record has the QUAL of the first VCF record with a non-MISSING QUAL value. The previous behavior was to take the max QUAL, which resulted in sometime strange downstream confusion.		2012-08-19 10:29:38 -04:00
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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	Update md5 in VariantRecalibrationWalkers test for BCF2 -- only encoding differences	2012-08-16 13:03:13 -04:00
variantutils	CombineVariants outputs the first non-MISSING qual, not the maximum	2012-08-19 10:29:38 -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