Christopher Hartl ba8622ff0d number of stashed changes are lurking in here. In order of importance: ... - Fix for M_Trieb's error report on the forum, and addition of integration tests to cover the walker. - Addition of StructuralIndel as a class of variation within the VariantContext. These are for variants with a full alt allele that's >150bp in length. - Adaptation of the MVLikelihoodRatio to work for a set of trios (takes the max over the trios of the MVLR) - InsertSizeDistribution changed to use the new gatk report output (it was previously broken) - RetrogeneDiscovery changed to be compatible with the new gatk report - A maxIndelSize argument added to SelectVariants - ByTranscriptEvaluator rewritten for cleanliness - VariantRecalibrator modified to not exclude structural indels from recalibration if the mode is INDEL - Documentation added to DepthOfCoverageIntegrationTest (no, don't yell at chartl ;_; ) Also sorry for the long commit history behind this that is the result of fixing merge conflicts. Because this *also* fixes a conflict (from git stash apply), for some reason I can't rebase all of them away. I'm pretty sure some of the commit notes say "this note isn't important because I'm going to rebase it anyway".		2012-08-21 07:08:58 -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	number of stashed changes are lurking in here. In order of importance:	2012-08-21 07:08:58 -04:00
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	number of stashed changes are lurking in here. In order of importance:	2012-08-21 07:08:58 -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