Mark DePristo f838815343 Updating MD5s for confidence ref site estimation in IndependentAllelesDiploidExactAFCalc ... -- Included logic to only add priors for alleles with sufficient evidence to be called polymorphic. If no alleles are poly make sure to add priors of first allele		2012-10-23 06:47:53 -04:00
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CNV	BCF2 with support symbolic alleles	2012-06-30 11:22:48 -04:00
annotator	Update MD5s with new FS score	2012-08-28 08:06:47 -04:00
beagle	Fixing remaining integration test errors. Adding missing ex2.bcf	2012-06-30 16:23:11 -04:00
bqsr	Bad news folks: BQSR scatter-gather was totally busted; you absolutely cannot trust any BQSR table that was a product of SG (for any version of BQSR). I fixed BQSR-gathering, rewrote (and enabled) the unit test, and confirmed that outputs are now identical whether or not SG is used to create the table.	2012-09-20 14:14:34 -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	Updating MD5s for confidence ref site estimation in IndependentAllelesDiploidExactAFCalc	2012-10-23 06:47:53 -04:00
indels	Allowing the GATK to have non-required outputs	2012-10-15 13:49:08 -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 md5s for VQSR, as VQSLOD is now a double and gets the standard double precision treatment in VCF	2012-08-30 19:41:49 -04:00
variantutils	Updating integration tests for minor changes due to switching to EXACT_INDEPENDENT model by default	2012-10-21 12:43:46 -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	Done GSA-282: Unindexed traversals crash if a read goes off the end of a contig	2012-09-05 21:10:03 -04:00
PrintReadsIntegrationTest.java	ReadShard are no longer allowed to span multiple contigs	2012-08-30 10:15:11 -04:00
PrintReadsUnitTest.java	Removed the "Walker" suffix from all walkers that had it.	2012-07-20 17:27:11 -04:00