Eric Banks 4f7fa3009a I forget why I thought that the VariantAnnotator couldn't run multi-threaded because it works just fine. Now you can specify -nt with VA.		2012-11-26 11:34:59 -05:00
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CNV	BCF2 with support symbolic alleles	2012-06-30 11:22:48 -04:00
annotator	I forget why I thought that the VariantAnnotator couldn't run multi-threaded because it works just fine. Now you can specify -nt with VA.	2012-11-26 11:34:59 -05:00
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	Fix bugs as reported on the forum: BED needs to be explicitly set as the default output format and the output didn't actually adhere to the BED spec.	2012-11-08 15:07:47 -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	Fixing problem reported on forum for VF: DP couldn't be filtered from the FORMAT field, only from the INFO field. Fixed and added integration test.	2012-10-26 00:57:40 -04:00
genotyper	Allow large-scale tests 5 hours each to run	2012-11-01 17:48:58 -04:00
indels	Allow large-scale tests 5 hours each to run	2012-11-01 17:48:58 -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	Fixing md5s to reflect the new HapMap file	2012-10-30 14:27:10 -04:00
variantrecalibration	Fixing md5s to reflect the new HapMap file	2012-10-30 14:27:10 -04:00
variantutils	Fixing md5s to reflect the new HapMap file	2012-10-30 14:27:10 -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