Eric Banks 35d9bd377c Moved (nearly) all Walkers from public to protected and removed GATKLite utils		2013-01-07 14:42:40 -05:00
..
CNV	BCF2 with support symbolic alleles	2012-06-30 11:22:48 -04:00
annotator	Remove AAL and update MD5s.	2013-01-04 16:46:14 -05:00
beagle	Fixing remaining integration test errors. Adding missing ex2.bcf	2012-06-30 16:23:11 -04:00
bqsr	Fixed precision problem in the Bayesian calculation of Qemp: we need to cap below max integer because the MathUtils code add +1.	2013-01-07 13:07:36 -05:00
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	Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package	2012-12-19 10:25:22 -05:00
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	Moved (nearly) all Walkers from public to protected and removed GATKLite utils	2013-01-07 14:42:40 -05:00
indels	Allow large-scale tests 5 hours each to run	2012-11-01 17:48:58 -04:00
phasing	Fix for PBT bug reported on the forum: the AD is actually output correctly now (rather than with 'null' or some gibberish memory pointer).	2012-12-13 23:28:30 +00:00
qc	Moved (nearly) all Walkers from public to protected and removed GATKLite utils	2013-01-07 14:42:40 -05:00
readutils	Moved (nearly) all Walkers from public to protected and removed GATKLite utils	2013-01-07 14:42:40 -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	Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package	2012-12-19 10:25:22 -05:00
variantrecalibration	Fixing md5s to reflect the new HapMap file	2012-10-30 14:27:10 -04:00
variantutils	Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package	2012-12-19 10:25:22 -05:00
BAQIntegrationTest.java	merge master	2011-10-25 16:08:39 -04:00