depristo ff66023d83 Trivial change to support filter field in VCF ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2636 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-19 22:56:22 +00:00
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HLAcaller	Looks bigger than it is:	2010-01-15 00:14:35 +00:00
contamination	Modified the walker documentation so that the stray punctuation wouldn't cause the GATK to stop parsing the help documenation early (aka I changed one word).	2009-12-22 20:50:01 +00:00
diagnostics	Added a forgotten column label	2010-01-18 01:00:52 +00:00
duplicates	Removed used routines in duputils; duplicatequals to archive; docs for new duplicate traversal code; general code cleanup; bug fixes for combineduplicates; integration tests for combine duplicates walker	2009-12-29 19:46:29 +00:00
graphalign	Walker for calculating non-independent base errors, v1. Will be moved to somewhere not in core	2009-12-15 02:40:15 +00:00
hybridselection	Update documentation in the new help system	2009-12-16 21:33:12 +00:00
papergenotyper	clean-up of the GATK paper genotyper, and better output formatting for the simple call format we emit.	2010-01-06 20:54:56 +00:00
poolseq	Added - new tests (Hapmap was re-added)	2009-12-14 21:57:20 +00:00
secondaryBases	SecondaryBaseTransitionTableWalker now breaks by genotype and read group, is javadoc annotated, and is compatible with ReadBackedPileup's methods.	2010-01-15 21:43:39 +00:00
varianteval	Trivial change to support filter field in VCF	2010-01-19 22:56:22 +00:00
variantoptimizer	Updated solid_recal_modes to work with bfast aligned data. Added an integration test that uses the BFAST file provided by TGen.	2010-01-19 21:18:02 +00:00
variantstovcf	Looks bigger than it is:	2010-01-15 00:14:35 +00:00
vcftools	New annotateUnion operation -- provides clearer annotations on where a call came from when unioning two VCF call sets	2010-01-16 20:20:37 +00:00
DeNovoSNPWalker.java	Update documentation in the new help system	2009-12-16 21:33:12 +00:00
LocusMismatchWalker.java	Misc. improvements to the LMW code. Support for emitting all sites, regardless of genotype. Min and max quality scores.	2009-12-19 23:20:57 +00:00
SnpCallRateByCoverageWalker.java	Update documentation in the new help system	2009-12-16 21:33:12 +00:00
package-info.java	Adding support to override the help text.	2009-12-07 00:16:26 +00:00