ebanks f742980864 1. Refactoring of GenoypeWriters so that parallelization now works again with VCF4.0. We now have just a single reference to the old VCF classes, and that one will be purged soon. ... 2. Moved Jared's VCFTool code into archive so that everything would compile. 3. Added the vcf reference base (needed for indels) as an attribute to the VariantContext from the reader. 4. TribbleRMDTrackBuilderUnitTest was complaining that a validation file didn'r exist, so I commented it out. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3835 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-20 06:16:45 +00:00
..
annotations	More archiving	2010-07-12 17:04:41 +00:00
mendelian	Deleting/archiving as instructed	2010-07-13 15:23:50 +00:00
multisamplecaller	Retiring multi-sample genotyper	2010-05-20 14:11:11 +00:00
oldepthofcoverage	CoverageStatistics has now replaced DepthOfCoverage -- old DoC is in the archive.	2010-04-01 16:27:23 +00:00
oldindels	Removing deprecated version of indel genotyper (putting it in archive in case we need to reproduce original 1KG indel calls for some reason).	2010-01-31 14:05:36 +00:00
oldsecondarybases	Removing deprecated code and walkers for which I had the green light from repository.	2009-12-01 05:58:20 +00:00
vcftools	1. Refactoring of GenoypeWriters so that parallelization now works again with VCF4.0. We now have just a single reference to the old VCF classes, and that one will be purged soon.	2010-07-20 06:16:45 +00:00
AlleleBalanceInspector.java	more clean-up: moving AlleleBalanceInspector to archive.	2010-04-16 20:53:33 +00:00
ConcordanceTruthTable.java	No longer used	2010-04-16 17:57:39 +00:00
DSBWalker.java	moving older versions of the oneoff project to archive, bye-bye	2010-02-04 19:46:27 +00:00
DSBWalkerV2.java	moving older versions of the oneoff project to archive, bye-bye	2010-02-04 19:46:27 +00:00
DuplicateQualsWalker.java	Home for retired duplicateQuals analysis utility	2010-01-06 15:05:00 +00:00
FisherStrand.java	Move VariantAnnotator over to use a StratifiedAlignmentContext split by sample.	2009-12-11 05:28:28 +00:00
HapmapPoolAllelicInfoWalker.java	No longer used	2010-04-16 17:57:39 +00:00