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
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AlleleUnitTest.java	Nearly finalize merging capabilities for CombineVariants. Support for dealing with inconsistent indel alleles at loci. Improvements to Allele and removal of addAllele to MutableGenotype. We are close to being able to merge all of 1000 genomes -- snps and indels -- into a single combined vcf	2010-07-02 13:32:33 +00:00
VariantContextIntegrationTest.java	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
VariantContextUnitTest.java	IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.	2010-07-01 04:40:31 +00:00
VariantJEXLContextUnitTest.java	JEXL2 upgrade. Improvements to JEXL processing including dynamically resolving variable -> value bindings instead of up front adding them to a map. Performance improvements and code cleanup throughout.	2010-06-07 00:33:02 +00:00