ebanks c6ad26e04f 1) When quals/GQs are really integers (x.00), strip off the floating points. ... 2) Keep track of whether vcf records are unfiltered vs. pass filters in the variant context so we can regenerate the records on output. 3) No more "ID" hard-coded all over the code to set the VariantContext ID. Use a static variable instead. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3840 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-20 18:01:45 +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) When quals/GQs are really integers (x.00), strip off the floating points.	2010-07-20 18:01:45 +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