delangel b6bdd61283 a) Fix bug when multi-base reference is homopolymeric when writing a VCF4.0 variant context: computation of number of trailing bases was incorrect and we ended up with incorrect position. ... b) Updated VCF4WriterTestWalker to take either VCF3 or VCF4 as inputs (this walker can also be used to convert from 3.3 to 4.0). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3711 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-02 15:19:42 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	a) Fix bug when multi-base reference is homopolymeric when writing a VCF4.0 variant context: computation of number of trailing bases was incorrect and we ended up with incorrect position.	2010-07-02 15:19:42 +00:00
test	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