delangel d932322190 More necessary fixes for VCF4.0 - now results look more sensible in realistic, bigger VCF files produced by say Dindel and not just the small test VCF: ... - Fixed and cleaned code to produce trailing and padding bases in alleles around indels. - Deal better with missing fields. Pending: - Chopping missing fields at end of genotypes. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3679 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-30 02:59:30 +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/org	More necessary fixes for VCF4.0 - now results look more sensible in realistic, bigger VCF files produced by say Dindel and not just the small test VCF:	2010-06-30 02:59:30 +00:00
test/org/broadinstitute/sting	Added ability to clean using only known indels. Added integration test for it. Fixed vcf->vc conversion for indels which was busted.	2010-06-30 01:20:56 +00:00