ebanks 0dd65461a1 Various improvements to plink, variant context, and VCF code. ... We almost completely support indels. Not yet done with plink stuff. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2926 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-04 17:58:01 +00:00
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alignment	oops - didn't mean to check this in	2010-03-02 20:28:22 +00:00
gatk	Various improvements to plink, variant context, and VCF code.	2010-03-04 17:58:01 +00:00
oneoffprojects/walkers	Quick commit in advance of Aaron's. Just a bunch of refactoring (private classes separated out, put in proper package). Also support added for coverage by read group rather than sample.	2010-02-26 16:39:47 +00:00
playground/gatk/walkers	1. To make indel calls, we need to get rid of the SNP-centricity of our code. First step is to have the reference be a String, not a char in the Genotype. Note that this is just a temporary patch until the genotype code is ported over to use VariantContext.	2010-03-02 20:26:40 +00:00
utils	Update to VCF code to get it up to spec.	2010-03-03 06:12:42 +00:00
BaseTest.java	added root GATKData variable	2010-02-12 15:25:34 +00:00
TrivialInstrumenter.java	fixed a bunch of comments and license headers.	2009-06-10 14:10:46 +00:00
WalkerTest.java	Waypoint check-in: a couple of changes to for Tribble, and adding some options to the integration test for passing in auxillary files that aren’t “%s” command line options.	2010-03-04 16:02:21 +00:00