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gatk-3.8/java/test/org/broadinstitute/sting
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ebanks 5f3c80d9aa 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. 
2. Significant refactoring of Plink code to work in the rods and use VariantContext.  More coming.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2913 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-03-02 20:26:40 +00:00
..
alignment 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
gatk docs, cleanup, and some improvements to the iterators. 2010-02-26 22:36:04 +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 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
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 Added the capability to allow expressions in an integration test command (i.e. -filter 'foo') by escaping them in the command. 2009-11-24 02:34:48 +00:00