hanna a7fe07c404 A few stopgap fixes to get the GATK to the point where the old sharding ... infrastructure can be torn down: 1) New sharding system emulates old MonolithicSharding mechanism. 2) Better awareness of differences between fasta and BAM files when creating shards. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2948 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-07 21:01:25 +00:00
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alignment	oops - didn't mean to check this in	2010-03-02 20:28:22 +00:00
gatk	A few stopgap fixes to get the GATK to the point where the old sharding	2010-03-07 21:01:25 +00:00
oneoffprojects/walkers	Forgot to check in fix this morning	2010-03-05 21:07:19 +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	another test-with-multiple outputs fix	2010-03-04 22:46:15 +00:00