ebanks ca5b274f16 Unit, integration, and performance tests are all busted, so this is a good time to make a big commit... ... Major cleanup of the genotype writer code from the calling end. UG no longer supports making calls in anything but VCF, and that allows us to use the VCFWriter more generically now. Putting the ball in Matt's court to finish collapsing everything. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3996 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-10 04:18:29 +00:00
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alignment	IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.	2010-07-01 04:40:31 +00:00
analyzecovariates	Changed logging level to default at INFO instead of WARN.	2010-08-09 16:42:48 +00:00
commandline	Changed logging level to default at INFO instead of WARN.	2010-08-09 16:42:48 +00:00
gatk	Unit, integration, and performance tests are all busted, so this is a good time to make a big commit...	2010-08-10 04:18:29 +00:00
oneoffprojects	Starting the clean up of the sting.utils.genotype code which is all either moving to Tribble, moving to sting.utils.vcf, or being removed.	2010-08-10 02:16:05 +00:00
playground	Starting the clean up of the sting.utils.genotype code which is all either moving to Tribble, moving to sting.utils.vcf, or being removed.	2010-08-10 02:16:05 +00:00
queue	Changed logging level to default at INFO instead of WARN.	2010-08-09 16:42:48 +00:00
utils	Unit, integration, and performance tests are all busted, so this is a good time to make a big commit...	2010-08-10 04:18:29 +00:00