gatk-3.8

Author	SHA1	Message	Date
ebanks	6b5c88d4d6	The GATK no longer writes vcf3.3; welcome to the world of vcf4.0. Needed to fix a few output bugs to get this to work, but it's looking great. Much more still to come. Guillermo: hopefully this doesn't break your local build too badly. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3786 348d0f76-0448-11de-a6fe-93d51630548a	2010-07-14 04:56:58 +00:00
aaron	43ca595d15	VCF headers now can be set to a particular VCF version after creation, which converts the header lines to the appropriate encoding on output. Plus some clean-up of the code. Also commented out the Tribble index out-of-date tests, the timing seems to be troublesome from the farm. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3702 348d0f76-0448-11de-a6fe-93d51630548a	2010-07-01 05:32:14 +00:00
aaron	d3848745ab	moving VCF 3.3 back into the GATK so Guillermo can make changes for VCF 4 output git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3639 348d0f76-0448-11de-a6fe-93d51630548a	2010-06-25 18:20:06 +00:00