gatk-3.8

Author	SHA1	Message	Date
ebanks	340bd0e2c1	Removed hard-coded pointers to references git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3934 348d0f76-0448-11de-a6fe-93d51630548a	2010-08-04 17:59:37 +00:00
hanna	4995950d04	IndexedFastaSequenceFile is now in Picard; transitioning to that implementation. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3701 348d0f76-0448-11de-a6fe-93d51630548a	2010-07-01 04:40:31 +00:00
hanna	8573b0bc6f	Refactoring intervals, separating the process of parsing interval lists, sorting and merging interval lists, and creating RODs from intervals. This gives Doug the ability to keep using our interval list parsing code when sorting intervals on our behalf. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3159 348d0f76-0448-11de-a6fe-93d51630548a	2010-04-13 15:50:38 +00:00
aaron	4014a8a674	A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: UnitTest and IntegrationTest are the two valid file name patterns for tests. Thanks! git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3135 348d0f76-0448-11de-a6fe-93d51630548a	2010-04-08 06:14:15 +00:00