gatk-3.8

Author	SHA1	Message	Date
aaron	3bf3c21ddd	Changed the assert code in the genome loc to throw exceptions, and deleted a function no one seems to be using. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@569 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-30 13:54:51 +00:00
aaron	96248cdec4	Added some output to all the classes, including build in runtime analysis git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@411 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-14 19:14:53 +00:00
hanna	0629f79049	Moved fasta support files into their own package. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@408 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-14 18:13:23 +00:00
kcibul	ce72932a45	* refactored GenomeLoc to use contigIndex internally for performance and fixed several calling classes * added basic unit test for GenomeLoc * fixed bug when parsing genome locations like chr1:5000 the start position was being left as maxint rather than being set to the same as the stop position. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@365 348d0f76-0448-11de-a6fe-93d51630548a	2009-04-12 02:25:17 +00:00