hanna ac5b7dd453 Fixed order-of-operations bug. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@919 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-06 03:22:56 +00:00
..
config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	Fixed order-of-operations bug.	2009-06-06 03:22:56 +00:00
test/org/broadinstitute/sting	major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps.	2009-06-05 23:34:37 +00:00