gatk-3.8

Commit Graph

Author	SHA1	Message	Date
hanna	96241c6637	More testng fallout: fixing another seemingly 'random' issue arising from an alternate test ordering. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5160 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-01 15:25:50 +00:00
hanna	4a33cdacde	Some basic integration tests detecting breakage in OTF BAM index generation. Doing it manually for the moment so that there's at least something testing this capability; will followup eventually with Mark to see whether we can shape the VCF index generation code in such a way that it supports BAM index testing as well. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5093 348d0f76-0448-11de-a6fe-93d51630548a	2011-01-26 23:48:04 +00:00
depristo	a51061fd96	Improved distributed processing analytics. Still not 100% ready for prime-time. More improvements incoming. Iterator claim now supports requests to obtain in a single atomic claim (one lock) multiple sequential shards, which radically reduces overhead. However, deadlocking is still possible... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5061 348d0f76-0448-11de-a6fe-93d51630548a	2011-01-23 16:17:25 +00:00
hanna	acfe83920b	'-L unmapped': adding integration tests for explicitly including (-L unmapped) unmapped reads and explicitly excluding (-XL unmapped) unmapped reads, augmenting the suite of unit tests already put in place. '-L unmapped' seems safe to use; go for it, but please validate results against samtools flagstat when the process finishes. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4849 348d0f76-0448-11de-a6fe-93d51630548a	2010-12-15 23:11:46 +00:00
hanna	861ee3e37a	Changing testing framework from junit -> testng, for its enhanced configurability. Initial test to see how Bamboo will respond. More detailed email to follow. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4609 348d0f76-0448-11de-a6fe-93d51630548a	2010-11-01 21:31:44 +00:00
hanna	78343be52c	At some time in the recent past, we lost our ability to process the '-L all' argument. Brought it back, and added an integrationtest to make sure it stays around. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4390 348d0f76-0448-11de-a6fe-93d51630548a	2010-09-30 15:58:43 +00:00

6 Commits (af09170167fa094fc43563848f92fc2fb3c3ae75)