carneiro 36db9bdcd5 Implemented and tested BWA alignment in the data processing pipeline. ... caveat: Right now bwa only supports one read group, so if the original file had multiple @RG lines, only the first one will be kept. (working on a solution to this) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5931 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-02 23:03:07 +00:00
..
qscript	Implemented and tested BWA alignment in the data processing pipeline.	2011-06-02 23:03:07 +00:00
src/org/broadinstitute/sting	Updated GridEngineJobRunner to return status RUNNING instead of PENDING when a job has been sent to GridEngine, even if it hasn't started.	2011-05-25 17:16:44 +00:00
test/org/broadinstitute/sting/queue	Minor update so the debug messages don't show temp files as chromosome 208799060637697164972	2011-05-26 22:56:33 +00:00