chartl 7bc2049031 Updates and bug fixes to private mutations qscript and pipeline libraries. Hand filter strings are now not busted (boo to having to escape quotes); convenience method added to VariantCalling to propagate standard trait data to a given GATK command line -- should be made more scala-esque in the future. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4824 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-13 04:55:13 +00:00
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chartl	Updates and bug fixes to private mutations qscript and pipeline libraries. Hand filter strings are now not busted (boo to having to escape quotes); convenience method added to VariantCalling to propagate standard trait data to a given GATK command line -- should be made more scala-esque in the future.	2010-12-13 04:55:13 +00:00
depristo	- After removing special code for intervals, instead of being of type File they are generated as List[File]. Changed previous checkin that was appending to this list and instead assigning a singleton list.	2010-10-21 06:37:28 +00:00
examples	- After removing special code for intervals, instead of being of type File they are generated as List[File]. Changed previous checkin that was appending to this list and instead assigning a singleton list.	2010-10-21 06:37:28 +00:00
hanna	Trying out Queue for the first time.	2010-11-18 18:29:12 +00:00
kshakir	Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects:	2010-12-10 04:36:06 +00:00
rpoplin	At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them.	2010-09-02 21:30:48 +00:00
fullCallingPipeline.q	Removing old arguments. We'll now be running with the defaults.	2010-12-09 18:58:56 +00:00
recalibrate.scala	- After removing special code for intervals, instead of being of type File they are generated as List[File]. Changed previous checkin that was appending to this list and instead assigning a singleton list.	2010-10-21 06:37:28 +00:00