chartl 0944184832 Major refactoring of library and full calling pipeline (v2) structure. ... Arguments to the full calling qscript (and indeed, any qscript that wants them) are now specified via the PipelineArgumentCollection Libraries require a Pipeline object for instantiation -- eliminating their previous dependence on yaml files Functions added to PipelineUtils to build out the proper Pipeline object from the PipelineArgumentCollection, which now contains additional arguments to specify pipeline properties (name, ref, bams, dbsnp, interval list); which are mutually exclusive with the yaml file. Pipeline length reduced to a mere 62 lines. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4790 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-05 02:33:54 +00:00
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chartl	Major refactoring of library and full calling pipeline (v2) structure.	2010-12-05 02:33:54 +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
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	Taking out recalibrating for now, since having these files is confusing people and we've not gone to dbsnp 132 yet so cluster generation's broken with these command lines.	2010-12-03 22:12:09 +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