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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BamProcessing.scala	Major refactoring of library and full calling pipeline (v2) structure.	2010-12-05 02:33:54 +00:00
PipelineArgumentCollection.scala	Major refactoring of library and full calling pipeline (v2) structure.	2010-12-05 02:33:54 +00:00
ProjectManagement.scala	Major refactoring of library and full calling pipeline (v2) structure.	2010-12-05 02:33:54 +00:00
QPipeline.scala	Somewhat major update. Changes:	2010-10-08 13:30:28 +00:00
VariantCalling.scala	Major refactoring of library and full calling pipeline (v2) structure.	2010-12-05 02:33:54 +00:00