chartl 220fb0c44a Added a pipeline for merging batches. For now takes a file containing a list of VCFs, and a file containing a list of bams. Does not do anything smart (e.g. if you leave out some .bams or add some extra ones, you will not be warned). Heavy lifting done in (the beginnings of) a library for managing multi-batch or multi-project tasks. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4771 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-02 07:31:59 +00:00
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BamProcessing.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
ProjectManagement.scala	Added a pipeline for merging batches. For now takes a file containing a list of VCFs, and a file containing a list of bams. Does not do anything smart (e.g. if you leave out some .bams or add some extra ones, you will not be warned). Heavy lifting done in (the beginnings of) a library for managing multi-batch or multi-project tasks.	2010-12-02 07:31:59 +00:00
QPipeline.scala	Somewhat major update. Changes:	2010-10-08 13:30:28 +00:00
VariantCalling.scala	Changes to V2 pipeline and libraries. AB dropped. Cleaning enabled. Project name now properly propagated to intermediate files (instead of the string repr of the object). Indel mask is now expanded prior to filtering at indels.	2010-12-01 18:55:48 +00:00