3 Commits (094418483241554323c1e60a03d250cf45412875)

Author	SHA1	Message	Date
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
chartl	670ae814b3	Get rid of files from the grep string ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4773 348d0f76-0448-11de-a6fe-93d51630548a	2010-12-02 18:39:59 +00:00
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