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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RefineGenotypesAndMerge.q	Commit for Ryan	2010-10-05 19:04:10 +00:00
batchMergePipeline.q	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
fullCallingPipelineV2.q	Major refactoring of library and full calling pipeline (v2) structure.	2010-12-05 02:33:54 +00:00
omni_qc.q	Bug fix to GenotypeConcordance. AC metrics get instantiated based on number of eval samples; if Comp has more samples, we can see AC indeces outside the bounds of the array.	2010-11-03 19:23:03 +00:00
private_mutations.q	Sometimes, inputs are really outputs in disguise.	2010-11-05 19:51:16 +00:00