VariantEvalWalker's logger is made public, so that variant eval modules can access it through the parent object.
DesignFileGenerator comment lists how best to bind things to it, and the feature accessor is better refined to grab the genome loc. (old change)
scala changes:
convenience addAll( List[CommandLineFunction] ) added to QScript class (and thus removed from the fCPV2)
useful command line functions added to a new library package for command line functions (these are fast simple VCF command lines)
bug fixed in ProjectManagement for the class where there's only one batch to be batch-merged (not really part of the use-case, but an edge-condition that came up during pipeline testing)
first draft of a private mutations pipeline which will be elaborated in future
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4823 348d0f76-0448-11de-a6fe-93d51630548a
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
- ProduceBeagleInputWalker
+ Now takes a validation ROD and a prior to give it, will use those genotypes in place of the variant genotypes if both are present
+ Takes a bootstrap argument -- can use some given %age of the validation sites
+ Optionally takes a bootstrap output argument -- re-prints the validation VCF, filtering those sites used as part of the bootstrap
-BeagleOutputToVCFWalker
+ Now filters sites where the genotypes have been reverted to hom ref
+ Now calls in to the new VCUtils to calculate AC/AN
-Queue
+ New pipeline libraries for easy qscript creation, still a work in progress, but this is a considerable prototype
+ full calling pipeline v2 uses the above libraries
+ minor changes to some of my own scripts
+ no more need for contig interval lists, these will be parsed out of your normal interval list when it is provided
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4459 348d0f76-0448-11de-a6fe-93d51630548a
chartl