Updated the Queue scatter/gather for read walkers to include -L unmapped on the last scatter job when intervals aren't specified, and to map it correctly when it is explicitly set.
Simplified the build.xml/ivy.xml to fix a bug reported with "ant clean dist test" where the scalac target wasn't found.
Now building all scala code at the same time, just like all java code is compiled at the same time.
Sped up the build for everyone by uncommenting a small bit of classes so that javac/scalac will not constantly launch trying to build .class files that will never compile.
Moved some source files to their expected location so that the .java/.scala -> .class is a one-to-one match, again keeping the compilers from wasting cycles.
Used <uptodate> and <touch> to skip extracting the help text and generating the GATK Queue extensions when the source files haven't been modified.
Fixed a couple errors when the <javadoc> task is run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4963 348d0f76-0448-11de-a6fe-93d51630548a
Additional ipf for expanding interval lists. Either there's heavy latency on the toro -- or it's not working properly yet (e.g. the system print in the same scope as the file print outputs a line, but no file shows up on the system)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4874 348d0f76-0448-11de-a6fe-93d51630548a
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
- More cleanup including removing the temporary classes and intermediate error files. Quieting any errors using Apache Commons IO 2.0.
- Counting the contigs during the QScript generation instead of the end user having to pass a separate contig interval list.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4539 348d0f76-0448-11de-a6fe-93d51630548a
Queue GATK generated .intervals is now a List(File) again removing special case handling in the generator.
Instead of using @Scatter annotation, using ScatterFunction instance to determine if a job can be scattered.
Implemented special VcfGatherFunction which only uses the header from the first file, even if the other files differ in their headers.
Added a -deleteIntermediates to Queue to delete the outputs from intermediate commands after a successful run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4536 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
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