kshakir d185c2961f Added pipeline for calling FCP in batches called MultiFullCallingPipeline. ... Bug smashes for the MCFP: Synchronized access to LSF library and modifications to the QGraph. If values are missing from the graph with -run make sure to exit with a non-zero. Refactored QGraph to pre-generate a unique Int for each QNode speeding up getHashCode/equals inside the graph. Added jobPriority and removed jobLimitSeconds from QFunction. All scatter gather is by default in a single sub directory queueScatterGather. Moved some FCPTest into BaseTest/PipelineTest for use by MFCPTest. Rev'ed the 1000G bams used for validation from v1 to v2 and added code to look for the bams before running other tests. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5247 348d0f76-0448-11de-a6fe-93d51630548a		2011-02-15 18:26:14 +00:00
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BatchMerge.q	Major revision of the batch merge script. All sites are now used, hooks for some UG settings, no longer reliant on the pipeline management library (pipeline libs are probably going to go away -- nobody uses them)	2011-02-14 23:52:05 +00:00
FullCallingPipeline.q	Renamed the pipeline yaml dbsnpFile to genotypeDbsnp, and added an evalDbsnp.	2011-02-07 22:01:09 +00:00
MultiFullCallingPipeline.scala	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +00:00
recalibrate.scala	Refactoring the qscript directory; oneoffs, playground, and core	2011-01-19 15:23:40 +00:00