kshakir 8040998c15 Renamed the pipeline yaml dbsnpFile to genotypeDbsnp, and added an evalDbsnp. ... Added a genotypeDbsnpType and evalDbsnpType to check the extensions for .vcf or .rod. Moved renaming of "recalibrated" bams to "cleaned" from sed to yaml generation template (see diff for more info). Renamed fCP.q to FCP.q. Though it's still disabled until VariantEval is updated, added changes above to the FCPTest. Removed refseq table from the queue.sh wrapper script. Only specified in the yaml. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5213 348d0f76-0448-11de-a6fe-93d51630548a		2011-02-07 22:01:09 +00:00
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qscript	Renamed the pipeline yaml dbsnpFile to genotypeDbsnp, and added an evalDbsnp.	2011-02-07 22:01:09 +00:00
src/org/broadinstitute/sting	Bug fixes in the in process function (spoiled by python: was not closing my writers). SortByRef now works somewhat like the perl script does, rather than doing a memory-expensive sort. Adding a QTools qscript which is kinda clunky, and will be used mostly for integration tests of these IPFs, pending some better way to construct argument collections and function accessors at compile-time.	2011-02-03 17:32:46 +00:00
test/org/broadinstitute/sting/queue	Renamed the pipeline yaml dbsnpFile to genotypeDbsnp, and added an evalDbsnp.	2011-02-07 22:01:09 +00:00