depristo 5c979633f0 Due to a problem in the way that dynamic type selection works, I've added an explicit (temporary) ability to restrict VE to specific variant types (SNPs, INDELs, etc), so that calculations will work when a site has a SNP in dbSNP but is called as an indel, causing the SNP site to mysteriously disappear from the comp track, a huge problem for validation report. VEU updated to allow both dynamic type (old) and just returning everything in the track. ... Also, created a standard Queue script that calculates a suite of standard indel and SNP assessment results. Will be the basis for a general evaluation Queue script with standardized data files for SNPs and Indels. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5385 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-06 19:31:12 +00:00
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core	gold standard creates its own tranches and vcf files now.	2011-03-01 17:48:40 +00:00
examples	Moved the maximum number of intervals check from FCP to the Queue core so that scatter gather will no longer blow up if you specify a scatter count that is too high.	2011-01-28 23:33:58 +00:00
lib	Thanks to mark: VCFInfoToTable removed in favor of a more flexible walker. Slight change to the argument structure of the walker to make it play more nicely with Queue: the field list parsing is pushed into the command line system (e.g. the variable is exposed as a List<String> and not a String, so Queue doesn't have to join a list into a string only to have it broken out again. This also allows the user to specify -F field1 -F field2 -F field3 if he/she so desires.	2010-12-15 03:33:36 +00:00
oneoffs	Due to a problem in the way that dynamic type selection works, I've added an explicit (temporary) ability to restrict VE to specific variant types (SNPs, INDELs, etc), so that calculations will work when a site has a SNP in dbSNP but is called as an indel, causing the SNP site to mysteriously disappear from the comp track, a huge problem for validation report. VEU updated to allow both dynamic type (old) and just returning everything in the track.	2011-03-06 19:31:12 +00:00
playground	MFCP waits for other pipelines to finish by using the previous log file of one pipeline as virtual input to the next pipeline.	2011-02-25 17:51:01 +00:00