depristo 165befd38a V1 of the post processing QC plotting scala script and R function. The scala script runs VariantEval on a VCF file, and computes QC metrics. The R script generates the report. Will discuss usage with data processing group. Ryan -- please add your additional plotting routines to this script, as you see fit. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5980 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-13 17:06:42 +00:00
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core	limiting the number of reads in memory for the SamValidateFile.jar	2011-06-10 20:14:30 +00:00
examples	When /etc/mailname is unreadable fall back to the hostname.	2011-04-11 20:22:44 +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	V1 of the post processing QC plotting scala script and R function. The scala script runs VariantEval on a VCF file, and computes QC metrics. The R script generates the report. Will discuss usage with data processing group. Ryan -- please add your additional plotting routines to this script, as you see fit.	2011-06-13 17:06:42 +00:00
playground	Added a samtools merge CLF.	2011-06-03 22:20:38 +00:00