andrewk e4546f802c Accumulates coverage across hybrid selection bait intervals to assess effect of bait adjacency. Requires input bait intervals that have an overhang beyond the actual bait interval to capture coverage data at these points. Outputs R parseable file that has all data in lists and then does some basic plotting. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2144 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-24 18:12:34 +00:00
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alignment	Convenience changes. If no -BWT option is specified, pull the BWT location from the reference.	2009-11-23 22:46:05 +00:00
gatk	I'm not sure I believe it, but JProfiler claims that calling FourBaseProbs.isVerbose() was taking 5% of my runtime...	2009-11-24 17:00:32 +00:00
playground	Accumulates coverage across hybrid selection bait intervals to assess effect of bait adjacency. Requires input bait intervals that have an overhang beyond the actual bait interval to capture coverage data at these points. Outputs R parseable file that has all data in lists and then does some basic plotting.	2009-11-24 18:12:34 +00:00
secondarybase	Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests.	2009-09-30 20:37:59 +00:00
utils	Optimizations:	2009-11-24 16:27:39 +00:00