chartl ec68ae3bc5 Added a filter that will split the read set by a threshold of mapping quality (Request from Jason Flannick) ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1812 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-12 20:58:37 +00:00
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contexts	Modifications:	2009-09-09 15:49:52 +00:00
examples	Update naming for consistency.	2009-06-30 22:03:21 +00:00
gatk	Recalibrator by NQS. Had this puppy running all afternoon. Thing had got through 100,000,000 reads before I decided to delete my sting tree. *sigh*, a little more delay.	2009-10-12 20:55:02 +00:00
indels	change paths to new ones	2009-07-24 07:28:43 +00:00
piecemealannotator	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
somaticcoverage	Cleanup: GATKEngine no longer needs to be lazy loaded, b/c the plugin directory no longer exists.	2009-07-21 18:50:51 +00:00
tools	Matthew Bainbridge's duplicate removal utility for 454 data. This code should eventually be moved into a read walker. For now, it's being introduced into the repository as-is (well, with one minor change to make the handling of command-line arguments a little more straightforward).	2009-10-08 18:32:37 +00:00
utils	Added a filter that will split the read set by a threshold of mapping quality (Request from Jason Flannick)	2009-10-12 20:58:37 +00:00