hanna 3dc78855fd Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax ... (-B:name,type file) as well as the old syntax. Also, a bonus feature: BAMs can now be tagged at the command-line, which should allow us to get rid of some of the hackier calls in GenomeAnalysisEngine. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4105 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-25 03:47:57 +00:00
..
storage	Okay, finally done with VCF compression. Now:	2010-08-24 16:36:54 +00:00
stubs	Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax	2010-08-25 03:47:57 +00:00
DirectOutputTracker.java	Output stream management fixes. I completely screwed up the output stream management system, but cleverly masked this fact by breaking some other stream management functionality that masked the problem.	2009-09-15 21:06:45 +00:00
OutputTracker.java	Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.	2010-08-22 14:27:05 +00:00
StingSAMFileWriter.java	Enhance the I/O management system to support custom headers and set the presorted flag	2010-01-12 18:21:42 +00:00
ThreadLocalOutputTracker.java	Support for initialize() and onTraversalDone() output from parallelized walkers.	2009-10-26 20:18:31 +00:00