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
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builders	adding the ability in Tribble to create indexes from a stream of features, so that we can create multiple indexes from one pass of the file. In the GATK we now create multiple indexes, and choose the	2010-08-23 06:54:59 +00:00
RMDTrackManagerUnitTest.java	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