aaron 9579aace1f updates to code dependent on Tribble, as well as the following Tribble changes: ... - makes writing to disk optional for indexes using the indexCreator classes (allow the user to specify the index file, if null don't write it) - removed some system.out debugging code - fixed version checking in interval tree - made indexes store and return a LinkedHashSet for sequence names (to ensure they've preserved the ordering in the file) - index creators now read the file before creating the index - changed the Index.write() method to take a LEDataStream instead of a file - removed the sequence dictionary code on the header - added utils for getting LEDataStreams - added a base Tribble exception git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3857 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-23 01:56:10 +00:00
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builders	updates to code dependent on Tribble, as well as the following Tribble changes:	2010-07-23 01:56:10 +00:00
RMDTrackManagerUnitTest.java	IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.	2010-07-01 04:40:31 +00:00