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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edu.mit.broad	Rev Picard with new IndexedFastaSequenceFile patch.	2010-07-01 03:05:43 +00:00
gov.nist	Adding Jama for Ryan.	2010-04-27 14:30:36 +00:00
net.sf	Rev Picard with new IndexedFastaSequenceFile patch.	2010-07-01 03:05:43 +00:00
org.broad	updates to code dependent on Tribble, as well as the following Tribble changes:	2010-07-23 01:56:10 +00:00
org.reflections	updating the reflections library; Matt found a problem where the reflections library doesn't sort out non-java objects from the classpath (affects only OS X so far). I'll push back the changes to	2010-05-06 02:08:41 +00:00