aaron 2d3b6d89dc 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 ... most appropriate based on feature density, and the longest feature in the file. Also: - Converted Tribble to TestNG; it has better features and is about 6x faster. - As much code clean-up as I could get done. More to do, especially in the example code. - Moved asserts in the code to throw exceptions. - Added getBinSize to the index interface; both indexes already implemented this. - Removed the abstract parts of the indexCreator interface; this is now more simple. - Added an IndexType enumeration; might be overkill but it is at least a single point of entry for index information. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4082 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-23 06:54:59 +00:00
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net/sf/picard/reference	IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.	2010-07-01 04:40:31 +00:00
org/broadinstitute/sting	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