hanna 433ad1f060 Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1196 348d0f76-0448-11de-a6fe-93d51630548a		2009-07-08 18:49:08 +00:00
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ArtificialResourcePool.java	Refactoring; make a better home for the MalformedReadFilteringIterator.	2009-07-08 16:54:20 +00:00
ReferenceOrderedDataPoolTest.java	Pooling of unmapped reads -- improves runtime of files with tons of unmapped reads by an order of magnitude.	2009-06-23 23:48:06 +00:00
SAMBAMDataSourceTest.java	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
SAMByIntervalTest.java	a couple of additions to the tests, plus a change to the artificial resource pool to support the queryContained flag	2009-06-25 18:30:32 +00:00
SAMByReadsTest.java	other fixes for some broken unit tests	2009-07-07 05:53:13 +00:00