aaron aacd72854f a fix for a bug Andrey discovered: in read-based interval traversals we're dupplicating reads in rare cases. The problem was that to accomidate a bug in SAM JDK indexing, we were forced to add one to the stop of our QueryOverlapping() calls to ensure we always got all of the overlapping reads. ... Added a PlusOneFixIterator that wraps other iterators, and eliminates reads that start outside of our intended interval (interval stop - 1). Updated and checked BamToFastqIntegrationTest MD5 sums. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1976 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-05 05:26:33 +00:00
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BoundedReadIteratorTest.java	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
IntervalOverlapIteratorTest.java	an iterator to fix the problem where read-based interval traversals are getting duplicate reads because reads span the two intervals.	2009-07-23 23:59:48 +00:00
PlusOneFixIteratorTest.java	a fix for a bug Andrey discovered: in read-based interval traversals we're dupplicating reads in rare cases. The problem was that to accomidate a bug in SAM JDK indexing, we were forced to add one to the stop of our QueryOverlapping() calls to ensure we always got all of the overlapping reads.	2009-11-05 05:26:33 +00:00
StingSAMIteratorAdapterTest.java	Switch TraverseByLoci over to new sharding system, and cleanup some code in passing read files along	2009-05-15 21:02:12 +00:00