aaron f5eae98af2 Fixed a bug where we could ask for a read when there were none in the pool (that's a bad thing). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@605 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-06 18:40:55 +00:00
..
BoundedReadIterator.java	Fixes to try and speed up unmapped read traversals. Still not nearly as fast as they should be, but the next step would be to modify samtools code.	2009-05-05 18:17:07 +00:00
BoundedReferenceIterator.java	Introduce new index-based fasta reader. Clean up MicroManager code, pushing necessary code back into TraversalEngine.	2009-04-24 19:40:21 +00:00
DownsampleIterator.java	Added iterator to randomly downsample to a given fraction of the reads.	2009-04-01 02:11:13 +00:00
LocusIterator.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
LocusIteratorByHanger.java	Fixed potential bug with next() operation returning empty contexts when a read contains a large deletion. We can now use the look ahead safely...	2009-04-15 21:38:28 +00:00
MergingSamRecordIterator2.java	Fixed a bug where we could ask for a read when there were none in the pool (that's a bad thing).	2009-05-06 18:40:55 +00:00
PushbackIterator.java	Enabled iterator() function	2009-04-30 22:15:14 +00:00
ReferenceIterator.java	Moved fasta support files into their own package.	2009-04-14 18:13:23 +00:00
SamQueryIterator.java	Fixing problems with SAMQueryIterator and reads	2009-04-02 18:04:28 +00:00
SortSamIterator.java	Uses the cleaner new GenomeLoc(read) syntax	2009-04-14 00:53:58 +00:00
ThreadedIterator.java	Make the operation 'read from the iterator and place on the queue' atomic with respect to hasNext(), next().	2009-04-23 20:16:26 +00:00
VerifyingSamIterator.java	Uses the cleaner new GenomeLoc(read) syntax	2009-04-14 00:53:58 +00:00