depristo cc75e8f712 Uses the cleaner new GenomeLoc(read) syntax ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@393 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-14 00:53:58 +00:00
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BoundedReferenceIterator.java	Added a constructor, took out a copy constructor, and changed some SAMBAM code.	2009-04-08 19:53:20 +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	* refactored GenomeLoc to use contigIndex internally for performance and fixed several calling classes	2009-04-12 02:25:17 +00:00
MergingSamRecordIterator2.java	Added a bunch of fixes: MSRI wasn't working, sharding had broken edge cases, and SAMBAM DS needed to close the file handles.	2009-04-09 00:20:15 +00:00
PushbackIterator.java	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
ReferenceIterator.java	seekForwardOffset changed (improved?): first, compareContigs does *not*, in general, return -1,0 or 1 if no dictionary is available; second, be more flexible in trying to jump to the right contig (current implementation of FastaFile2 will still through an exception if there's no dictionary, but iterator itself behaves transparently)	2009-04-07 21:42:33 +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	Push core / playground lower into the tree.	2009-03-23 23:19:54 +00:00
VerifyingSamIterator.java	Uses the cleaner new GenomeLoc(read) syntax	2009-04-14 00:53:58 +00:00