aaron 7fc4472e6d A big fix for MergingSamRecordIterator, where we weren't correctly handling the comparisons of SAMRecords correctly (we weren't applying the new reference index first, so sometimes the MT contig would be ID 23, sometimes 24 in different records). ... Also a fix to the GLF tests, and a correction to PrintReadsWalker to remove the close() on the output source, the source handles that itself (and you get a double close). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1758 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-02 19:35:35 +00:00
..
BoundedReadIterator.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
DownsampleIterator.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
GenomeLocusIterator.java	Cleaned division of responsibilities between arguments to map function. Reference has been changed	2009-08-04 21:01:37 +00:00
IntervalOverlapIterator.java	Added the interator to SAMDataSource to prevent seeing dupplicate reads, only in a byReads traversal. The iterator discards any reads in the current interval that would have been seen in the previous interval.	2009-07-25 22:36:29 +00:00
LocusIterator.java	Cleaned division of responsibilities between arguments to map function. Reference has been changed	2009-08-04 21:01:37 +00:00
LocusIteratorByHanger.java	fixed locus pile-up limiting problem	2009-09-02 16:56:44 +00:00
LocusIteratorByState.java	1) now is tolerant to sloppy cigar strings with 0-length elements (at the price of extra recursive call)	2009-09-09 20:04:04 +00:00
MalformedSAMFilteringIterator.java	Filter reads whose alignment starts past the end of the contig to which it allegedly aligns.	2009-07-07 22:27:44 +00:00
MergingSamRecordIterator2.java	A big fix for MergingSamRecordIterator, where we weren't correctly handling the comparisons of SAMRecords correctly (we weren't applying the new reference index first, so sometimes the MT contig would be ID 23, sometimes 24 in different records).	2009-10-02 19:35:35 +00:00
NullSAMIterator.java	@Required / @Allows flags for main arguments.	2009-05-19 23:26:17 +00:00
PeekingIterator.java	added changes to support alec toUnmappedRead seek. Huge improvements (orders of magnitude) in unmapped read performance.	2009-06-16 22:15:56 +00:00
PositionTrackingIterator.java	Refactoring; make a better home for the MalformedReadFilteringIterator.	2009-07-08 16:54:20 +00:00
PushbackIterator.java	Enabled iterator() function	2009-04-30 22:15:14 +00:00
QueryIterator.java	added changes to support alec toUnmappedRead seek. Huge improvements (orders of magnitude) in unmapped read performance.	2009-06-16 22:15:56 +00:00
StingSAMIterator.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
StingSAMIteratorAdapter.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
VerifyingSamIterator.java	Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future.	2009-06-22 14:39:41 +00:00
package.html	More package-level documentation.	2009-06-17 16:28:45 +00:00