depristo 449a6ba75a Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1885 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-20 12:23:36 +00:00
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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
LocusIteratorByState.java	Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered.	2009-10-20 12:23:36 +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	Improved error messages -- now easier to read, points to the GATK Error Messages wiki, and avoids double printing of stack traces	2009-10-15 12:07:44 +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