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gatk-3.8/java/src/org/broadinstitute/sting/gatk/iterators
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hanna 3d922a019f Basic support for very simple index-driven locus traversals. Interface has been changed to 
support batched intervals in a single shard, but intervals are not yet compressed into a single
shard.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2730 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-01-29 03:14:26 +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 Basic support for very simple index-driven locus traversals. Interface has been changed to 2010-01-29 03:14:26 +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
IterableIterator.java Restructuring and interface change to ReadBackedPileup. We now lower support the Pileup interface, the BasicPileup static methods, and the ReadBackedPileup class. Now everything is a ReadBackedPileup and all methods to manipulate pileups are off of it. Also provides the recommended iterable() interface of pileup elements so you can use the syntax for (PileupElement p : pileup) and access directly from p.getBase() and p.getQual() and p.getSecondBase(). Only a few straggler walkers use the old style interface -- but those walkers will be retired soon. Documentation coming in the AM. Please everyone use the new syntax, it's safer, and will be more efficient as soon as the LocusIteratorByState directly emits the ReadBackedPileup for the Alignment context, as opposed to the current interface. In the process of the change over, discovered several bugs in the second-best base code due to things getting out of sync, but these changes were resolved manually. All other integrationtests passed without modification. 2009-11-25 03:51:41 +00:00
LocusIterator.java added a method to AlignmentContext called hasExceededMaxPileup, which you can use to determine if the current site exceeded the maximum pileup size (reads were dropped). Added this as a check to unified genotyper according to Eric's instructions, and added the plumbing to the engine. 2010-01-27 05:17:01 +00:00
LocusIteratorByState.java added a method to AlignmentContext called hasExceededMaxPileup, which you can use to determine if the current site exceeded the maximum pileup size (reads were dropped). Added this as a check to unified genotyper according to Eric's instructions, and added the plumbing to the engine. 2010-01-27 05:17:01 +00:00
LocusOverflowTracker.java AnalyzeAnnotations seems to be popular so I've rewritten the guts to be easier to extend and maintain. 2010-01-27 19:30:31 +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 added a better message for the SO flag error in MergingSAMIterator2 2010-01-25 22:57:18 +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
PlusOneFixIterator.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
PositionTrackingIterator.java Refactoring; make a better home for the MalformedReadFilteringIterator. 2009-07-08 16:54:20 +00:00
PushbackIterator.java Fixing a bug that Steven uncovered; we had an abigous contract for peek() in PushbackIterator, and SeekableRODIterator wasn't checking to see if it's PushbackIterator hasNext() was true before calling peek(). 2009-12-15 23:04:40 +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
ReadWrappingIterator.java Completing the optimization started by Matt: we now wrap SAMRecords and SAMReadGroupRecords with our own versions which cache oft-used variables (e.g. platform, readString, strand flag). All walkers automagically get this speedup since the wrapping occurs in the engine. 2009-11-30 17:39:29 +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-info.java Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file 2009-12-04 20:08:41 +00:00