hanna 41d57b7139 Massive cleanup of read filtering. ... - Eliminate reduncancy of filter application. - Track filter metrics per-shard to facitate per merging. - Flatten counting iterator hierarchy for easier debugging. - Rename Reads class to ReadProperties and track it outside of the Sting iterators. Note: because shards are currently tied so closely to reads and not the merged triplet of <reads,ref,RODs>, the metrics classes are managed by the SAMDataSource when they should be managed by something more general. For now, we're hacking the reads data source to manage the metrics; in the future, something more general should manage the metrics classes. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4015 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-11 20:17:11 +00:00
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BoundedReadIterator.java	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
BufferingReadIterator.java	The sharding system now buffers reads, with a size determined by command-line argument. Will investigate whether/how this	2010-07-01 22:28:55 +00:00
DownsampleIterator.java	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
GenomeLocusIterator.java	Clean up the code a bit following the introduction of reduceByInterval.	2010-02-25 01:20:22 +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	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
LocusIteratorFilter.java	GATK now does automatic adaptor filtering in locus iterators (but not expt. downsampling iterator). General support for LocusIteratorFilters just like read filters but only applying at particular bases. Updated tools with new MD5 sums due to adaptor bases in their integrationtest data. Not that as a side effect here reads close to each other with odd orientations are also filtered out. Updated minor argument to VariantRecalibrator to change the qStep value on the command line	2010-06-02 22:26:32 +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
NullSAMIterator.java	Massive cleanup of read filtering.	2010-08-11 20:17:11 +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	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
PushbackIterator.java	fixes for parallel processing problems with Tribble, a small bug in the resource pool, and some more documentation.	2010-05-12 06:13:26 +00:00
ReadFormattingIterator.java	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
StingSAMIterator.java	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
StingSAMIteratorAdapter.java	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
VerifyingSamIterator.java	Massive cleanup of read filtering.	2010-08-11 20:17:11 +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