ebanks 47a42b1507 trivial cleanup ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3736 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-08 04:42:32 +00:00
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AlignmentStartComparator.java	Rev the reservoir downsampler to support partitioning through a functor.	2010-04-21 19:50:26 +00:00
AlignmentUtils.java	trivial cleanup	2010-07-08 04:42:32 +00:00
ArtificialPatternedSAMIterator.java	Fix minor bug introduced in filtration, and cleaned up the artificial sam records so that they use SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX and SAMRecord.NO_ALIGNMENT_START rather than hardcoded -1's.	2009-07-22 22:37:41 +00:00
ArtificialReadsTraversal.java	Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK	2010-05-19 23:27:55 +00:00
ArtificialSAMFileReader.java	Rev Picard with performance enhancements.	2010-06-22 22:54:23 +00:00
ArtificialSAMFileWriter.java	A rogue QualityUtils.MAX_REASONABLE_Q_SCORE managed to get through my previous bug fix. It should instead check the command line -maxQ argument.	2010-01-07 21:17:39 +00:00
ArtificialSAMIterator.java	Fix minor bug introduced in filtration, and cleaned up the artificial sam records so that they use SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX and SAMRecord.NO_ALIGNMENT_START rather than hardcoded -1's.	2009-07-22 22:37:41 +00:00
ArtificialSAMQueryIterator.java	First pass at eliminating the old sharding system. Classes required for the original sharding system	2010-06-17 20:17:31 +00:00
ArtificialSAMUtils.java	First pass at eliminating the old sharding system. Classes required for the original sharding system	2010-06-17 20:17:31 +00:00
ComparableSAMRecord.java	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
GATKSAMReadGroupRecord.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
GATKSAMRecord.java	Switched over to reviewed version of Picard patch. In process, did some optimization to the IntervalSharder	2010-05-08 14:12:22 +00:00
ReadUtils.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
SAMFileReaderBuilder.java	Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very*	2009-07-29 16:11:45 +00:00
SAMReadValidationException.java	Basic infrastructure for filtering malformed reads.	2009-07-06 22:50:22 +00:00
SAMReadValidator.java	Fix minor bug introduced in filtration, and cleaned up the artificial sam records so that they use SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX and SAMRecord.NO_ALIGNMENT_START rather than hardcoded -1's.	2009-07-22 22:37:41 +00:00
SAMReadViolationHistogram.java	Basic infrastructure for filtering malformed reads.	2009-07-06 22:50:22 +00:00
package-info.java	Put a major.minor version into the GATK Javadoc for reading. Also,	2010-01-15 21:48:30 +00:00