ebanks 660998065b 'Okay, now I'm absolutely certain that there are no more bugs in the constrained writer.' ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5353 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-02 03:48:40 +00:00
..
AlignmentStartComparator.java	Rev the reservoir downsampler to support partitioning through a functor.	2010-04-21 19:50:26 +00:00
AlignmentUtils.java	Fix for the HaplotypeScore optimization in AlignmentUtils	2011-02-24 20:40:18 +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	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
ArtificialSAMFileReader.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +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	Massive cleanup of read filtering.	2010-08-11 20:17:11 +00:00
ArtificialSAMQueryIterator.java	Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.	2010-09-12 15:07:38 +00:00
ArtificialSAMUtils.java	Fixed Umapped misspelling	2011-02-04 22:21:41 +00:00
ComparableSAMRecord.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
ConstrainedMateFixingSAMFileWriter.java	'Okay, now I'm absolutely certain that there are no more bugs in the constrained writer.'	2011-03-02 03:48:40 +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	SAMFileWriter that allows the user to move reads, but only a bit, in an incoming coordinated sorted BAM files. Does some local reordering and local mate fixing, under specified constrained. These constrains allow us to make a special -- under testing for Eric, who promised to try this out a bit, expand test cases and integration tests -- but soon to be the default and only model of the realigner that only moves reads with ISIZE < 3000 that directly emits a coordinate sorted, mate fixed validating BAM file without needing FixMates externally. Preliminary testing shows this runs in a totally fine amount of memory and produces equivalent results to the previous version.	2011-02-04 22:27:05 +00:00
GATKSAMRecordFilter.java	Experimental code for better filtering of bases in sam records. Not hooked up yet.	2010-10-11 02:19:51 +00:00
ReadUtils.java	Fixes for constrained movement Indel Realigner. Now sorts all of the reads in the interval before handing them to ConstrainedMateFixingSAMFileWriter to maintain correct contract between the two pieces of software	2011-02-28 03:52:18 +00:00
SAMFileReaderBuilder.java	Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.	2010-09-12 15:07:38 +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