ebanks cf7d932a17 Fix for f***ed up BWA alignments that adhere to SAM specs ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4834 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-14 17:12:25 +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	Fix for f***ed up BWA alignments that adhere to SAM specs	2010-12-14 17:12:25 +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	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
ComparableSAMRecord.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +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	Reverting Matt's change from yesterday which I accidentally blew away when trying to cope with the stupid svn update issues we've been plagued with recently.	2010-10-14 14:40:42 +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	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	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