hanna 199b43fcf2 Reduce by interval alterations to interface with new sharding system. This checkin with be followed by a ... simplification of some of the locus traversal code. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2886 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-25 00:16:50 +00:00
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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	Reduce by interval alterations to interface with new sharding system. This checkin with be followed by a	2010-02-25 00:16:50 +00:00
ArtificialSAMFileReader.java	Fix CleanedReadInjectorTest to work with new CleanedReadInjector.	2009-07-01 15:48:06 +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	made a fake fasta generator, so we can now generate a complete bam / fasta combo of made up data.	2009-07-01 21:35:34 +00:00
ArtificialSAMUtils.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
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	Optimization - Added method to Covariates: void getValues( SAMRecord read, Comparable[] comparable ) which takes an array of size (at least) read.getReadLength() and fills it with covariate values for all positions in the given read. Made CovariateCounterWalker and TableRecalibrationWalker use this method instead of calling getValue(..) for each covariate and each offset.	2010-02-22 17:35:25 +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