aaron c3c001e02e cleanup of the traversal output code ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2026 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-12 06:18:10 +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	cleanup of the traversal output code	2009-11-12 06:18:10 +00:00
ArtificialSAMFileReader.java	Fix CleanedReadInjectorTest to work with new CleanedReadInjector.	2009-07-01 15:48:06 +00:00
ArtificialSAMFileWriter.java	adding an artificial sam file writer, used to unit test some of the walkers (mainly the PrintReadsWalker)	2009-06-09 21:47:49 +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
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.html	Package level documentation -- helps new users get acclimated to the codebase more quickly.	2009-06-17 16:27:48 +00:00