gatk-3.8/java/src/org/broadinstitute/sting/utils/sam
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
..
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