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ArtificialPatternedSAMIterator.java
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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.
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2009-07-22 22:37:41 +00:00 |
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ArtificialReadsTraversal.java
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Rework the way the MicroScheduler handles locus shards to handle intervals that span shards
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2010-03-11 18:40:31 +00:00 |
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ArtificialSAMFileReader.java
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Fix CleanedReadInjectorTest to work with new CleanedReadInjector.
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2009-07-01 15:48:06 +00:00 |
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ArtificialSAMFileWriter.java
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A rogue QualityUtils.MAX_REASONABLE_Q_SCORE managed to get through my previous bug fix. It should instead check the command line -maxQ argument.
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2010-01-07 21:17:39 +00:00 |
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ArtificialSAMIterator.java
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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.
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2009-07-22 22:37:41 +00:00 |
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ArtificialSAMQueryIterator.java
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made a fake fasta generator, so we can now generate a complete bam / fasta combo of made up data.
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2009-07-01 21:35:34 +00:00 |
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ArtificialSAMUtils.java
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a little clean-up: move setting the bases of generated reads into Artificial SAM Utils now that the clean read injector test is gone.
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2010-03-03 16:31:45 +00:00 |
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GATKSAMReadGroupRecord.java
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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.
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2009-11-30 17:39:29 +00:00 |
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GATKSAMRecord.java
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-Pushed base quals back down into SAMRecord; if -OQ is used, the SAMRecord quals get updated automatically
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2010-03-17 16:00:10 +00:00 |
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SAMFileReaderBuilder.java
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Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very*
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2009-07-29 16:11:45 +00:00 |
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SAMReadValidationException.java
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Basic infrastructure for filtering malformed reads.
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2009-07-06 22:50:22 +00:00 |
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SAMReadValidator.java
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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.
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2009-07-22 22:37:41 +00:00 |
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SAMReadViolationHistogram.java
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Basic infrastructure for filtering malformed reads.
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2009-07-06 22:50:22 +00:00 |
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package-info.java
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Put a major.minor version into the GATK Javadoc for reading. Also,
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2010-01-15 21:48:30 +00:00 |
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