├── .directory ├── .gitignore ├── CITE ├── COPYING ├── COPYING.DOC ├── COPYING.LESSER ├── README.md ├── bin └── edu │ └── gatech │ └── kestrel │ ├── KestrelConstants.class │ ├── LogLevel.class │ ├── align │ └── AlignmentWeight.class │ ├── clui │ └── Main.class │ ├── io │ ├── InputSample.class │ └── StreamableOutput.class │ ├── refreader │ ├── ReferenceReader$ReadCollectorRunner.class │ ├── ReferenceReader$ReaderRunner.class │ ├── ReferenceReader$UncaughtHandler.class │ ├── ReferenceReader.class │ ├── ReferenceReaderInitException.class │ └── ReferenceSequence.class │ ├── runner │ ├── ConfigurationErrorException.class │ ├── KestrelArgumentParser$ConfigurationConditionListener.class │ ├── KestrelArgumentParser$HelpCite.class │ ├── KestrelArgumentParser$HelpFormat.class │ ├── KestrelArgumentParser$HelpReader.class │ ├── KestrelArgumentParser$HelpRefReader.class │ ├── KestrelArgumentParser$InputSourceFile.class │ ├── KestrelArgumentParser$OptAlignmentWeightVector.class │ ├── KestrelArgumentParser$OptBatchCacheSize.class │ ├── KestrelArgumentParser$OptCharset.class │ ├── KestrelArgumentParser$OptFilesPerSample.class │ ├── KestrelArgumentParser$OptFormat.class │ ├── KestrelArgumentParser$OptKmerBatchSize.class │ ├── KestrelArgumentParser$OptKmerQueueSize.class │ ├── KestrelArgumentParser$OptKmerSize.class │ ├── KestrelArgumentParser$OptKmerThreads.class │ ├── KestrelArgumentParser$OptLoadLibraryFile.class │ ├── KestrelArgumentParser$OptLoadLibraryUrl.class │ ├── KestrelArgumentParser$OptLogFileName.class │ ├── KestrelArgumentParser$OptLogLevel.class │ ├── KestrelArgumentParser$OptLogStderr.class │ ├── KestrelArgumentParser$OptLogStdout.class │ ├── KestrelArgumentParser$OptMinKmerCount.class │ ├── KestrelArgumentParser$OptNoSequenceFilter.class │ ├── KestrelArgumentParser$OptOutFileName.class │ ├── KestrelArgumentParser$OptQuality.class │ ├── KestrelArgumentParser$OptReference.class │ ├── KestrelArgumentParser$OptSampleSet.class │ ├── KestrelArgumentParser$OptSegmentSize.class │ ├── KestrelArgumentParser$OptSequenceBatchSize.class │ ├── KestrelArgumentParser$OptSequenceFilter.class │ ├── KestrelArgumentParser$OptSequenceFilterBase.class │ ├── KestrelArgumentParser$OptSequenceQueueSize.class │ ├── KestrelArgumentParser$OptSplitThreads.class │ ├── KestrelArgumentParser$OptTempFileLocation.class │ ├── KestrelArgumentParser$OptWriteStdout.class │ ├── KestrelArgumentParser.class │ ├── KestrelRunner$KestrelRunnerException.class │ ├── KestrelRunner.class │ ├── KestrelRunnerBase.class │ ├── KmerCountRunner$CountRunnerConditionListener.class │ ├── KmerCountRunner.class │ └── RunnerFailException.class │ ├── test │ ├── ValidateAll.class │ ├── files │ │ └── refreader │ │ │ ├── DESCRIPTION │ │ │ ├── allchars.us-ascii.fasta │ │ │ ├── allchars.us-ascii.fastq │ │ │ ├── general.us-ascii.fasta │ │ │ ├── general.us-ascii.fastq │ │ │ └── randread.py │ └── refreader │ │ ├── ExpectedSequence$Record.class │ │ ├── ExpectedSequence.class │ │ ├── FormatType.class │ │ ├── ReaderTestCase.class │ │ └── TestReferenceReader.class │ └── util │ ├── InfoUtil$InfoMode.class │ └── InfoUtil.class ├── docsrc └── manual │ ├── abbrvnat.bst │ ├── img │ ├── ARIllustration.eps │ ├── KestrelOverview.eps │ └── src │ │ ├── ARIllustration │ │ ├── NOTES │ │ └── rseq.table │ │ ├── KestrelOverview.xcf │ │ ├── KmerCount.xcf │ │ └── overview │ │ ├── ActiveRegionIllustration.eps │ │ ├── KmerShift.eps │ │ ├── KmerShift.xcf │ │ └── NOTES │ ├── main.bib │ ├── main.tex │ ├── natbib.bst │ ├── natbib.sty │ └── sections │ ├── api.tex │ ├── cmdline.tex │ ├── extending.tex │ ├── implementation.tex │ ├── intro.tex │ ├── license.tex │ ├── process.tex │ └── suppl.tex ├── files ├── launch │ ├── linux │ │ ├── cite │ │ └── kestrel │ └── win │ │ ├── cite_launch.xml │ │ └── kestrel_launch.xml └── readme │ └── README ├── lib ├── GETOPT.LICENSE ├── JUNIT.LICENSE ├── XSTREAM.LICENSE ├── commons-lang3-3.4.jar ├── hamcrest-core-1.3.jar ├── java-getopt-1.0.14.jar ├── junit-4.11.jar ├── kanalyze.jar ├── logback-classic-1.1.3.jar ├── logback-core-1.1.3.jar ├── slf4j-api-1.7.12.jar └── xstream-1.4.5.jar └── src └── edu └── gatech └── kestrel ├── KestrelConstants.java ├── LogLevel.java ├── activeregion ├── ActiveRegion.java ├── ActiveRegionContainer.java ├── ActiveRegionDetector.java ├── Haplotype.java ├── RegionHaplotype.java ├── RegionStats.java └── package-info.java ├── align ├── AlignNode.java ├── AlignmentWeight.java ├── HaplotypeContainer.java ├── KmerAligner.java ├── KmerAlignmentBuilder.java ├── MaxAlignmentScoreNode.java ├── TraceMatrix.java ├── TraceNode.java ├── TypeList.java ├── package-info.java └── state │ ├── RestoredState.java │ ├── StateStackNode.java │ ├── TraceNodeContainer.java │ └── package-info.java ├── clui └── Main.java ├── counter ├── CountMap.java ├── IkcCountMap.java ├── MemoryCountMap.java └── package-info.java ├── hapwriter ├── HaplotypeWriter.java ├── HaplotypeWriterInitException.java ├── NullHaplotypeWriter.java ├── package-info.java └── sam │ ├── SamHaplotypeWriter.java │ └── package-info.java ├── interval ├── IntervalReader.java ├── IntervalReaderInitException.java ├── RegionInterval.java ├── RegionIntervalContainer.java ├── bed │ ├── BedIntervalReader.java │ └── package-info.java └── package-info.java ├── io ├── InputSample.java └── StreamableOutput.java ├── refreader ├── ReadCollectorRunner.java ├── ReadCollectorRunnerException.java ├── ReaderRunner.java ├── ReaderThreadRunner.java ├── ReferenceReader.java ├── ReferenceReaderInitException.java ├── ReferenceRegion.java ├── ReferenceRegionContainer.java └── ReferenceSequence.java ├── runner ├── ConfigurationErrorException.java ├── KestrelArgumentParser.java ├── KestrelRunner.java ├── KestrelRunnerBase.java └── RunnerConditionListener.java ├── util ├── InfoUtil.java ├── NumberUtil.java ├── SystemUtil.java └── digest │ ├── ArrayUtil.java │ ├── Digest.java │ ├── NullMessageDigest.java │ └── package-info.java ├── varfilter ├── VariantFilter.java ├── VariantFilterInitException.java ├── VariantFilterRunner.java ├── coverage │ ├── CoverageVariantFilter.java │ └── package-info.java ├── location │ ├── LocationVariantFilter.java │ └── package-info.java ├── package-info.java └── type │ ├── TypeVariantFilter.java │ └── package-info.java ├── variant ├── VariantCall.java ├── VariantCaller.java ├── VariantDeletion.java ├── VariantInsertion.java ├── VariantSNP.java ├── VariantType.java └── package-info.java └── writer ├── VariantWriter.java ├── VariantWriterInitException.java ├── package-info.java ├── table ├── TableVariantWriter.java └── package-info.java ├── txt ├── TxtVariantWriter.java └── package-info.java └── vcf ├── VcfRecordContainer.java ├── VcfVariantWriter.java └── package-info.java /.directory: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/paudano/kestrel/HEAD/.directory -------------------------------------------------------------------------------- /.gitignore: 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