├── .classpath ├── .gitignore ├── .project ├── META-INF └── MANIFEST.MF ├── README.rdoc ├── dist └── java-genomics-toolkit.jar ├── galaxy-conf ├── Add.xml ├── Autocorrelation.xml ├── Average.xml ├── BaseAlignCounts.xml ├── Correlate.xml ├── DNAPropertyCalculator.xml ├── Divide.xml ├── Downsample.xml ├── DynaPro.xml ├── ExtractDataFromRegion.xml ├── FastqIlluminaToSanger.xml ├── FindAbsoluteMaxima.xml ├── FindBoundaryNucleosomes.xml ├── FindNMers.xml ├── FindOutlierRegions.xml ├── GaussianSmooth.xml ├── GeneTrackToBedGraph.xml ├── GeneTrackToWig.xml ├── GreedyCaller.xml ├── InterpolateDiscontinuousData.xml ├── IntervalAverager.xml ├── IntervalLengthDistribution.xml ├── IntervalStats.xml ├── IntervalToBed.xml ├── IntervalToWig.xml ├── KMeans.xml ├── LogTransform.xml ├── MapDyads.xml ├── MatrixAligner.xml ├── MovingAverageSmooth.xml ├── Multiply.xml ├── PairOverlappingNucleosomes.xml ├── PercusDecomposition.xml ├── Phasogram.xml ├── PowerSpectrum.xml ├── ReadLengthDistributionMatrix.xml ├── RollingReadLength.xml ├── RomanNumeralize.xml ├── Scale.xml ├── Shift.xml ├── StripMatrix.xml ├── Subsample.xml ├── Subtract.xml ├── Summary.xml ├── ValueDistribution.xml ├── WaveletTransform.xml ├── ZScore.xml ├── galaxyToolRunner.sh ├── log4j.properties └── matrix2png.xml ├── galaxyToolConf.xml ├── lib ├── BigWig.jar ├── JLargeArrays-1.2.jar ├── JTransforms-3.0.jar ├── commons-lang3-3.1.jar ├── commons-math3-3.0.jar ├── dnaproperties-1732.jar ├── hamcrest-core-1.1.0.jar ├── java-genomics-io.jar ├── jcommander-1.27.jar ├── junit.jar ├── log4j-1.2.15.jar ├── picard-1.67.jar └── sam-1.67.jar ├── license.txt ├── log4j.properties ├── resources └── assemblies │ ├── ce10.len │ ├── ce2.len │ ├── ce3.len │ ├── ce4.len │ ├── ce5.len │ ├── ce6.len │ ├── ce7.len │ ├── ce8.len │ ├── ce9.len │ ├── dm1.len │ ├── dm2.len │ ├── dm3.len │ ├── hg15.len │ ├── hg16.len │ ├── hg17.len │ ├── hg18.len │ ├── hg19.len │ ├── hg19Haps.len │ ├── hg19Patch2.len │ ├── hg38.len │ ├── klac.len │ ├── kwal.len │ ├── sacCer1.len │ ├── sacCer2.len │ └── sacCer3.len ├── sam_fa_indices.loc.sample ├── src ├── edu │ └── unc │ │ ├── genomics │ │ ├── AssemblyConverter.java │ │ ├── AssemblyFactory.java │ │ ├── CommandLineTool.java │ │ ├── CommandLineToolException.java │ │ ├── KMeansRow.java │ │ ├── NucleosomeCall.java │ │ ├── NucleosomeCallsFileReader.java │ │ ├── PathConverter.java │ │ ├── PathFactory.java │ │ ├── ReadMapperTool.java │ │ ├── ReadablePathValidator.java │ │ ├── WigAnalysisTool.java │ │ ├── WigMathTool.java │ │ ├── converters │ │ │ ├── FastqIlluminaToSanger.java │ │ │ ├── GeneTrackToBedGraph.java │ │ │ ├── GeneTrackToWig.java │ │ │ ├── InterpolateDiscontinuousData.java │ │ │ ├── IntervalToBed.java │ │ │ ├── IntervalToWig.java │ │ │ └── RomanNumeralize.java │ │ ├── dna │ │ │ ├── DNAPropertyCalculator.java │ │ │ └── FindNMers.java │ │ ├── ngs │ │ │ ├── Autocorrelation.java │ │ │ ├── BaseAlignCounts.java │ │ │ ├── ExtractDataFromRegion.java │ │ │ ├── FilterRegions.java │ │ │ ├── FindAbsoluteMaxima.java │ │ │ ├── FindOutlierRegions.java │ │ │ ├── FragmentLengthDistributionByGene.java │ │ │ ├── IntervalLengthDistribution.java │ │ │ ├── IntervalStats.java │ │ │ ├── PowerSpectrum.java │ │ │ ├── ReadLengthDistributionMatrix.java │ │ │ ├── RollingReadLength.java │ │ │ ├── SplitReads.java │ │ │ ├── SplitWigIntervals.java │ │ │ ├── Subsample.java │ │ │ └── WaveletTransform.java │ │ ├── nucleosomes │ │ │ ├── DynaPro.java │ │ │ ├── FindBoundaryNucleosomes.java │ │ │ ├── GreedyCaller.java │ │ │ ├── IntervalEntropy.java │ │ │ ├── MapDyads.java │ │ │ ├── PairOverlappingNucleosomes.java │ │ │ ├── PercusDecomposition.java │ │ │ ├── Phasogram.java │ │ │ └── PredictDinucleosomes.java │ │ ├── visualization │ │ │ ├── IntervalAverager.java │ │ │ ├── KMeans.java │ │ │ ├── MatrixAligner.java │ │ │ └── StripMatrix.java │ │ └── wigmath │ │ │ ├── Add.java │ │ │ ├── Average.java │ │ │ ├── Correlate.java │ │ │ ├── Divide.java │ │ │ ├── Downsample.java │ │ │ ├── ExtractRegion.java │ │ │ ├── GaussianSmooth.java │ │ │ ├── LogTransform.java │ │ │ ├── MovingAverageSmooth.java │ │ │ ├── MovingEntropy.java │ │ │ ├── Multiply.java │ │ │ ├── Root.java │ │ │ ├── Scale.java │ │ │ ├── Shift.java │ │ │ ├── StandardDeviation.java │ │ │ ├── Subtract.java │ │ │ ├── Summary.java │ │ │ ├── ValueDistribution.java │ │ │ └── ZScore.java │ │ └── utils │ │ ├── ArrayScaler.java │ │ ├── ArrayUtils.java │ │ ├── FFTUtils.java │ │ ├── FloatCorrelation.java │ │ ├── FloatHistogram.java │ │ ├── RomanNumeral.java │ │ ├── Samtools.java │ │ ├── SequenceUtils.java │ │ ├── SortUtils.java │ │ └── WigStatistic.java └── log4j.properties ├── test-data ├── baseAlignCounts1.wig ├── bedGraphToWig.input.bedGraph ├── divide1.wig ├── divide2.wig ├── divide3.wig ├── downsample1.wig ├── downsample2.wig ├── downsample3.wig ├── gaussian1.wig ├── gaussian2.wig ├── gaussian3.wig ├── geneTrackToBedGraph.bedGraph ├── geneTrackToWig1.wig ├── geneTrackToWig2.wig ├── intervallengthdistribution1.txt ├── intervallengthdistribution2.txt ├── intervallengthdistribution3.txt ├── logger1.wig ├── logger2.wig ├── logger3.wig ├── logger4.wig ├── logger5.wig ├── logger6.wig ├── romanNumeralize.input ├── romanNumeralize.output ├── stripMatrix.txt ├── test.bed ├── test.fasta ├── test.fasta.fai ├── test.fastqillumina ├── test.fastqsanger ├── test.genetrack ├── test.matrix2png.txt ├── test2.bed ├── twist.normalized.wig ├── twist.wig ├── wigmath1.bw ├── wigmath1.wig ├── wigmath2.bw ├── wigmath2.wig ├── wigmath3.bw ├── wigmath3.wig ├── wigsummary1.txt ├── wigsummary2.txt ├── wigsummary3.txt ├── zscorer1.wig ├── zscorer2.wig ├── zscorer3.wig ├── zscorer4.wig ├── zscorer5.wig └── zscorer6.wig ├── test └── edu │ └── unc │ └── utils │ ├── ArrayScalerTest.java │ ├── ArrayUtilsTest.java │ ├── FloatCorrelationTest.java │ ├── FloatHistogramTest.java │ ├── RomanNumeralTest.java │ └── SortUtilsTest.java ├── toolRunner.bat ├── toolRunner.sh └── tool_data_table_conf.xml.sample /.classpath: 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