Download java genomics toolkit Free Java Code

.classpath// w w w.j ava 2  s.c  o  m
.gitignore
.project
META-INF/MANIFEST.MF
README.rdoc
build.xml
galaxy-conf/Add.xml
galaxy-conf/Autocorrelation.xml
galaxy-conf/Average.xml
galaxy-conf/BaseAlignCounts.xml
galaxy-conf/Correlate.xml
galaxy-conf/DNAPropertyCalculator.xml
galaxy-conf/Divide.xml
galaxy-conf/Downsample.xml
galaxy-conf/DynaPro.xml
galaxy-conf/ExtractDataFromRegion.xml
galaxy-conf/FastqIlluminaToSanger.xml
galaxy-conf/FindAbsoluteMaxima.xml
galaxy-conf/FindBoundaryNucleosomes.xml
galaxy-conf/FindNMers.xml
galaxy-conf/FindOutlierRegions.xml
galaxy-conf/GaussianSmooth.xml
galaxy-conf/GeneTrackToBedGraph.xml
galaxy-conf/GeneTrackToWig.xml
galaxy-conf/GreedyCaller.xml
galaxy-conf/InterpolateDiscontinuousData.xml
galaxy-conf/IntervalAverager.xml
galaxy-conf/IntervalLengthDistribution.xml
galaxy-conf/IntervalStats.xml
galaxy-conf/IntervalToBed.xml
galaxy-conf/IntervalToWig.xml
galaxy-conf/KMeans.xml
galaxy-conf/LogTransform.xml
galaxy-conf/MapDyads.xml
galaxy-conf/MatrixAligner.xml
galaxy-conf/MovingAverageSmooth.xml
galaxy-conf/Multiply.xml
galaxy-conf/PairOverlappingNucleosomes.xml
galaxy-conf/PercusDecomposition.xml
galaxy-conf/Phasogram.xml
galaxy-conf/PowerSpectrum.xml
galaxy-conf/ReadLengthDistributionMatrix.xml
galaxy-conf/RollingReadLength.xml
galaxy-conf/RomanNumeralize.xml
galaxy-conf/Scale.xml
galaxy-conf/Shift.xml
galaxy-conf/StripMatrix.xml
galaxy-conf/Subsample.xml
galaxy-conf/Subtract.xml
galaxy-conf/Summary.xml
galaxy-conf/ValueDistribution.xml
galaxy-conf/WaveletTransform.xml
galaxy-conf/ZScore.xml
galaxy-conf/galaxyToolRunner.sh
galaxy-conf/log4j.properties
galaxy-conf/matrix2png.xml
galaxyToolConf.xml
lib/BigWig.jar
lib/commons-lang3-3.1.jar
lib/commons-math3-3.0.jar
lib/dnaproperties-1732.jar
lib/hamcrest-core-1.1.0.jar
lib/java-genomics-io.jar
lib/jcommander-1.27.jar
lib/jtransforms-2.4.jar
lib/junit.jar
lib/log4j-1.2.15.jar
lib/picard-1.67.jar
lib/sam-1.67.jar
license.txt
log4j.properties
resources/assemblies/ce10.len
resources/assemblies/ce2.len
resources/assemblies/ce3.len
resources/assemblies/ce4.len
resources/assemblies/ce5.len
resources/assemblies/ce6.len
resources/assemblies/ce7.len
resources/assemblies/ce8.len
resources/assemblies/ce9.len
resources/assemblies/dm1.len
resources/assemblies/dm2.len
resources/assemblies/dm3.len
resources/assemblies/hg15.len
resources/assemblies/hg16.len
resources/assemblies/hg17.len
resources/assemblies/hg18.len
resources/assemblies/hg19.len
resources/assemblies/hg19Haps.len
resources/assemblies/hg19Patch2.len
resources/assemblies/klac.len
resources/assemblies/kwal.len
resources/assemblies/sacCer1.len
resources/assemblies/sacCer2.len
resources/assemblies/sacCer3.len
sam_fa_indices.loc.sample
src/edu/unc/genomics/AssemblyConverter.java
src/edu/unc/genomics/AssemblyFactory.java
src/edu/unc/genomics/CommandLineTool.java
src/edu/unc/genomics/CommandLineToolException.java
src/edu/unc/genomics/KMeansRow.java
src/edu/unc/genomics/NucleosomeCall.java
src/edu/unc/genomics/NucleosomeCallsFileReader.java
src/edu/unc/genomics/PathConverter.java
src/edu/unc/genomics/PathFactory.java
src/edu/unc/genomics/ReadMapperTool.java
src/edu/unc/genomics/ReadablePathValidator.java
src/edu/unc/genomics/WigAnalysisTool.java
src/edu/unc/genomics/WigMathTool.java
src/edu/unc/genomics/converters/FastqIlluminaToSanger.java
src/edu/unc/genomics/converters/GeneTrackToBedGraph.java
src/edu/unc/genomics/converters/GeneTrackToWig.java
src/edu/unc/genomics/converters/InterpolateDiscontinuousData.java
src/edu/unc/genomics/converters/IntervalToBed.java
src/edu/unc/genomics/converters/IntervalToWig.java
src/edu/unc/genomics/converters/RomanNumeralize.java
src/edu/unc/genomics/dna/DNAPropertyCalculator.java
src/edu/unc/genomics/dna/FindNMers.java
src/edu/unc/genomics/ngs/Autocorrelation.java
src/edu/unc/genomics/ngs/BaseAlignCounts.java
src/edu/unc/genomics/ngs/ExtractDataFromRegion.java
src/edu/unc/genomics/ngs/FilterRegions.java
src/edu/unc/genomics/ngs/FindAbsoluteMaxima.java
src/edu/unc/genomics/ngs/FindOutlierRegions.java
src/edu/unc/genomics/ngs/FragmentLengthDistributionByGene.java
src/edu/unc/genomics/ngs/IntervalLengthDistribution.java
src/edu/unc/genomics/ngs/IntervalStats.java
src/edu/unc/genomics/ngs/PowerSpectrum.java
src/edu/unc/genomics/ngs/ReadLengthDistributionMatrix.java
src/edu/unc/genomics/ngs/RollingReadLength.java
src/edu/unc/genomics/ngs/SplitReads.java
src/edu/unc/genomics/ngs/Subsample.java
src/edu/unc/genomics/ngs/WaveletTransform.java
src/edu/unc/genomics/nucleosomes/DynaPro.java
src/edu/unc/genomics/nucleosomes/FindBoundaryNucleosomes.java
src/edu/unc/genomics/nucleosomes/GreedyCaller.java
src/edu/unc/genomics/nucleosomes/MapDyads.java
src/edu/unc/genomics/nucleosomes/PairOverlappingNucleosomes.java
src/edu/unc/genomics/nucleosomes/PercusDecomposition.java
src/edu/unc/genomics/nucleosomes/Phasogram.java
src/edu/unc/genomics/nucleosomes/PredictDinucleosomes.java
src/edu/unc/genomics/visualization/IntervalAverager.java
src/edu/unc/genomics/visualization/KMeans.java
src/edu/unc/genomics/visualization/MatrixAligner.java
src/edu/unc/genomics/visualization/StripMatrix.java
src/edu/unc/genomics/wigmath/Add.java
src/edu/unc/genomics/wigmath/Average.java
src/edu/unc/genomics/wigmath/Correlate.java
src/edu/unc/genomics/wigmath/Divide.java
src/edu/unc/genomics/wigmath/Downsample.java
src/edu/unc/genomics/wigmath/ExtractRegion.java
src/edu/unc/genomics/wigmath/GaussianSmooth.java
src/edu/unc/genomics/wigmath/LogTransform.java
src/edu/unc/genomics/wigmath/MovingAverageSmooth.java
src/edu/unc/genomics/wigmath/Multiply.java
src/edu/unc/genomics/wigmath/Scale.java
src/edu/unc/genomics/wigmath/Shift.java
src/edu/unc/genomics/wigmath/StandardDeviation.java
src/edu/unc/genomics/wigmath/Subtract.java
src/edu/unc/genomics/wigmath/Summary.java
src/edu/unc/genomics/wigmath/ValueDistribution.java
src/edu/unc/genomics/wigmath/ZScore.java
src/edu/unc/utils/ArrayScaler.java
src/edu/unc/utils/ArrayUtils.java
src/edu/unc/utils/FFTUtils.java
src/edu/unc/utils/FloatCorrelation.java
src/edu/unc/utils/FloatHistogram.java
src/edu/unc/utils/RomanNumeral.java
src/edu/unc/utils/Samtools.java
src/edu/unc/utils/SequenceUtils.java
src/edu/unc/utils/SortUtils.java
src/edu/unc/utils/WigStatistic.java
src/log4j.properties
test-data/baseAlignCounts1.wig
test-data/bedGraphToWig.input.bedGraph
test-data/divide1.wig
test-data/divide2.wig
test-data/divide3.wig
test-data/downsample1.wig
test-data/downsample2.wig
test-data/downsample3.wig
test-data/gaussian1.wig
test-data/gaussian2.wig
test-data/gaussian3.wig
test-data/geneTrackToBedGraph.bedGraph
test-data/geneTrackToWig1.wig
test-data/geneTrackToWig2.wig
test-data/intervallengthdistribution1.txt
test-data/intervallengthdistribution2.txt
test-data/intervallengthdistribution3.txt
test-data/logger1.wig
test-data/logger2.wig
test-data/logger3.wig
test-data/logger4.wig
test-data/logger5.wig
test-data/logger6.wig
test-data/romanNumeralize.input
test-data/romanNumeralize.output
test-data/stripMatrix.txt
test-data/test.bed
test-data/test.fasta
test-data/test.fasta.fai
test-data/test.fastqillumina
test-data/test.fastqsanger
test-data/test.genetrack
test-data/test.matrix2png.txt
test-data/test2.bed
test-data/twist.normalized.wig
test-data/twist.wig
test-data/wigmath1.bw
test-data/wigmath1.wig
test-data/wigmath2.bw
test-data/wigmath2.wig
test-data/wigmath3.bw
test-data/wigmath3.wig
test-data/wigsummary1.txt
test-data/wigsummary2.txt
test-data/wigsummary3.txt
test-data/zscorer1.wig
test-data/zscorer2.wig
test-data/zscorer3.wig
test-data/zscorer4.wig
test-data/zscorer5.wig
test-data/zscorer6.wig
test/edu/unc/utils/ArrayScalerTest.java
test/edu/unc/utils/ArrayUtilsTest.java
test/edu/unc/utils/FloatCorrelationTest.java
test/edu/unc/utils/FloatHistogramTest.java
test/edu/unc/utils/RomanNumeralTest.java
test/edu/unc/utils/SortUtilsTest.java
toolRunner.sh
tool_data_table_conf.xml.sample