INSTALL
KNOWN_BUGS
LICENSE
MANIFEST.in
README.rst
README.txt
THANKS.txt
install_requisites.sh
requires.txt
setup.py
CGAT/AGP.py
CGAT/AString.py
CGAT/AlignedPairs.py
CGAT/Bed.py
CGAT/Bioprospector.py
CGAT/BlastAlignments.py
CGAT/Blat.py
CGAT/BlatTest.py
CGAT/CBioPortal.py
CGAT/CSV.py
CGAT/CSV2DB.py
CGAT/Cluster.py
CGAT/CorrespondenceAnalysis.py
CGAT/Database.py
CGAT/Exons.py
CGAT/Experiment.py
CGAT/Expression.py
CGAT/ExternalList.py
CGAT/Fasta.py
CGAT/FastaIterator.py
CGAT/Fastq.py
CGAT/GDLDraw.py
CGAT/GO.py
CGAT/GTF.py
CGAT/GenomicIO.py
CGAT/Genomics.py
CGAT/Glam2.py
CGAT/Glam2Scan.py
CGAT/GraphTools.py
CGAT/Histogram.py
CGAT/Histogram2D.py
CGAT/IGV.py
CGAT/IOTools.py
CGAT/IndexedFasta.py
CGAT/IndexedGenome.py
CGAT/Intervalls.py
CGAT/IntervallsWeighted.py
CGAT/Intervals.py
CGAT/Iterators.py
CGAT/Local.py
CGAT/Logfile.py
CGAT/MAST.py
CGAT/Mali.py
CGAT/MaliIO.py
CGAT/Maq.py
CGAT/Masker.py
CGAT/MatlabTools.py
CGAT/MatrixTools.py
CGAT/Metaphlan.py
CGAT/Motifs.py
CGAT/Nucmer.py
CGAT/Orthologs.py
CGAT/PamMatrices.py
CGAT/Pipeline.py
CGAT/Prediction.py
CGAT/PredictionFile.py
CGAT/PredictionParser.py
CGAT/Predictor.py
CGAT/ProfileLibrary.py
CGAT/ProfileLibraryCompass.py
CGAT/ProgressBar.py
CGAT/RLE.py
CGAT/RateEstimation.py
CGAT/Regions.py
CGAT/SVGDuplicationsWheel.py
CGAT/SVGTree.py
CGAT/SVGdraw.py
CGAT/SaryFasta.py
CGAT/SequencePairProperties.py
CGAT/SequenceProperties.py
CGAT/SetTools.py
CGAT/Sockets.py
CGAT/Stats.py
CGAT/SuffixArray.py
CGAT/Synteny.py
CGAT/Tophat.py
CGAT/Tree.py
CGAT/TreeTools.py
CGAT/VCF.py
CGAT/Variants.py
CGAT/Wiggle.py
CGAT/WrapperAdaptiveCAI.py
CGAT/WrapperBaseML.py
CGAT/WrapperBl2Seq.py
CGAT/WrapperBlastZ.py
CGAT/WrapperClustal.py
CGAT/WrapperCodeML.py
CGAT/WrapperDBA.py
CGAT/WrapperDialign.py
CGAT/WrapperENC.py
CGAT/WrapperExonerate.py
CGAT/WrapperGblocks.py
CGAT/WrapperHmmer.py
CGAT/WrapperIDR.py
CGAT/WrapperMACS.py
CGAT/WrapperMEDIPS.py
CGAT/WrapperMuscle.py
CGAT/WrapperNJTree.py
CGAT/WrapperPhylip.py
CGAT/WrapperSPP.py
CGAT/WrapperSlr.py
CGAT/WrapperZinba.py
CGAT/__init__.py
CGAT/dictzip.py
CGAT.egg-info/PKG-INFO
CGAT.egg-info/SOURCES.txt
CGAT.egg-info/dependency_links.txt
CGAT.egg-info/entry_points.txt
CGAT.egg-info/not-zip-safe
CGAT.egg-info/requires.txt
CGAT.egg-info/top_level.txt
CGAT/Components/Components.cpp
CGAT/Components/Components.pyx
CGAT/Components/connected_components.cpp
CGAT/Components/connected_components.h
CGAT/NCL/__init__.py
CGAT/NCL/_cnestedlist.pxd
CGAT/NCL/cnestedlist.pyx
CGAT/NCL/default.h
CGAT/NCL/intervaldb.c
CGAT/NCL/intervaldb.h
CGAT/Nubiscan/__init__.py
CGAT/Nubiscan/cnubiscan.pyx
scripts/__init__.py
scripts/_bam2bam.pyx
scripts/_bam2bam.pyxbld
scripts/_bam2bed.pyx
scripts/_bam2bed.pyxbld
scripts/_bam2geneprofile.pyx
scripts/_bam2geneprofile.pyxbld
scripts/_bam2peakshape.pyx
scripts/_bam2peakshape.pyxbld
scripts/_bam2stats.pyx
scripts/_bam2stats.pyxbld
scripts/_bams2bam.pyx
scripts/_bams2bam.pyxbld
scripts/_gtf2table.pyx
scripts/_gtf2table.pyxbld
scripts/bam2bam.py
scripts/bam2bed.py
scripts/bam2fastq.py
scripts/bam2geneprofile.py
scripts/bam2peakshape.py
scripts/bam2stats.py
scripts/bam2wiggle.py
scripts/bam_vs_bam.py
scripts/bam_vs_bed.py
scripts/bam_vs_gtf.py
scripts/bed2bed.py
scripts/bed2fasta.py
scripts/bed2gff.py
scripts/bed2stats.py
scripts/bed2table.py
scripts/beds2beds.py
scripts/beds2counts.py
scripts/cgat.py
scripts/chain2psl.py
scripts/chain2stats.py
scripts/diff_bam.py
scripts/diff_bed.py
scripts/diff_chains.py
scripts/diff_fasta.py
scripts/diff_gtf.py
scripts/fasta2bed.py
scripts/fasta2fasta.py
scripts/fasta2kmercontent.py
scripts/fasta2table.py
scripts/fasta2variants.py
scripts/fastas2fasta.py
scripts/fastq2fastq.py
scripts/fastq2table.py
scripts/fastqs2fasta.py
scripts/fastqs2fastqs.py
scripts/gff2bed.py
scripts/gff2coverage.py
scripts/gff2fasta.py
scripts/gff2gff.py
scripts/gff2histogram.py
scripts/gff2psl.py
scripts/gff2stats.py
scripts/gtf2fasta.py
scripts/gtf2gff.py
scripts/gtf2gtf.py
scripts/gtf2table.py
scripts/gtf2tsv.py
scripts/gtfs2tsv.py
scripts/index_fasta.py
scripts/split_gff.py
scripts/vcf2vcf.py
scripts/version.py