INSTALL
KNOWN_BUGS
LICENSE
MANIFEST.in
README.rst
THANKS.txt
install-CGAT-tools.sh
requires.txt
setup.py
CGAT/AGP.py
CGAT/AString.py
CGAT/BamTools.py
CGAT/Bed.py
CGAT/Biomart.py
CGAT/Bioprospector.py
CGAT/Blat.py
CGAT/CBioPortal.py
CGAT/CSV.py
CGAT/CSV2DB.py
CGAT/CorrespondenceAnalysis.py
CGAT/Counts.py
CGAT/Database.py
CGAT/Diamond.py
CGAT/Experiment.py
CGAT/Expression.py
CGAT/FastaIterator.py
CGAT/Fastq.py
CGAT/GFF3.py
CGAT/GO.py
CGAT/GTF.py
CGAT/GWAS.py
CGAT/GeneModelAnalysis.pyx
CGAT/Genomics.py
CGAT/Glam2.py
CGAT/Glam2Scan.py
CGAT/Histogram.py
CGAT/Histogram2D.py
CGAT/IGV.py
CGAT/IOTools.py
CGAT/IndexedFasta.py
CGAT/IndexedGenome.py
CGAT/Intervals.py
CGAT/Iterators.py
CGAT/LCA.py
CGAT/Logfile.py
CGAT/MAST.py
CGAT/MEME.py
CGAT/Mali.py
CGAT/Maq.py
CGAT/Masker.py
CGAT/MatlabTools.py
CGAT/MatrixTools.py
CGAT/Metaphlan.py
CGAT/Motifs.py
CGAT/R.py
CGAT/RLE.py
CGAT/RateEstimation.py
CGAT/Requirements.py
CGAT/SVGdraw.py
CGAT/SequencePairProperties.py
CGAT/SequenceProperties.py
CGAT/SetTools.py
CGAT/Sra.py
CGAT/Stats.py
CGAT/Style.py
CGAT/Tophat.py
CGAT/Tree.py
CGAT/TreeTools.py
CGAT/VCF.py
CGAT/Variants.py
CGAT/WrapperCodeML.py
CGAT/WrapperIDR.py
CGAT/WrapperMACS.py
CGAT/WrapperMuscle.py
CGAT/WrapperZinba.py
CGAT/__init__.py
CGAT/cgat.py
CGAT/dictzip.py
CGAT/makeGeneset.py
CGAT/version.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/Timeseries/__init__.py
CGAT/Timeseries/cmetrics.pyx
CGAT/scripts/__init__.py
CGAT/scripts/_bam2bam.pyx
CGAT/scripts/_bam2bam.pyxbld
CGAT/scripts/_bam2bed.pyx
CGAT/scripts/_bam2bed.pyxbld
CGAT/scripts/_bam2geneprofile.pyx
CGAT/scripts/_bam2geneprofile.pyxbld
CGAT/scripts/_bam2peakshape.pyx
CGAT/scripts/_bam2peakshape.pyxbld
CGAT/scripts/_bam2stats.pyx
CGAT/scripts/_bam2stats.pyxbld
CGAT/scripts/_bams2bam.pyx
CGAT/scripts/_bams2bam.pyxbld
CGAT/scripts/_gtf2table.pyx
CGAT/scripts/_gtf2table.pyxbld
CGAT/scripts/bam2bam.py
CGAT/scripts/bam2bed.py
CGAT/scripts/bam2fastq.py
CGAT/scripts/bam2geneprofile.py
CGAT/scripts/bam2peakshape.py
CGAT/scripts/bam2stats.py
CGAT/scripts/bam2wiggle.py
CGAT/scripts/bam_vs_bam.py
CGAT/scripts/bam_vs_bed.py
CGAT/scripts/bam_vs_gtf.py
CGAT/scripts/bed2bed.py
CGAT/scripts/bed2fasta.py
CGAT/scripts/bed2gff.py
CGAT/scripts/bed2stats.py
CGAT/scripts/bed2table.py
CGAT/scripts/beds2beds.py
CGAT/scripts/beds2counts.py
CGAT/scripts/chain2psl.py
CGAT/scripts/chain2stats.py
CGAT/scripts/diff_bam.py
CGAT/scripts/diff_bed.py
CGAT/scripts/diff_chains.py
CGAT/scripts/diff_fasta.py
CGAT/scripts/diff_gtf.py
CGAT/scripts/fasta2bed.py
CGAT/scripts/fasta2fasta.py
CGAT/scripts/fasta2kmercontent.py
CGAT/scripts/fasta2table.py
CGAT/scripts/fasta2variants.py
CGAT/scripts/fastas2fasta.py
CGAT/scripts/fastq2fastq.py
CGAT/scripts/fastq2table.py
CGAT/scripts/fastqs2fasta.py
CGAT/scripts/fastqs2fastqs.py
CGAT/scripts/gff2bed.py
CGAT/scripts/gff2coverage.py
CGAT/scripts/gff2fasta.py
CGAT/scripts/gff2gff.py
CGAT/scripts/gff2histogram.py
CGAT/scripts/gff2psl.py
CGAT/scripts/gff2stats.py
CGAT/scripts/gtf2fasta.py
CGAT/scripts/gtf2gff.py
CGAT/scripts/gtf2gtf.py
CGAT/scripts/gtf2table.py
CGAT/scripts/gtf2tsv.py
CGAT/scripts/gtfs2tsv.py
CGAT/scripts/index_fasta.py
CGAT/scripts/randomize_lines.py
CGAT/scripts/split_gff.py
CGAT/scripts/vcf2vcf.py