INSTALL
KNOWN_BUGS
LICENSE
MANIFEST.in
README.rst
THANKS.txt
install.sh
requires.txt
setup.py
cgat/AGP.py
cgat/AString.py
cgat/Bed.py
cgat/Blat.py
cgat/CBioPortal.py
cgat/CorrespondenceAnalysis.py
cgat/Diamond.py
cgat/FastaIterator.py
cgat/Fastq.py
cgat/GFF3.py
cgat/GO.py
cgat/GTF.py
cgat/GeneModelAnalysis.pyx
cgat/Genomics.py
cgat/Glam2.py
cgat/Glam2Scan.py
cgat/Histogram.py
cgat/Histogram2D.py
cgat/IGV.py
cgat/IndexedFasta.py
cgat/IndexedGenome.py
cgat/Intervals.py
cgat/Iterators.py
cgat/LCA.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/RLE.py
cgat/RateEstimation.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/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/top_level.txt
cgat/BamTools/bamtools.pyx
cgat/BamTools/geneprofile.pyx
cgat/BamTools/peakshape.pyx
cgat/Components/Components.pyx
cgat/Components/connected_components.cpp
cgat/Components/connected_components.h
cgat/FastqTools/fastqtools.pyx
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/Plots/VariantPlots.py
cgat/Plots/__init__.py
cgat/VCFTools/vcftools.pyx
cgat/tools/__init__.py
cgat/tools/bam2UniquePairs.py
cgat/tools/bam2bam.py
cgat/tools/bam2bam_split_reads.py
cgat/tools/bam2bed.py
cgat/tools/bam2depth.py
cgat/tools/bam2fasta.py
cgat/tools/bam2fastq.py
cgat/tools/bam2geneprofile.py
cgat/tools/bam2libtype.py
cgat/tools/bam2peakshape.py
cgat/tools/bam2stats.py
cgat/tools/bam2wiggle.py
cgat/tools/bam2window_stats.py
cgat/tools/bam_compare_alignments.py
cgat/tools/bam_pileup2tsv.py
cgat/tools/bam_vs_bam.py
cgat/tools/bam_vs_bed.py
cgat/tools/bam_vs_gtf.py
cgat/tools/bams2bam.py
cgat/tools/bed2annotator.py
cgat/tools/bed2bed.py
cgat/tools/bed2fasta.py
cgat/tools/bed2gff.py
cgat/tools/bed2graph.py
cgat/tools/bed2plot.py
cgat/tools/bed2stats.py
cgat/tools/bed2table.py
cgat/tools/bed_vs_bed.py
cgat/tools/beds2beds.py
cgat/tools/beds2counts.py
cgat/tools/cat_tables.py
cgat/tools/cgat2dot.py
cgat/tools/cgat2rdf.py
cgat/tools/cgat_fasta2cDNA.py
cgat/tools/cgat_galaxy_wrapper.py
cgat/tools/cgat_get_options.py
cgat/tools/cgat_pep8_code_quality.py
cgat/tools/cgat_rebuild_extensions.py
cgat/tools/cgat_script_template.py
cgat/tools/chain2psl.py
cgat/tools/clean.py
cgat/tools/combine_tables.py
cgat/tools/csv2csv.py
cgat/tools/csv2db.py
cgat/tools/csv_cut.py
cgat/tools/csv_intersection.py
cgat/tools/csv_rename.py
cgat/tools/csv_select.py
cgat/tools/csv_set.py
cgat/tools/csvs2csv.py
cgat/tools/data2histogram.py
cgat/tools/diamond2counts.py
cgat/tools/diff_bam.py
cgat/tools/diff_bed.py
cgat/tools/diff_chains.py
cgat/tools/diff_fasta.py
cgat/tools/diff_gtf.py
cgat/tools/extract_stats.py
cgat/tools/fasta2bed.py
cgat/tools/fasta2fasta.py
cgat/tools/fasta2fastq.py
cgat/tools/fasta2kmercontent.py
cgat/tools/fasta2stats.py
cgat/tools/fasta2table.py
cgat/tools/fasta2variants.py
cgat/tools/fasta2vcf.py
cgat/tools/fastas2fasta.py
cgat/tools/fastq2fasta.py
cgat/tools/fastq2fastq.py
cgat/tools/fastq2summary.py
cgat/tools/fastq2table.py
cgat/tools/fastq2tpm.py
cgat/tools/fastq2tsv.py
cgat/tools/fastqs2fasta.py
cgat/tools/fastqs2fastq.py
cgat/tools/fastqs2fastqs.py
cgat/tools/genome_bed.py
cgat/tools/gff2bed.py
cgat/tools/gff2coverage.py
cgat/tools/gff2fasta.py
cgat/tools/gff2gff.py
cgat/tools/gff2histogram.py
cgat/tools/gff2psl.py
cgat/tools/gff2stats.py
cgat/tools/gff2table.py
cgat/tools/gff32gtf.py
cgat/tools/gtf2fasta.py
cgat/tools/gtf2gff.py
cgat/tools/gtf2gtf.py
cgat/tools/gtf2table.py
cgat/tools/gtf2tsv.py
cgat/tools/gtfs2tsv.py
cgat/tools/index2bed.py
cgat/tools/index_fasta.py
cgat/tools/lca2table.py
cgat/tools/maf2maf.py
cgat/tools/medip_merge_intervals.py
cgat/tools/metaphlan2table.py
cgat/tools/plot_variant_stats.py
cgat/tools/randomize_lines.py
cgat/tools/rnaseq_junction_bam2bam.py
cgat/tools/runGO.py
cgat/tools/split_fasta.py
cgat/tools/split_file.py
cgat/tools/split_gff.py
cgat/tools/table2stats.py
cgat/tools/table2table.py
cgat/tools/tables2table.py
cgat/tools/transfac2transfac.py
cgat/tools/vcf2tsv.py
cgat/tools/vcf2vcf.py
cgat/tools/vcf_compare_phase.py
cgat/tools/vcf_stats.py
cgat/tools/vcf_vs_vcf.py
cgat/tools/vcfstats2db.py
cgat/tools/wig2bed.py