├── .github └── workflows │ └── main.yml ├── .gitignore ├── LICENSE.txt ├── MANIFEST.in ├── README.rst ├── dev-requirements.txt ├── docker ├── full-test.sh ├── harness.sh ├── pbt-test-py2 │ └── Dockerfile └── pbt-test-py3 │ └── Dockerfile ├── docs ├── Makefile ├── README.rst ├── make.bat └── source │ ├── 3-brief-examples.rst │ ├── FAQs.rst │ ├── _static │ └── custom.css │ ├── _templates │ └── layout.html │ ├── autodoc_source.rst │ ├── autodocs │ └── pybedtools.contrib.plotting.Track.rst │ ├── changes.rst │ ├── conf.py │ ├── create-a-bedtool-tutorial.rst │ ├── default-arguments.rst │ ├── each.rst │ ├── example-script │ ├── example-script-nocomments │ ├── example_3 │ ├── example_3_no_comments │ ├── filtering.rst │ ├── flow-of-commands.rst │ ├── history.rst │ ├── images │ ├── downloads.png │ ├── gchart.png │ └── mpl.png │ ├── includeme.rst │ ├── index.rst │ ├── intersections.rst │ ├── intervals.rst │ ├── intro.rst │ ├── main.rst │ ├── piping.rst │ ├── pybedtools-dev-history.rst │ ├── pybedtools.featurefuncs.TSS.rst │ ├── pybedtools.featurefuncs.add_color.rst │ ├── pybedtools.featurefuncs.bed2gff.rst │ ├── pybedtools.featurefuncs.bedgraph_scale.rst │ ├── pybedtools.featurefuncs.center.rst │ ├── pybedtools.featurefuncs.extend_fields.rst │ ├── pybedtools.featurefuncs.five_prime.rst │ ├── pybedtools.featurefuncs.gff2bed.rst │ ├── pybedtools.featurefuncs.greater_than.rst │ ├── pybedtools.featurefuncs.less_than.rst │ ├── pybedtools.featurefuncs.midpoint.rst │ ├── pybedtools.featurefuncs.normalized_to_length.rst │ ├── pybedtools.featurefuncs.rename.rst │ ├── pybedtools.featurefuncs.three_prime.rst │ ├── save-results.rst │ ├── scripts.rst │ ├── sh-comparison.rst │ ├── topical-bam-semantics.rst │ ├── topical-bam.rst │ ├── topical-comparisons.rst │ ├── topical-create-a-bedtool.rst │ ├── topical-design-principles.rst │ ├── topical-documentation-contents.rst │ ├── topical-genome.rst │ ├── topical-iterators.rst │ ├── topical-low-level-ops.rst │ ├── topical-random.rst │ ├── topical-saving.rst │ ├── topical-wrapping.rst │ └── tutorial-contents.rst ├── ez_setup.py ├── optional-requirements.txt ├── pybedtools ├── _Window.pyx ├── __init__.py ├── bedtool.py ├── cbedtools.pxd ├── cbedtools.pyx ├── contrib │ ├── __init__.py │ ├── bigbed.py │ ├── bigwig.py │ ├── intersection_matrix.py │ ├── long_range_interaction.py │ ├── plotting.py │ └── venn_maker.py ├── featurefuncs.pyx ├── filenames.py ├── genome_registry.py ├── helpers.py ├── include │ ├── bedFile.cpp │ ├── bedFile.h │ ├── fileType.cpp │ ├── fileType.h │ ├── gzstream.cpp │ ├── gzstream.h │ └── lineFileUtilities.h ├── logger.py ├── parallel.py ├── paths.py ├── scripts │ ├── annotate.py │ ├── examples │ │ └── pbt_plotting_example.py │ ├── intersection_matrix.py │ ├── intron_exon_reads.py │ ├── peak_pie.py │ ├── py_ms_example.py │ ├── pybedtools │ ├── sh_ms_example.sh │ ├── venn_gchart.py │ └── venn_mpl.py ├── settings.py ├── stats.py ├── test │ ├── __init__.py │ ├── data │ │ ├── 1000genomes-example.vcf │ │ ├── 164.gtf │ │ ├── BEAF_Kc_Bushey_2009.bed │ │ ├── BEAF_Mbn2_Bushey_2009.bed │ │ ├── CTCF_Kc_Bushey_2009.bed │ │ ├── CTCF_Mbn2_Bushey_2009.bed │ │ ├── Cp190_Kc_Bushey_2009.bed │ │ ├── Cp190_Mbn2_Bushey_2009.bed │ │ ├── SuHw_Kc_Bushey_2009.bed │ │ ├── SuHw_Mbn2_Bushey_2009.bed │ │ ├── __init__.py │ │ ├── a.bed │ │ ├── a.igv_script │ │ ├── a.links.html │ │ ├── b.bed │ │ ├── bedpe.bed │ │ ├── bedpe2.bed │ │ ├── c.gff │ │ ├── d.gff │ │ ├── democonfig.yaml │ │ ├── dm3-chr2L-5M-invalid.gff.gz │ │ ├── dm3-chr2L-5M.gff.gz │ │ ├── example.narrowPeak │ │ ├── exons.gff │ │ ├── expand_test.bed │ │ ├── gdc.1.100.bam │ │ ├── gdc.1.100.bam.bai │ │ ├── gdc.50.200.bam │ │ ├── gdc.50.200.bam.bai │ │ ├── gdc.bam │ │ ├── gdc.bed │ │ ├── gdc.cram │ │ ├── gdc.gff │ │ ├── gdc.gff.gz │ │ ├── gdc.othersort.bam │ │ ├── gdc.sorted.bam │ │ ├── gdc.sorted.bam.bai │ │ ├── genome.fa │ │ ├── hg19.gff │ │ ├── hg38-base.bed │ │ ├── hg38-problem.bed │ │ ├── issue319.bed │ │ ├── issue319.out.bed │ │ ├── issue319.vcf.gz │ │ ├── issue_121.bam │ │ ├── m1.bed │ │ ├── mm9.bed12 │ │ ├── multibamcov_test.bed │ │ ├── reads.bam │ │ ├── rmsk.hg18.chr21.small.bed │ │ ├── rmsk.hg18.chr21.small.bed.gz │ │ ├── small.bam │ │ ├── small.fastq │ │ ├── snps.bed.gz │ │ ├── tag_test1.bed │ │ ├── tag_test2.bed │ │ ├── test.fa │ │ ├── test.fa.fai │ │ ├── test_bedpe.bed │ │ ├── test_peaks.bed │ │ ├── test_tsses.bed │ │ ├── v.vcf │ │ ├── vcf-stderr-test.bed │ │ ├── vcf-stderr-test.vcf │ │ ├── venn.b.bed │ │ ├── venn.c.bed │ │ ├── x.bam │ │ ├── x.bed │ │ └── y.bam │ ├── gchart-expected.png │ ├── genomepy_integration.py │ ├── mpl-expected.png │ ├── prevent_open_file_regression │ ├── regression_tests.py │ ├── test_1.py │ ├── test_cases.yaml │ ├── test_cbedtools.py │ ├── test_contrib.py │ ├── test_gzip_support.py │ ├── test_helpers.py │ ├── test_issues.py │ ├── test_iter.py │ ├── test_len_leak.py │ ├── test_merge215.yaml │ ├── test_merge227.yaml │ ├── test_pathlib.py │ ├── test_shuffle215.yaml │ ├── test_shuffle227.yaml │ └── 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