LICENSE.txt
MANIFEST.in
README.rst
ez_setup.py
setup.cfg
setup.py
docs/Makefile
docs/make.bat
docs/source/3-brief-examples.rst
docs/source/FAQs.rst
docs/source/autodoc_source.rst
docs/source/changes.rst
docs/source/conf.py
docs/source/create-a-bedtool-tutorial.rst
docs/source/default-arguments.rst
docs/source/each.rst
docs/source/filtering.rst
docs/source/flow-of-commands.rst
docs/source/history.rst
docs/source/includeme.rst
docs/source/index.rst
docs/source/intersections.rst
docs/source/intervals.rst
docs/source/intro.rst
docs/source/main.rst
docs/source/piping.rst
docs/source/pybedtools-dev-history.rst
docs/source/pybedtools.featurefuncs.TSS.rst
docs/source/pybedtools.featurefuncs.add_color.rst
docs/source/pybedtools.featurefuncs.bed2gff.rst
docs/source/pybedtools.featurefuncs.bedgraph_scale.rst
docs/source/pybedtools.featurefuncs.center.rst
docs/source/pybedtools.featurefuncs.extend_fields.rst
docs/source/pybedtools.featurefuncs.five_prime.rst
docs/source/pybedtools.featurefuncs.gff2bed.rst
docs/source/pybedtools.featurefuncs.greater_than.rst
docs/source/pybedtools.featurefuncs.less_than.rst
docs/source/pybedtools.featurefuncs.midpoint.rst
docs/source/pybedtools.featurefuncs.normalized_to_length.rst
docs/source/pybedtools.featurefuncs.rename.rst
docs/source/pybedtools.featurefuncs.three_prime.rst
docs/source/save-results.rst
docs/source/scripts.rst
docs/source/sh-comparison.rst
docs/source/topical-bam-semantics.rst
docs/source/topical-bam.rst
docs/source/topical-comparisons.rst
docs/source/topical-create-a-bedtool.rst
docs/source/topical-design-principles.rst
docs/source/topical-documentation-contents.rst
docs/source/topical-genome.rst
docs/source/topical-iterators.rst
docs/source/topical-low-level-ops.rst
docs/source/topical-random.rst
docs/source/topical-saving.rst
docs/source/topical-wrapping.rst
docs/source/tutorial-contents.rst
docs/source/_templates/layout.html
docs/source/autodocs/pybedtools.contrib.plotting.Track.rst
docs/source/images/downloads.png
docs/source/images/gchart.png
docs/source/images/mpl.png
pybedtools/_Window.c
pybedtools/_Window.pyx
pybedtools/__init__.py
pybedtools/__main__.py
pybedtools/bedtool.py
pybedtools/cbedtools.cxx
pybedtools/cbedtools.pxd
pybedtools/cbedtools.pyx
pybedtools/featurefuncs.cxx
pybedtools/featurefuncs.pyx
pybedtools/filenames.py
pybedtools/genome_registry.py
pybedtools/helpers.py
pybedtools/logger.py
pybedtools/parallel.py
pybedtools/settings.py
pybedtools/stats.py
pybedtools/version.py
pybedtools.egg-info/PKG-INFO
pybedtools.egg-info/SOURCES.txt
pybedtools.egg-info/dependency_links.txt
pybedtools.egg-info/not-zip-safe
pybedtools.egg-info/requires.txt
pybedtools.egg-info/top_level.txt
pybedtools/contrib/__init__.py
pybedtools/contrib/bigbed.py
pybedtools/contrib/bigwig.py
pybedtools/contrib/classifier.py
pybedtools/contrib/intersection_matrix.py
pybedtools/contrib/long_range_interaction.py
pybedtools/contrib/plotting.py
pybedtools/contrib/venn_maker.py
pybedtools/scripts/__init__.py
pybedtools/scripts/annotate.py
pybedtools/scripts/intersection_matrix.py
pybedtools/scripts/intron_exon_reads.py
pybedtools/scripts/peak_pie.py
pybedtools/scripts/py_ms_example.py
pybedtools/scripts/pybedtools
pybedtools/scripts/venn_gchart.py
pybedtools/scripts/venn_mpl.py
pybedtools/scripts/examples/pbt_plotting_example.py
pybedtools/test/__init__.py
pybedtools/test/gchart-expected.png
pybedtools/test/mpl-expected.png
pybedtools/test/prevent_open_file_regression
pybedtools/test/regression_tests.py
pybedtools/test/test1.py
pybedtools/test/test_cases.yaml
pybedtools/test/test_cbedtools.py
pybedtools/test/test_contrib.py
pybedtools/test/test_gzip_support.py
pybedtools/test/test_helpers.py
pybedtools/test/test_iter.py
pybedtools/test/test_len_leak.py
pybedtools/test/test_scripts.py
pybedtools/test/tfuncs.py
pybedtools/test/data/1000genomes-example.vcf
pybedtools/test/data/164.gtf
pybedtools/test/data/BEAF_Kc_Bushey_2009.bed
pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed
pybedtools/test/data/CTCF_Kc_Bushey_2009.bed
pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed
pybedtools/test/data/Cp190_Kc_Bushey_2009.bed
pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed
pybedtools/test/data/SuHw_Kc_Bushey_2009.bed
pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed
pybedtools/test/data/__init__.py
pybedtools/test/data/a.bed
pybedtools/test/data/a.igv_script
pybedtools/test/data/a.links.html
pybedtools/test/data/b.bed
pybedtools/test/data/bedpe.bed
pybedtools/test/data/bedpe2.bed
pybedtools/test/data/c.gff
pybedtools/test/data/d.gff
pybedtools/test/data/democonfig.yaml
pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz
pybedtools/test/data/dm3-chr2L-5M.gff.gz
pybedtools/test/data/exons.gff
pybedtools/test/data/expand_test.bed
pybedtools/test/data/gdc.1.100.bam
pybedtools/test/data/gdc.1.100.bam.bai
pybedtools/test/data/gdc.50.200.bam
pybedtools/test/data/gdc.50.200.bam.bai
pybedtools/test/data/gdc.bam
pybedtools/test/data/gdc.bed
pybedtools/test/data/gdc.gff
pybedtools/test/data/gdc.gff.gz
pybedtools/test/data/gdc.othersort.bam
pybedtools/test/data/gdc.sorted.bam
pybedtools/test/data/gdc.sorted.bam.bai
pybedtools/test/data/hg19.gff
pybedtools/test/data/hg38-base.bed
pybedtools/test/data/hg38-problem.bed
pybedtools/test/data/issue_121.bam
pybedtools/test/data/m1.bed
pybedtools/test/data/mm9.bed12
pybedtools/test/data/multibamcov_test.bed
pybedtools/test/data/reads.bam
pybedtools/test/data/rmsk.hg18.chr21.small.bed
pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz
pybedtools/test/data/small.bam
pybedtools/test/data/small.fastq
pybedtools/test/data/snps.bed.gz
pybedtools/test/data/tag_test1.bed
pybedtools/test/data/tag_test2.bed
pybedtools/test/data/test.fa
pybedtools/test/data/test.fa.fai
pybedtools/test/data/test_bedpe.bed
pybedtools/test/data/test_peaks.bed
pybedtools/test/data/test_tsses.bed
pybedtools/test/data/v.vcf
pybedtools/test/data/vcf-stderr-test.bed
pybedtools/test/data/vcf-stderr-test.vcf
pybedtools/test/data/venn.b.bed
pybedtools/test/data/venn.c.bed
pybedtools/test/data/x.bam
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pybedtools/test/data/y.bam
src/bedFile.cpp
src/bedFile.h
src/fileType.cpp
src/fileType.h
src/gzstream.cpp
src/gzstream.h
src/lineFileUtilities.h