.coveragerc
.gitignore
.readthedocs.yml
AUTHORS.rst
CHANGELOG.rst
CONTRIBUTING.rst
LICENSE.txt
README.md
README.rst
pyproject.toml
setup.cfg
setup.py
tox.ini
docs/Makefile
docs/authors.rst
docs/changelog.rst
docs/conf.py
docs/contributing.rst
docs/index.rst
docs/license.rst
docs/readme.rst
docs/requirements.txt
docs/_static/.gitignore
rscripts/diff_expr_DESeq2.R
rscripts/diff_expr_edgeR.R
rscripts/diff_expr_plot.R
rscripts/peak_anno.R
rscripts/plot_FRiPs.R
rscripts/plot_bar.R
rscripts/plot_corr.R
rscripts/plot_deeptools_fragmentsize.R
rscripts/plot_hist.R
rscripts/plot_peak_width.R
rscripts/plot_rep_cor.R
rscripts/plot_summary.R
rscripts/plot_venn.R
scripts/fasta_len.sh
scripts/fasta_u2t.sh
scripts/fastq_len.sh
scripts/get_chrom_length.sh
scripts/gtfparser.sh
scripts/merge_subseq.sh
scripts/remove_duplicates.sh
src/bx/binBits.c
src/bx/binBits.h
src/bx/bits.c
src/bx/bits.h
src/bx/bitset.pyx
src/bx/cluster.c
src/bx/cluster.h
src/bx/cluster.pyx
src/bx/common.c
src/bx/common.h
src/bx/intersection.pyx
src/pybiotk/__init__.py
src/pybiotk.egg-info/PKG-INFO
src/pybiotk.egg-info/SOURCES.txt
src/pybiotk.egg-info/dependency_links.txt
src/pybiotk.egg-info/entry_points.txt
src/pybiotk.egg-info/not-zip-safe
src/pybiotk.egg-info/requires.txt
src/pybiotk.egg-info/top_level.txt
src/pybiotk/annodb/__init__.py
src/pybiotk/annodb/anno.py
src/pybiotk/annodb/gene.py
src/pybiotk/annodb/merged_transcript.py
src/pybiotk/annodb/transcript.py
src/pybiotk/convert/__init__.py
src/pybiotk/convert/bam2fastx.py
src/pybiotk/convert/bampe_order_by_name.py
src/pybiotk/convert/bed2bedgraph.py
src/pybiotk/convert/fq2fasta.py
src/pybiotk/convert/gtf2bed.py
src/pybiotk/data/__init__.py
src/pybiotk/data/hg38.chrom.sizes
src/pybiotk/data/mm10.chrom.sizes
src/pybiotk/intervals/__init__.py
src/pybiotk/intervals/grange.py
src/pybiotk/intervals/merge_bed3.py
src/pybiotk/intervals/merge_intervals.py
src/pybiotk/io/__init__.py
src/pybiotk/io/bam.py
src/pybiotk/io/bed.py
src/pybiotk/io/bw.py
src/pybiotk/io/fasta.py
src/pybiotk/io/fastq.py
src/pybiotk/io/gtf.py
src/pybiotk/utils/__init__.py
src/pybiotk/utils/bam_random.py
src/pybiotk/utils/fasta_filter.py
src/pybiotk/utils/fastq_join.py
src/pybiotk/utils/fastq_uniq.py
src/pybiotk/utils/fragment_size.py
src/pybiotk/utils/gtf_filter.py
src/pybiotk/utils/merge_row.py
src/pybiotk/utils/merge_subseq.py
src/pybiotk/utils/normalize.py
src/pybiotk/utils/pyanno.py
src/pybiotk/utils/read_tables.py
src/pybiotk/utils/reference_count.py
src/pybiotk/utils/reverse_fastx.py
src/pybiotk/utils/rmats_filter.py
src/pybiotk/utils/seq_random.py
src/pybiotk/utils/subseq_analysis.py
src/pybiotk/utils/summary_log.py
src/pybiotk/utils/utils.py
src/stream/__init__.py
src/stream/pipe.py
src/stream/stream.py
tests/__init__.py
tests/conftest.py
tests/test_stream/test_pipe.py