CHANGES.md
LICENSE
MANIFEST.in
README.md
requirements.txt
requirements_doc.txt
setup.py
/home/runner/work/pairtools/pairtools/pairtools/lib/dedup_cython.c
/home/runner/work/pairtools/pairtools/pairtools/lib/parse_pysam.c
/home/runner/work/pairtools/pairtools/pairtools/lib/regions.cpp
doc/Makefile
doc/cli_tools.rst
doc/conf.py
doc/formats.rst
doc/index.rst
doc/installation.rst
doc/parsing.rst
doc/quickstart.rst
doc/sorting.rst
doc/technotes.rst
doc/_static/hic-processing-pipeline.png
doc/_static/hic-processing-pipeline.svg
doc/_static/read-vs-alignment-vs-pairs.svg
doc/_static/read_pair_MU.png
doc/_static/read_pair_MU_MM_NM.png
doc/_static/read_pair_NU.png
doc/_static/read_pair_NU_NN.png
doc/_static/read_pair_UR.png
doc/_static/read_pair_UR_MorN.png
doc/_static/read_pair_UR_criteria.png
doc/_static/read_pair_WW.png
doc/_static/read_pair_gaps_vs_null_alignment.png
doc/_static/report-orientation.svg
doc/_static/report-positions.svg
doc/_static/rescue_modes.svg
doc/_static/rescue_modes_readthrough.svg
doc/_static/terminology.png
doc/examples/example_pipeline.sh
doc/examples/example_singlecell_pipeline.sh
doc/examples/pairtools_phase_walkthrough.ipynb
doc/examples/pairtools_restrict_walkthrough.ipynb
doc/examples/pairtools_walkthrough.ipynb
doc/examples/scalings_example.ipynb
doc/examples/benchmark/Snakefile
doc/examples/benchmark/benchmark.ipynb
doc/examples/benchmark/benchmarking_1mln.csv
pairtools/__init__.py
pairtools/__main__.py
pairtools/_logging.py
pairtools.egg-info/PKG-INFO
pairtools.egg-info/SOURCES.txt
pairtools.egg-info/dependency_links.txt
pairtools.egg-info/entry_points.txt
pairtools.egg-info/not-zip-safe
pairtools.egg-info/requires.txt
pairtools.egg-info/top_level.txt
pairtools/cli/__init__.py
pairtools/cli/dedup.py
pairtools/cli/filterbycov.py
pairtools/cli/flip.py
pairtools/cli/header.py
pairtools/cli/markasdup.py
pairtools/cli/merge.py
pairtools/cli/parse.py
pairtools/cli/parse2.py
pairtools/cli/phase.py
pairtools/cli/restrict.py
pairtools/cli/sample.py
pairtools/cli/scaling.py
pairtools/cli/select.py
pairtools/cli/sort.py
pairtools/cli/split.py
pairtools/cli/stats.py
pairtools/lib/__init__.py
pairtools/lib/dedup.py
pairtools/lib/dedup_cython.pyx
pairtools/lib/fileio.py
pairtools/lib/filterbycov.py
pairtools/lib/headerops.py
pairtools/lib/pairsam_format.py
pairtools/lib/parse.py
pairtools/lib/parse_pysam.pyx
pairtools/lib/phase.py
pairtools/lib/regions.pyx
pairtools/lib/restrict.py
pairtools/lib/scaling.py
pairtools/lib/select.py
pairtools/lib/stats.py
tests/test_dedup.py
tests/test_filterbycov.py
tests/test_flip.py
tests/test_header.py
tests/test_headerops.py
tests/test_markasdup.py
tests/test_merge.py
tests/test_parse.py
tests/test_parse2.py
tests/test_restrict.py
tests/test_scaling.py
tests/test_select.py
tests/test_sort.py
tests/test_split.py
tests/test_stats.py
tests/data/mock.2.pairsam
tests/data/mock.4dedup.pairsam
tests/data/mock.4filterbycov.pairs
tests/data/mock.4flip.pairs
tests/data/mock.4stats.pairs
tests/data/mock.chrom.sizes
tests/data/mock.pairsam
tests/data/mock.parse-all.sam
tests/data/mock.parse2.sam
tests/data/mock.rsites.bed
tests/data/mock.sam
tests/data/mock.test-restr.pairs