CHANGES.md
LICENSE
MANIFEST.in
README.md
requirements.txt
requirements_doc.txt
setup.py
doc/.cli_tools.rst.un~
doc/.conf.py.un~
doc/.formats.rst.un~
doc/.index.rst.un~
doc/.installation.rst.un~
doc/.overview.rst.un~
doc/.parsing.rst.un~
doc/.quickstart.rst.un~
doc/.sorting.rst.un~
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/terminology.png
pairtools/__init__.py
pairtools/__main__.py
pairtools/_dedup.c
pairtools/_dedup.pyx
pairtools/_fileio.py
pairtools/_headerops.py
pairtools/_pairsam_format.py
pairtools/pairtools_dedup.py
pairtools/pairtools_filterbycov.py
pairtools/pairtools_flip.py
pairtools/pairtools_markasdup.py
pairtools/pairtools_merge.py
pairtools/pairtools_parse.py
pairtools/pairtools_phase.py
pairtools/pairtools_restrict.py
pairtools/pairtools_select.py
pairtools/pairtools_sort.py
pairtools/pairtools_split.py
pairtools/pairtools_stats.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
tests/test_dedup.py
tests/test_filterbycov.py
tests/test_flip.py
tests/test_headerops.py
tests/test_markasdup.py
tests/test_merge.py
tests/test_parse.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.chrom.sizes
tests/data/mock.pairsam
tests/data/mock.sam