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.gitmodules
.mergify.yml
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CHANGELOG.rst
LICENSE
MANIFEST.in
Makefile
README.md
README.rst
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convert_hdf5.py
dev.py
evaluation.py
pytest.ini
setup.py
visualisation.py
.circleci/config.yml
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.github/workflows/wheels.yml
.github/workflows/docker/buildwheel.sh
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docs/Makefile
docs/api.rst
docs/cli.rst
docs/conf.py
docs/development.rst
docs/file_formats.rst
docs/index.rst
docs/inference.rst
docs/installation.rst
docs/introduction.rst
docs/simulation-example.py
docs/toy-example.py
docs/tutorial.rst
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docs/_static/P_dom_chr24_phased.vcf.gz
docs/_static/P_dom_chr24_phased.vcf.gz.tbi
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docs/_templates/.README
lib/.clang-format
lib/ancestor_builder.c
lib/ancestor_matcher.c
lib/avl.c
lib/avl.h
lib/err.c
lib/err.h
lib/meson.build
lib/object_heap.c
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lib/tree_sequence_builder.c
lib/tsinfer.h
lib/subprojects/kastore/kastore.c
lib/subprojects/kastore/kastore.h
lib/subprojects/tskit/tskit.h
lib/subprojects/tskit/tskit/convert.h
lib/subprojects/tskit/tskit/core.c
lib/subprojects/tskit/tskit/core.h
lib/subprojects/tskit/tskit/genotypes.h
lib/subprojects/tskit/tskit/haplotype_matching.h
lib/subprojects/tskit/tskit/stats.h
lib/subprojects/tskit/tskit/tables.h
lib/subprojects/tskit/tskit/trees.h
lib/tests/tests.c
requirements/development.txt
requirements/readthedocs.txt
requirements/CI-tests-complete/requirements.txt
requirements/CI-tests-conda/requirements.txt
requirements/CI-tests-pip/requirements.txt
tests/conftest.py
tests/test_cli.py
tests/test_evaluation.py
tests/test_formats.py
tests/test_inference.py
tests/test_low_level.py
tests/test_provenance.py
tests/tsutil.py
tests/data/bugs/invalid_pc_ancestor_time.samples
tsinfer/__init__.py
tsinfer/__main__.py
tsinfer/_version.py
tsinfer/algorithm.py
tsinfer/cli.py
tsinfer/constants.py
tsinfer/eval_util.py
tsinfer/exceptions.py
tsinfer/formats.py
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tsinfer/progress.py
tsinfer/provenance.py
tsinfer/threads.py
tsinfer.egg-info/PKG-INFO
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tsinfer.egg-info/dependency_links.txt
tsinfer.egg-info/entry_points.txt
tsinfer.egg-info/requires.txt
tsinfer.egg-info/top_level.txt