CMakeLists.txt
LICENSE
README.md
setup.py
extra/gtime.cpp
extra/vcftime.cpp
include/grgl/common.h
include/grgl/grg.h
include/grgl/grgnode.h
include/grgl/map_mutations.h
include/grgl/mut_iterator.h
include/grgl/mutation.h
include/grgl/serialize.h
include/grgl/ts2grg.h
include/grgl/version.h
include/grgl/visitor.h
pygrgl/__init__.py
pygrgl/cli.py
pygrgl/display.py
pygrgl/grg.py
pygrgl.egg-info/PKG-INFO
pygrgl.egg-info/SOURCES.txt
pygrgl.egg-info/dependency_links.txt
pygrgl.egg-info/entry_points.txt
pygrgl.egg-info/not-zip-safe
pygrgl.egg-info/top_level.txt
pygrgl/clicmd/__init__.py
pygrgl/clicmd/common.py
pygrgl/clicmd/construct.py
pygrgl/clicmd/convert.py
pygrgl/clicmd/process.py
src/build_shape.cpp
src/build_shape.h
src/calculations.cpp
src/calculations.h
src/common_visitors.h
src/gconverter.cpp
src/gindexer.cpp
src/grg.cpp
src/grg_helpers.h
src/grg_merge.cpp
src/grgl.cpp
src/grgp.cpp
src/hap_helpers.h
src/hap_index.cpp
src/hap_index.h
src/lean_bk_tree.h
src/map_mutations.cpp
src/merge.cpp
src/mut_iterator.cpp
src/node_unique_hash.h
src/serialize.cpp
src/ts2grg.cpp
src/tskit_util.h
src/util.h
src/varint.h
src/python/.clang-tidy
src/python/_grgl.cpp
src/similarity/bf_hash.h
test/endtoend/run_tests.py
test/endtoend/__pycache__/run_tests.cpython-310-pytest-7.4.3.pyc
test/endtoend/expect/test-200-samples.freq.txt
test/endtoend/input/test-200-samples.vcf.gz
test/inputs/msprime.example.vcf
test/inputs/msprime.example.vcf.gz
test/unit/common_grgs.h
test/unit/test_bloom_filter.cpp
test/unit/test_common.cpp
test/unit/test_construct.cpp
test/unit/test_grg.cpp
test/unit/test_main.cpp
test/unit/test_mutation.cpp
test/unit/test_serialize.cpp
test/unit/test_util.cpp
test/unit/test_visitor.cpp
test/unit/testing_utilities.h
third-party/CMakeLists.txt
third-party/args/.buckconfig
third-party/args/.git
third-party/args/.gitignore
third-party/args/.gitlab-ci.yml
third-party/args/.gitmodules
third-party/args/.travis.yml
third-party/args/.ycm_extra_conf.py
third-party/args/BUCK
third-party/args/CHANGELOG
third-party/args/CMakeLists.txt
third-party/args/CONTRIBUTING.md
third-party/args/Doxyfile
third-party/args/LICENSE
third-party/args/Makefile
third-party/args/README.md
third-party/args/appveyor.yml
third-party/args/args.hxx
third-party/args/catch.hpp
third-party/args/conanfile.py
third-party/args/meson.build
third-party/args/meson_options.txt
third-party/args/test.cxx
third-party/args/.tipi/deps
third-party/args/.tipi/opts
third-party/args/examples/BUCK
third-party/args/examples/CMakeLists.txt
third-party/args/examples/bash_completion.sh
third-party/args/examples/completion.cxx
third-party/args/examples/gitlike.cxx
third-party/args/examples/.tipi/deps
third-party/args/packaging/pkgconfig.pc.in
third-party/args/test/BUCK
third-party/args/test/multiple_inclusion_1.cxx
third-party/args/test/multiple_inclusion_2.cxx
third-party/args/test/windows_h.cxx
third-party/bgen/.clang-format
third-party/bgen/.git
third-party/bgen/.gitignore
third-party/bgen/.pre-commit-config.yaml
third-party/bgen/CMakeLists.txt
third-party/bgen/LICENSE.md
third-party/bgen/README.md
third-party/bgen/bgen-config.cmake.in
third-party/bgen/bgen-file-format.pdf
third-party/bgen/.github/workflows/deploy.yml
third-party/bgen/.github/workflows/test.yml
third-party/bgen/cmake/CPM.cmake
third-party/bgen/cmake/compiler-options.cmake
third-party/bgen/cmake/sanitizers.cmake
third-party/bgen/doc/.gitignore
third-party/bgen/doc/Doxyfile
third-party/bgen/doc/Makefile
third-party/bgen/doc/conf.py
third-party/bgen/doc/index.rst
third-party/bgen/doc/install.rst
third-party/bgen/doc/interface.rst
third-party/bgen/doc/make.bat
third-party/bgen/doc/requirements.txt
third-party/bgen/include/bgen/bgen.h
third-party/bgen/include/bgen/bstring.h
third-party/bgen/include/bgen/file.h
third-party/bgen/include/bgen/genotype.h
third-party/bgen/include/bgen/metafile.h
third-party/bgen/include/bgen/partition.h
third-party/bgen/include/bgen/samples.h
third-party/bgen/include/bgen/variant.h
third-party/bgen/src/bmath.h
third-party/bgen/src/bstring.c
third-party/bgen/src/bstring.h
third-party/bgen/src/file.c
third-party/bgen/src/file.h
third-party/bgen/src/free.h
third-party/bgen/src/genotype.c
third-party/bgen/src/genotype.h
third-party/bgen/src/io.c
third-party/bgen/src/io.h
third-party/bgen/src/layout1.c
third-party/bgen/src/layout1.h
third-party/bgen/src/layout2.c
third-party/bgen/src/layout2.h
third-party/bgen/src/mem.h
third-party/bgen/src/metafile.c
third-party/bgen/src/metafile.h
third-party/bgen/src/metafile_write.h
third-party/bgen/src/partition.c
third-party/bgen/src/partition.h
third-party/bgen/src/platform.h
third-party/bgen/src/report.c
third-party/bgen/src/report.h
third-party/bgen/src/samples.c
third-party/bgen/src/samples.h
third-party/bgen/src/unzlib.c
third-party/bgen/src/unzlib.h
third-party/bgen/src/unzstd.c
third-party/bgen/src/unzstd.h
third-party/bgen/src/variant.c
third-party/bgen/src/variant.h
third-party/bgen/test/.gitignore
third-party/bgen/test/CMakeLists.txt
third-party/bgen/test/data/complex.23bits.bgen
third-party/bgen/test/data/example.14bits.bgen
third-party/bgen/test/data/example.14bits.bgen.index
third-party/bgen/test/data/example.14bits.bgen.metafile
third-party/bgen/test/data/example.14bits.bgen.metafile.truncated
third-party/bgen/test/data/example.14bits.bgen.truncated
third-party/bgen/test/data/example.1bits.bgen
third-party/bgen/test/data/example.1bits.bgen.index
third-party/bgen/test/data/example.1bits.bgen.metafile
third-party/bgen/test/data/example.32bits.bgen
third-party/bgen/test/data/example.32bits.bgen.index
third-party/bgen/test/data/example.32bits.bgen.metafile
third-party/bgen/test/data/example.matrix
third-party/bgen/test/data/example.v11.bgen
third-party/bgen/test/data/example.v11.bgen.index
third-party/bgen/test/data/haplotypes.bgen
third-party/bgen/test/data/pbgen_example.pgen
third-party/bgen/test/data/random.bgen
third-party/bgen/test/data/random.bgen.metafile
third-party/bgen/test/data/roundtrip1.bgen
third-party/bgen/test/data/wrong.metafile
third-party/bgen/test/data/zero_len_chrom_id.bgen
third-party/bgen/test/src/assert_interface_2.c
third-party/bgen/test/src/assert_interface_3.c
third-party/bgen/test/src/assert_interface_3_complex.c
third-party/bgen/test/src/cass.h
third-party/bgen/test/src/complex.c
third-party/bgen/test/src/create_metafile.c
third-party/bgen/test/src/haplotype.c
third-party/bgen/test/src/index.c
third-party/bgen/test/src/metadata_example.c
third-party/bgen/test/src/one_million.c
third-party/bgen/test/src/open_genotype.c
third-party/bgen/test/src/pbgen_example.c
third-party/bgen/test/src/v12_zlib_layout2.c
third-party/bgen/test/src/variant_position_overflow.c
third-party/bgen/test/src/wrong_bgen_files.c
third-party/bgen/test/src/wrong_metadata_files.c
third-party/bgen/test/src/zero_len_chrom_id.c
third-party/picohash/README.md
third-party/picohash/picohash.h
third-party/picovcf/picovcf.hpp
third-party/pybind11/.appveyor.yml
third-party/pybind11/.clang-format
third-party/pybind11/.clang-tidy
third-party/pybind11/.cmake-format.yaml
third-party/pybind11/.codespell-ignore-lines
third-party/pybind11/.git
third-party/pybind11/.gitattributes
third-party/pybind11/.gitignore
third-party/pybind11/.pre-commit-config.yaml
third-party/pybind11/.readthedocs.yml
third-party/pybind11/CMakeLists.txt
third-party/pybind11/LICENSE
third-party/pybind11/MANIFEST.in
third-party/pybind11/README.rst
third-party/pybind11/SECURITY.md
third-party/pybind11/noxfile.py
third-party/pybind11/pyproject.toml
third-party/pybind11/setup.cfg
third-party/pybind11/setup.py
third-party/pybind11/.github/CODEOWNERS
third-party/pybind11/.github/CONTRIBUTING.md
third-party/pybind11/.github/dependabot.yml
third-party/pybind11/.github/labeler.yml
third-party/pybind11/.github/labeler_merged.yml
third-party/pybind11/.github/pull_request_template.md
third-party/pybind11/.github/ISSUE_TEMPLATE/bug-report.yml
third-party/pybind11/.github/ISSUE_TEMPLATE/config.yml
third-party/pybind11/.github/matchers/pylint.json
third-party/pybind11/.github/workflows/ci.yml
third-party/pybind11/.github/workflows/configure.yml
third-party/pybind11/.github/workflows/format.yml
third-party/pybind11/.github/workflows/labeler.yml
third-party/pybind11/.github/workflows/pip.yml
third-party/pybind11/.github/workflows/upstream.yml
third-party/pybind11/docs/Doxyfile
third-party/pybind11/docs/Makefile
third-party/pybind11/docs/basics.rst
third-party/pybind11/docs/benchmark.py
third-party/pybind11/docs/benchmark.rst
third-party/pybind11/docs/changelog.rst
third-party/pybind11/docs/classes.rst
third-party/pybind11/docs/compiling.rst
third-party/pybind11/docs/conf.py
third-party/pybind11/docs/faq.rst
third-party/pybind11/docs/index.rst
third-party/pybind11/docs/installing.rst
third-party/pybind11/docs/limitations.rst
third-party/pybind11/docs/pybind11-logo.png
third-party/pybind11/docs/pybind11_vs_boost_python1.png
third-party/pybind11/docs/pybind11_vs_boost_python1.svg
third-party/pybind11/docs/pybind11_vs_boost_python2.png
third-party/pybind11/docs/pybind11_vs_boost_python2.svg
third-party/pybind11/docs/reference.rst
third-party/pybind11/docs/release.rst
third-party/pybind11/docs/requirements.in
third-party/pybind11/docs/requirements.txt
third-party/pybind11/docs/upgrade.rst
third-party/pybind11/docs/_static/css/custom.css
third-party/pybind11/docs/advanced/classes.rst
third-party/pybind11/docs/advanced/embedding.rst
third-party/pybind11/docs/advanced/exceptions.rst
third-party/pybind11/docs/advanced/functions.rst
third-party/pybind11/docs/advanced/misc.rst
third-party/pybind11/docs/advanced/smart_ptrs.rst
third-party/pybind11/docs/advanced/cast/chrono.rst
third-party/pybind11/docs/advanced/cast/custom.rst
third-party/pybind11/docs/advanced/cast/eigen.rst
third-party/pybind11/docs/advanced/cast/functional.rst
third-party/pybind11/docs/advanced/cast/index.rst
third-party/pybind11/docs/advanced/cast/overview.rst
third-party/pybind11/docs/advanced/cast/stl.rst
third-party/pybind11/docs/advanced/cast/strings.rst
third-party/pybind11/docs/advanced/pycpp/index.rst
third-party/pybind11/docs/advanced/pycpp/numpy.rst
third-party/pybind11/docs/advanced/pycpp/object.rst
third-party/pybind11/docs/advanced/pycpp/utilities.rst
third-party/pybind11/docs/cmake/index.rst
third-party/pybind11/include/pybind11/attr.h
third-party/pybind11/include/pybind11/buffer_info.h
third-party/pybind11/include/pybind11/cast.h
third-party/pybind11/include/pybind11/chrono.h
third-party/pybind11/include/pybind11/common.h
third-party/pybind11/include/pybind11/complex.h
third-party/pybind11/include/pybind11/eigen.h
third-party/pybind11/include/pybind11/embed.h
third-party/pybind11/include/pybind11/eval.h
third-party/pybind11/include/pybind11/functional.h
third-party/pybind11/include/pybind11/gil.h
third-party/pybind11/include/pybind11/gil_safe_call_once.h
third-party/pybind11/include/pybind11/iostream.h
third-party/pybind11/include/pybind11/numpy.h
third-party/pybind11/include/pybind11/operators.h
third-party/pybind11/include/pybind11/options.h
third-party/pybind11/include/pybind11/pybind11.h
third-party/pybind11/include/pybind11/pytypes.h
third-party/pybind11/include/pybind11/stl.h
third-party/pybind11/include/pybind11/stl_bind.h
third-party/pybind11/include/pybind11/type_caster_pyobject_ptr.h
third-party/pybind11/include/pybind11/typing.h
third-party/pybind11/include/pybind11/detail/class.h
third-party/pybind11/include/pybind11/detail/common.h
third-party/pybind11/include/pybind11/detail/descr.h
third-party/pybind11/include/pybind11/detail/init.h
third-party/pybind11/include/pybind11/detail/internals.h
third-party/pybind11/include/pybind11/detail/type_caster_base.h
third-party/pybind11/include/pybind11/detail/typeid.h
third-party/pybind11/include/pybind11/eigen/common.h
third-party/pybind11/include/pybind11/eigen/matrix.h
third-party/pybind11/include/pybind11/eigen/tensor.h
third-party/pybind11/include/pybind11/stl/filesystem.h
third-party/pybind11/pybind11/__init__.py
third-party/pybind11/pybind11/__main__.py
third-party/pybind11/pybind11/_version.py
third-party/pybind11/pybind11/commands.py
third-party/pybind11/pybind11/py.typed
third-party/pybind11/pybind11/setup_helpers.py
third-party/pybind11/tests/CMakeLists.txt
third-party/pybind11/tests/conftest.py
third-party/pybind11/tests/constructor_stats.h
third-party/pybind11/tests/cross_module_gil_utils.cpp
third-party/pybind11/tests/cross_module_interleaved_error_already_set.cpp
third-party/pybind11/tests/eigen_tensor_avoid_stl_array.cpp
third-party/pybind11/tests/env.py
third-party/pybind11/tests/local_bindings.h
third-party/pybind11/tests/object.h
third-party/pybind11/tests/pybind11_cross_module_tests.cpp
third-party/pybind11/tests/pybind11_tests.cpp
third-party/pybind11/tests/pybind11_tests.h
third-party/pybind11/tests/pytest.ini
third-party/pybind11/tests/requirements.txt
third-party/pybind11/tests/test_async.cpp
third-party/pybind11/tests/test_async.py
third-party/pybind11/tests/test_buffers.cpp
third-party/pybind11/tests/test_buffers.py
third-party/pybind11/tests/test_builtin_casters.cpp
third-party/pybind11/tests/test_builtin_casters.py
third-party/pybind11/tests/test_call_policies.cpp
third-party/pybind11/tests/test_call_policies.py
third-party/pybind11/tests/test_callbacks.cpp
third-party/pybind11/tests/test_callbacks.py
third-party/pybind11/tests/test_chrono.cpp
third-party/pybind11/tests/test_chrono.py
third-party/pybind11/tests/test_class.cpp
third-party/pybind11/tests/test_class.py
third-party/pybind11/tests/test_const_name.cpp
third-party/pybind11/tests/test_const_name.py
third-party/pybind11/tests/test_constants_and_functions.cpp
third-party/pybind11/tests/test_constants_and_functions.py
third-party/pybind11/tests/test_copy_move.cpp
third-party/pybind11/tests/test_copy_move.py
third-party/pybind11/tests/test_custom_type_casters.cpp
third-party/pybind11/tests/test_custom_type_casters.py
third-party/pybind11/tests/test_custom_type_setup.cpp
third-party/pybind11/tests/test_custom_type_setup.py
third-party/pybind11/tests/test_docstring_options.cpp
third-party/pybind11/tests/test_docstring_options.py
third-party/pybind11/tests/test_eigen_matrix.cpp
third-party/pybind11/tests/test_eigen_matrix.py
third-party/pybind11/tests/test_eigen_tensor.cpp
third-party/pybind11/tests/test_eigen_tensor.inl
third-party/pybind11/tests/test_eigen_tensor.py
third-party/pybind11/tests/test_enum.cpp
third-party/pybind11/tests/test_enum.py
third-party/pybind11/tests/test_eval.cpp
third-party/pybind11/tests/test_eval.py
third-party/pybind11/tests/test_eval_call.py
third-party/pybind11/tests/test_exceptions.cpp
third-party/pybind11/tests/test_exceptions.h
third-party/pybind11/tests/test_exceptions.py
third-party/pybind11/tests/test_factory_constructors.cpp
third-party/pybind11/tests/test_factory_constructors.py
third-party/pybind11/tests/test_gil_scoped.cpp
third-party/pybind11/tests/test_gil_scoped.py
third-party/pybind11/tests/test_iostream.cpp
third-party/pybind11/tests/test_iostream.py
third-party/pybind11/tests/test_kwargs_and_defaults.cpp
third-party/pybind11/tests/test_kwargs_and_defaults.py
third-party/pybind11/tests/test_local_bindings.cpp
third-party/pybind11/tests/test_local_bindings.py
third-party/pybind11/tests/test_methods_and_attributes.cpp
third-party/pybind11/tests/test_methods_and_attributes.py
third-party/pybind11/tests/test_modules.cpp
third-party/pybind11/tests/test_modules.py
third-party/pybind11/tests/test_multiple_inheritance.cpp
third-party/pybind11/tests/test_multiple_inheritance.py
third-party/pybind11/tests/test_numpy_array.cpp
third-party/pybind11/tests/test_numpy_array.py
third-party/pybind11/tests/test_numpy_dtypes.cpp
third-party/pybind11/tests/test_numpy_dtypes.py
third-party/pybind11/tests/test_numpy_vectorize.cpp
third-party/pybind11/tests/test_numpy_vectorize.py
third-party/pybind11/tests/test_opaque_types.cpp
third-party/pybind11/tests/test_opaque_types.py
third-party/pybind11/tests/test_operator_overloading.cpp
third-party/pybind11/tests/test_operator_overloading.py
third-party/pybind11/tests/test_pickling.cpp
third-party/pybind11/tests/test_pickling.py
third-party/pybind11/tests/test_python_multiple_inheritance.cpp
third-party/pybind11/tests/test_python_multiple_inheritance.py
third-party/pybind11/tests/test_pytypes.cpp
third-party/pybind11/tests/test_pytypes.py
third-party/pybind11/tests/test_sequences_and_iterators.cpp
third-party/pybind11/tests/test_sequences_and_iterators.py
third-party/pybind11/tests/test_smart_ptr.cpp
third-party/pybind11/tests/test_smart_ptr.py
third-party/pybind11/tests/test_stl.cpp
third-party/pybind11/tests/test_stl.py
third-party/pybind11/tests/test_stl_binders.cpp
third-party/pybind11/tests/test_stl_binders.py
third-party/pybind11/tests/test_tagbased_polymorphic.cpp
third-party/pybind11/tests/test_tagbased_polymorphic.py
third-party/pybind11/tests/test_thread.cpp
third-party/pybind11/tests/test_thread.py
third-party/pybind11/tests/test_type_caster_pyobject_ptr.cpp
third-party/pybind11/tests/test_type_caster_pyobject_ptr.py
third-party/pybind11/tests/test_union.cpp
third-party/pybind11/tests/test_union.py
third-party/pybind11/tests/test_unnamed_namespace_a.cpp
third-party/pybind11/tests/test_unnamed_namespace_a.py
third-party/pybind11/tests/test_unnamed_namespace_b.cpp
third-party/pybind11/tests/test_unnamed_namespace_b.py
third-party/pybind11/tests/test_vector_unique_ptr_member.cpp
third-party/pybind11/tests/test_vector_unique_ptr_member.py
third-party/pybind11/tests/test_virtual_functions.cpp
third-party/pybind11/tests/test_virtual_functions.py
third-party/pybind11/tests/valgrind-numpy-scipy.supp
third-party/pybind11/tests/valgrind-python.supp
third-party/pybind11/tests/extra_python_package/pytest.ini
third-party/pybind11/tests/extra_python_package/test_files.py
third-party/pybind11/tests/extra_setuptools/pytest.ini
third-party/pybind11/tests/extra_setuptools/test_setuphelper.py
third-party/pybind11/tests/test_cmake_build/CMakeLists.txt
third-party/pybind11/tests/test_cmake_build/embed.cpp
third-party/pybind11/tests/test_cmake_build/main.cpp
third-party/pybind11/tests/test_cmake_build/test.py
third-party/pybind11/tests/test_cmake_build/installed_embed/CMakeLists.txt
third-party/pybind11/tests/test_cmake_build/installed_function/CMakeLists.txt
third-party/pybind11/tests/test_cmake_build/installed_target/CMakeLists.txt
third-party/pybind11/tests/test_cmake_build/subdirectory_embed/CMakeLists.txt
third-party/pybind11/tests/test_cmake_build/subdirectory_function/CMakeLists.txt
third-party/pybind11/tests/test_cmake_build/subdirectory_target/CMakeLists.txt
third-party/pybind11/tests/test_embed/CMakeLists.txt
third-party/pybind11/tests/test_embed/catch.cpp
third-party/pybind11/tests/test_embed/external_module.cpp
third-party/pybind11/tests/test_embed/test_interpreter.cpp
third-party/pybind11/tests/test_embed/test_interpreter.py
third-party/pybind11/tests/test_embed/test_trampoline.py
third-party/pybind11/tools/FindCatch.cmake
third-party/pybind11/tools/FindEigen3.cmake
third-party/pybind11/tools/FindPythonLibsNew.cmake
third-party/pybind11/tools/JoinPaths.cmake
third-party/pybind11/tools/check-style.sh
third-party/pybind11/tools/cmake_uninstall.cmake.in
third-party/pybind11/tools/codespell_ignore_lines_from_errors.py
third-party/pybind11/tools/libsize.py
third-party/pybind11/tools/make_changelog.py
third-party/pybind11/tools/pybind11.pc.in
third-party/pybind11/tools/pybind11Common.cmake
third-party/pybind11/tools/pybind11Config.cmake.in
third-party/pybind11/tools/pybind11GuessPythonExtSuffix.cmake
third-party/pybind11/tools/pybind11NewTools.cmake
third-party/pybind11/tools/pybind11Tools.cmake
third-party/pybind11/tools/pyproject.toml
third-party/pybind11/tools/setup_global.py.in
third-party/pybind11/tools/setup_main.py.in
third-party/pybind11/tools/test-pybind11GuessPythonExtSuffix.cmake
third-party/tskit/.clang-format
third-party/tskit/.codecov.yml
third-party/tskit/.git
third-party/tskit/.gitignore
third-party/tskit/.mergify.yml
third-party/tskit/.pre-commit-config.yaml
third-party/tskit/.pyup.yml
third-party/tskit/CONTRIBUTING.md
third-party/tskit/LICENSE
third-party/tskit/README.md
third-party/tskit/ROADMAP.md
third-party/tskit/.circleci/config.yml
third-party/tskit/.circleci/images/32bit/Dockerfile
third-party/tskit/.github/PULL_REQUEST_TEMPLATE.md
third-party/tskit/.github/workflows/docs.yml
third-party/tskit/.github/workflows/release.yml
third-party/tskit/.github/workflows/tests.yml
third-party/tskit/.github/workflows/wheels.yml
third-party/tskit/.github/workflows/docker/buildwheel.sh
third-party/tskit/.github/workflows/docker/shared.env
third-party/tskit/c/.gitignore
third-party/tskit/c/CHANGELOG.rst
third-party/tskit/c/VERSION.txt
third-party/tskit/c/meson.build
third-party/tskit/c/meson_options.txt
third-party/tskit/c/tskit.h
third-party/tskit/c/examples/Makefile
third-party/tskit/c/examples/api_structure.c
third-party/tskit/c/examples/cpp_sorting_example.cpp
third-party/tskit/c/examples/error_handling.c
third-party/tskit/c/examples/haploid_wright_fisher.c
third-party/tskit/c/examples/streaming.c
third-party/tskit/c/examples/take_ownership.c
third-party/tskit/c/examples/tree_iteration.c
third-party/tskit/c/examples/tree_traversal.c
third-party/tskit/c/subprojects/kastore/README.md
third-party/tskit/c/subprojects/kastore/VERSION.txt
third-party/tskit/c/subprojects/kastore/kastore.c
third-party/tskit/c/subprojects/kastore/kastore.h
third-party/tskit/c/subprojects/kastore/meson.build
third-party/tskit/c/tests/test_convert.c
third-party/tskit/c/tests/test_core.c
third-party/tskit/c/tests/test_file_format.c
third-party/tskit/c/tests/test_genotypes.c
third-party/tskit/c/tests/test_haplotype_matching.c
third-party/tskit/c/tests/test_minimal_cpp.cpp
third-party/tskit/c/tests/test_stats.c
third-party/tskit/c/tests/test_tables.c
third-party/tskit/c/tests/test_trees.c
third-party/tskit/c/tests/testlib.c
third-party/tskit/c/tests/testlib.h
third-party/tskit/c/tests/meson-subproject/example.c
third-party/tskit/c/tests/meson-subproject/meson.build
third-party/tskit/c/tskit/convert.c
third-party/tskit/c/tskit/convert.h
third-party/tskit/c/tskit/core.c
third-party/tskit/c/tskit/core.h
third-party/tskit/c/tskit/genotypes.c
third-party/tskit/c/tskit/genotypes.h
third-party/tskit/c/tskit/haplotype_matching.c
third-party/tskit/c/tskit/haplotype_matching.h
third-party/tskit/c/tskit/stats.c
third-party/tskit/c/tskit/stats.h
third-party/tskit/c/tskit/tables.c
third-party/tskit/c/tskit/tables.h
third-party/tskit/c/tskit/trees.c
third-party/tskit/c/tskit/trees.h
third-party/tskit/docs/.gitignore
third-party/tskit/docs/Makefile
third-party/tskit/docs/_config.yml
third-party/tskit/docs/_toc.yml
third-party/tskit/docs/build.sh
third-party/tskit/docs/c-api.rst
third-party/tskit/docs/changelogs.rst
third-party/tskit/docs/cli.md
third-party/tskit/docs/convert_changelog.py
third-party/tskit/docs/data-model.md
third-party/tskit/docs/development.md
third-party/tskit/docs/export.md
third-party/tskit/docs/file-formats.md
third-party/tskit/docs/glossary.md
third-party/tskit/docs/ibd.md
third-party/tskit/docs/installation.md
third-party/tskit/docs/introduction.md
third-party/tskit/docs/logo.svg
third-party/tskit/docs/metadata.md
third-party/tskit/docs/provenance.md
third-party/tskit/docs/python-api.md
third-party/tskit/docs/quickstart.md
third-party/tskit/docs/stats.md
third-party/tskit/docs/topological-analysis.md
third-party/tskit/docs/_static/README
third-party/tskit/docs/_static/bespoke.css
third-party/tskit/docs/_static/four_leaf_tree_shapes.png
third-party/tskit/docs/_static/tskit_logo_pale.svg
third-party/tskit/docs/data/basic_tree_seq.trees
third-party/tskit/docs/doxygen/Doxyfile
third-party/tskit/docs/substitutions/linear_traversal_warning.rst
third-party/tskit/docs/substitutions/table_edit_warning.rst
third-party/tskit/docs/substitutions/table_keep_rows_main.rst
third-party/tskit/docs/substitutions/tree_array_warning.rst
third-party/tskit/docs/substitutions/virtual_root_array_note.rst
third-party/tskit/python/.flake8
third-party/tskit/python/.gitignore
third-party/tskit/python/CHANGELOG.rst
third-party/tskit/python/LICENSE
third-party/tskit/python/MANIFEST.in
third-party/tskit/python/Makefile
third-party/tskit/python/README.rst
third-party/tskit/python/_tskitmodule.c
third-party/tskit/python/pyproject.toml
third-party/tskit/python/setup.py
third-party/tskit/python/stress_lowlevel.py
third-party/tskit/python/benchmark/config.yaml
third-party/tskit/python/benchmark/run-for-all-releases.py
third-party/tskit/python/benchmark/run.py
third-party/tskit/python/lwt_interface/CHANGELOG.rst
third-party/tskit/python/lwt_interface/Makefile
third-party/tskit/python/lwt_interface/README.md
third-party/tskit/python/lwt_interface/dict_encoding_testlib.py
third-party/tskit/python/lwt_interface/example_c_module.c
third-party/tskit/python/lwt_interface/setup.py
third-party/tskit/python/lwt_interface/test_example_c_module.py
third-party/tskit/python/lwt_interface/tskit_lwt_interface.h
third-party/tskit/python/requirements/benchmark.txt
third-party/tskit/python/requirements/development.txt
third-party/tskit/python/requirements/development.yml
third-party/tskit/python/requirements/CI-complete/requirements.txt
third-party/tskit/python/requirements/CI-docs/requirements.txt
third-party/tskit/python/requirements/CI-tests-conda/requirements.txt
third-party/tskit/python/requirements/CI-tests-pip/requirements.txt
third-party/tskit/python/tests/__init__.py
third-party/tskit/python/tests/conftest.py
third-party/tskit/python/tests/ibd.py
third-party/tskit/python/tests/simplify.py
third-party/tskit/python/tests/test_avl_tree.py
third-party/tskit/python/tests/test_balance_metrics.py
third-party/tskit/python/tests/test_cli.py
third-party/tskit/python/tests/test_coalrate.py
third-party/tskit/python/tests/test_combinatorics.py
third-party/tskit/python/tests/test_dict_encoding.py
third-party/tskit/python/tests/test_divmat.py
third-party/tskit/python/tests/test_drawing.py
third-party/tskit/python/tests/test_extend_edges.py
third-party/tskit/python/tests/test_file_format.py
third-party/tskit/python/tests/test_fileobj.py
third-party/tskit/python/tests/test_genotype_matching.py
third-party/tskit/python/tests/test_genotypes.py
third-party/tskit/python/tests/test_haplotype_matching.py
third-party/tskit/python/tests/test_highlevel.py
third-party/tskit/python/tests/test_ibd.py
third-party/tskit/python/tests/test_intervals.py
third-party/tskit/python/tests/test_ld_matrix.py
third-party/tskit/python/tests/test_lowlevel.py
third-party/tskit/python/tests/test_metadata.py
third-party/tskit/python/tests/test_ms.py
third-party/tskit/python/tests/test_parsimony.py
third-party/tskit/python/tests/test_phylo_formats.py
third-party/tskit/python/tests/test_provenance.py
third-party/tskit/python/tests/test_reference_sequence.py
third-party/tskit/python/tests/test_stats.py
third-party/tskit/python/tests/test_table_transforms.py
third-party/tskit/python/tests/test_tables.py
third-party/tskit/python/tests/test_text_formats.py
third-party/tskit/python/tests/test_threads.py
third-party/tskit/python/tests/test_topology.py
third-party/tskit/python/tests/test_tree_positioning.py
third-party/tskit/python/tests/test_tree_stats.py
third-party/tskit/python/tests/test_util.py
third-party/tskit/python/tests/test_utilities.py
third-party/tskit/python/tests/test_vcf.py
third-party/tskit/python/tests/test_version.py
third-party/tskit/python/tests/test_wright_fisher.py
third-party/tskit/python/tests/tsutil.py
third-party/tskit/python/tests/data/SLiM/README
third-party/tskit/python/tests/data/SLiM/minimal-example.trees
third-party/tskit/python/tests/data/SLiM/minimal-example.txt
third-party/tskit/python/tests/data/SLiM/single-locus-example.trees
third-party/tskit/python/tests/data/SLiM/single-locus-example.txt
third-party/tskit/python/tests/data/dict-encodings/generate_msprime.py
third-party/tskit/python/tests/data/dict-encodings/msprime-0.7.4.pkl
third-party/tskit/python/tests/data/hdf5-formats/msprime-0.3.0_v2.0.hdf5
third-party/tskit/python/tests/data/hdf5-formats/msprime-0.4.0_v3.1.hdf5
third-party/tskit/python/tests/data/hdf5-formats/msprime-0.5.0_v10.0.hdf5
third-party/tskit/python/tests/data/old-formats/tskit-0.3.3.trees
third-party/tskit/python/tests/data/simplify-bugs/01-edges.txt
third-party/tskit/python/tests/data/simplify-bugs/01-mutations.txt
third-party/tskit/python/tests/data/simplify-bugs/01-nodes.txt
third-party/tskit/python/tests/data/simplify-bugs/01-sites.txt
third-party/tskit/python/tests/data/simplify-bugs/02-edges.txt
third-party/tskit/python/tests/data/simplify-bugs/02-mutations.txt
third-party/tskit/python/tests/data/simplify-bugs/02-nodes.txt
third-party/tskit/python/tests/data/simplify-bugs/02-sites.txt
third-party/tskit/python/tests/data/simplify-bugs/03-edges.txt
third-party/tskit/python/tests/data/simplify-bugs/03-mutations.txt
third-party/tskit/python/tests/data/simplify-bugs/03-nodes.txt
third-party/tskit/python/tests/data/simplify-bugs/03-sites.txt
third-party/tskit/python/tests/data/simplify-bugs/04-edges.txt
third-party/tskit/python/tests/data/simplify-bugs/04-mutations.txt
third-party/tskit/python/tests/data/simplify-bugs/04-nodes.txt
third-party/tskit/python/tests/data/simplify-bugs/04-sites.txt
third-party/tskit/python/tests/data/simplify-bugs/05-edges.txt
third-party/tskit/python/tests/data/simplify-bugs/05-mutations.txt
third-party/tskit/python/tests/data/simplify-bugs/05-nodes.txt
third-party/tskit/python/tests/data/simplify-bugs/05-sites.txt
third-party/tskit/python/tests/data/svg/internal_sample_ts.svg
third-party/tskit/python/tests/data/svg/tree.svg
third-party/tskit/python/tests/data/svg/tree_both_axes.svg
third-party/tskit/python/tests/data/svg/tree_muts.svg
third-party/tskit/python/tests/data/svg/tree_muts_all_edge.svg
third-party/tskit/python/tests/data/svg/tree_timed_muts.svg
third-party/tskit/python/tests/data/svg/tree_x_axis.svg
third-party/tskit/python/tests/data/svg/tree_y_axis_rank.svg
third-party/tskit/python/tests/data/svg/ts.svg
third-party/tskit/python/tests/data/svg/ts_max_trees.svg
third-party/tskit/python/tests/data/svg/ts_max_trees_treewise.svg
third-party/tskit/python/tests/data/svg/ts_multiroot.svg
third-party/tskit/python/tests/data/svg/ts_mut_highlight.svg
third-party/tskit/python/tests/data/svg/ts_mut_times.svg
third-party/tskit/python/tests/data/svg/ts_mut_times_logscale.svg
third-party/tskit/python/tests/data/svg/ts_mutations_no_edges.svg
third-party/tskit/python/tests/data/svg/ts_mutations_timed_no_edges.svg
third-party/tskit/python/tests/data/svg/ts_no_axes.svg
third-party/tskit/python/tests/data/svg/ts_nonbinary.svg
third-party/tskit/python/tests/data/svg/ts_plain.svg
third-party/tskit/python/tests/data/svg/ts_plain_no_xlab.svg
third-party/tskit/python/tests/data/svg/ts_plain_y.svg
third-party/tskit/python/tests/data/svg/ts_rank.svg
third-party/tskit/python/tests/data/svg/ts_x_lim.svg
third-party/tskit/python/tests/data/svg/ts_xlabel.svg
third-party/tskit/python/tests/data/svg/ts_y_axis.svg
third-party/tskit/python/tests/data/svg/ts_y_axis_log.svg
third-party/tskit/python/tests/data/svg/ts_y_axis_regular.svg
third-party/tskit/python/tskit/__init__.py
third-party/tskit/python/tskit/__main__.py
third-party/tskit/python/tskit/_version.py
third-party/tskit/python/tskit/cli.py
third-party/tskit/python/tskit/combinatorics.py
third-party/tskit/python/tskit/drawing.py
third-party/tskit/python/tskit/exceptions.py
third-party/tskit/python/tskit/formats.py
third-party/tskit/python/tskit/genotypes.py
third-party/tskit/python/tskit/intervals.py
third-party/tskit/python/tskit/metadata.py
third-party/tskit/python/tskit/metadata_schema.schema.json
third-party/tskit/python/tskit/provenance.py
third-party/tskit/python/tskit/provenance.schema.json
third-party/tskit/python/tskit/stats.py
third-party/tskit/python/tskit/tables.py
third-party/tskit/python/tskit/text_formats.py
third-party/tskit/python/tskit/trees.py
third-party/tskit/python/tskit/util.py
third-party/tskit/python/tskit/vcf.py