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Merge pull request #105 from jeromekelleher/C-api-docs-final
C api docs final
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‎LICENSE

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MIT License
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Copyright (c) 2018 tskit-dev
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Copyright (c) 2018-2019 Tskit Developers
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal

‎c/CHANGELOG.rst

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---------------------
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[0.99.1] - 2019-XX-XX
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[0.99.1] - 2019-01-24
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---------------------
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Refinements to the C API as we move towards 1.0.0. Changes:
@@ -19,6 +19,7 @@ Refinements to the C API as we move towards 1.0.0. Changes:
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currently be marked as samples. (https://github.com/tskit-dev/tskit/issues/72)
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- Allow ``tsk_table_collection_simplify`` to take a NULL samples argument to
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specify "all samples in the current tables".
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- Add support for building as a meson subproject.
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---------------------
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[0.99.0] - 2019-01-14

‎c/examples/haploid_wright_fisher.c

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if (t % simplify_interval == 0) {
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printf("Simplify at generation %d: (%d nodes %d edges)", t,
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tables->nodes.num_rows, tables->edges.num_rows);
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ret = tsk_table_collection_sort(tables, 0, 0); /* FIXME; should take position. */
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/* Note: Edges must be sorted for simplify to work, and we use a brute force
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* approach of sorting each time here for simplicity. This is inefficient. */
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ret = tsk_table_collection_sort(tables, NULL, 0);
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check_tsk_error(ret);
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ret = tsk_table_collection_simplify(tables, children, N, 0, NULL);
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check_tsk_error(ret);

‎c/tests/meson-subproject/example.c

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/*
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* MIT License
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*
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* Copyright (c) 2019 Tskit Developers
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal
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* in the Software without restriction, including without limitation the rights
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the Software is
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* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in all
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* copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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* SOFTWARE.
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*/
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/* Simple example testing that we compile and link in tskit and kastore
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* when we use meson submodules.
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*/

‎c/tests/test_convert.c

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/*
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* MIT License
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*
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* Copyright (c) 2019 Tskit Developers
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal
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* in the Software without restriction, including without limitation the rights
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the Software is
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* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in all
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* copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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* SOFTWARE.
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*/
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#include "testlib.h"
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#include <tskit/convert.h>
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‎c/tests/test_core.c

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/*
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* MIT License
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*
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* Copyright (c) 2019 Tskit Developers
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal
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* in the Software without restriction, including without limitation the rights
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the Software is
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* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in all
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* copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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* SOFTWARE.
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*/
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#include "testlib.h"
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#include <tskit/core.h>
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‎c/tests/test_genotypes.c

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/*
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* MIT License
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*
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* Copyright (c) 2019 Tskit Developers
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal
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* in the Software without restriction, including without limitation the rights
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the Software is
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* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in all
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* copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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* SOFTWARE.
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*/
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#include "testlib.h"
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#include <tskit/genotypes.h>
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‎c/tests/test_minimal_cpp.cpp

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/*
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* MIT License
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*
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* Copyright (c) 2019 Tskit Developers
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal
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* in the Software without restriction, including without limitation the rights
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the Software is
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* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in all
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* copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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* SOFTWARE.
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*/
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/* Minimal tests to make sure that tskit at least compiles and links
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* in a simple C++ program */
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‎c/tests/test_stats.c

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/*
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* MIT License
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*
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* Copyright (c) 2019 Tskit Developers
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal
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* in the Software without restriction, including without limitation the rights
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the Software is
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* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in all
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* copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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* SOFTWARE.
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*/
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#include "testlib.h"
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#include <tskit/stats.h>
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‎c/tests/test_tables.c

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/*
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* MIT License
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*
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* Copyright (c) 2019 Tskit Developers
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal
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* in the Software without restriction, including without limitation the rights
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* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the Software is
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* furnished to do so, subject to the following conditions:
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*
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* The above copyright notice and this permission notice shall be included in all
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* copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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* SOFTWARE.
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*/
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#include "testlib.h"
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#include <tskit/tables.h>
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