├── .gitignore ├── LICENSE.txt ├── README.md ├── example ├── ACB_chr_1_subset.vcf.gz ├── ACB_chr_1_subset.vcf.gz.tbi ├── ACB_pop_sizes.csv └── example.sh ├── pyrho ├── __init__.py ├── compute_r2.py ├── data │ └── pyrho_hapmap_maps.txt ├── frontend.py ├── haplotype_reader.py ├── hyperparameter_optimizer.py ├── make_table.py ├── objective_function.py ├── optimizer.py ├── rho_splines.py ├── size_reader.py └── utility.py ├── setup.py ├── smcpp_popsizes_1kg.csv └── tests ├── ACB_pop_sizes.csv ├── issue6_msmc.txt ├── locs.txt ├── msmc_test.final.txt ├── n_10_test_table.hdf ├── n_15_test_table.hdf ├── short.vcf.gz ├── short.vcf.gz.tbi ├── sites.txt ├── test.fa ├── test.hdf ├── test_check.hdf ├── test_dna.fa └── tests.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/popgenmethods/pyrho/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE.txt: 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