.gitattributes
.gitignore
.pre-commit-config.yaml
LICENSE
README.md
pixi.lock
pyproject.toml
benchmarks/published/compare_gurgy_pedigrees.py
benchmarks/published/compare_nepluyevsky_pedigrees.py
benchmarks/published/run_evaluations.py
benchmarks/published/data/gurgy/citation.md
benchmarks/published/data/gurgy/inferred_relations_READv2.csv
benchmarks/published/data/gurgy/nodes.csv
benchmarks/published/data/gurgy/published_exact_relations.csv
benchmarks/published/data/hazleton_north/citation.md
benchmarks/published/data/hazleton_north/inferred_relations_coeffs.csv
benchmarks/published/data/hazleton_north/inferred_relations_custom.csv
benchmarks/published/data/hazleton_north/nodes.csv
benchmarks/published/data/hazleton_north/published_exact_relations.csv
benchmarks/published/data/nepluyevsky/citation.md
benchmarks/published/data/nepluyevsky/inferred_relations_KIN.csv
benchmarks/published/data/nepluyevsky/inferred_relations_custom.csv
benchmarks/published/data/nepluyevsky/nodes.csv
benchmarks/published/data/nepluyevsky/published_exact_relations.csv
benchmarks/published/evaluator/__init__.py
benchmarks/published/evaluator/comparison_utils.py
benchmarks/published/evaluator/pedigree_evaluator.py
benchmarks/published/results/results.csv
benchmarks/published/results/gurgy_comparison/inferred_pedigree.svg
benchmarks/published/results/gurgy_comparison/inferred_pedigree_repositioned_cropped.pdf
benchmarks/published/results/gurgy_comparison/inferred_pedigree_repositioned_cropped.svg
benchmarks/published/results/gurgy_comparison/published_pedigree.svg
benchmarks/published/results/gurgy_comparison/published_pedigree_cropped.pdf
benchmarks/published/results/gurgy_comparison/published_pedigree_cropped.svg
benchmarks/published/results/gurgy_comparison/relation_differences.csv
benchmarks/published/results/nepluyevsky_comparison/inferred_pedigree.svg
benchmarks/published/results/nepluyevsky_comparison/inferred_pedigree_cropped.pdf
benchmarks/published/results/nepluyevsky_comparison/inferred_pedigree_cropped.svg
benchmarks/published/results/nepluyevsky_comparison/published_pedigree.svg
benchmarks/published/results/nepluyevsky_comparison/published_pedigree_cropped.pdf
benchmarks/published/results/nepluyevsky_comparison/published_pedigree_cropped.svg
benchmarks/published/results/nepluyevsky_comparison/relation_differences.csv
benchmarks/simulations/plot_parameter_data.py
benchmarks/simulations/plot_sampling_data.py
benchmarks/simulations/run_parameter_experiment.py
benchmarks/simulations/run_sampling_experiment.py
benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.0_error_rate_scale=0.0.csv
benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.0_error_rate_scale=0.5.csv
benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.0_error_rate_scale=1.0.csv
benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.0_error_rate_scale=2.0.csv
benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.2_error_rate_scale=0.0.csv
benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.2_error_rate_scale=0.5.csv
benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.2_error_rate_scale=1.0.csv
benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.2_error_rate_scale=2.0.csv
benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.4_error_rate_scale=0.0.csv
benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.4_error_rate_scale=0.5.csv
benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.4_error_rate_scale=1.0.csv
benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.4_error_rate_scale=2.0.csv
benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.6_error_rate_scale=0.0.csv
benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.6_error_rate_scale=0.5.csv
benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.6_error_rate_scale=1.0.csv
benchmarks/simulations/results/parameter_experiment/data/p_mask_node=0.6_error_rate_scale=2.0.csv
benchmarks/simulations/results/parameter_experiment/plots/degree_f1_heatmap.pdf
benchmarks/simulations/results/parameter_experiment/plots/pedigree_summary_statistics.pdf
benchmarks/simulations/results/parameter_experiment/plots/relation_f1_heatmap.pdf
benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=10000_epsilon=0.0.csv
benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=10000_epsilon=0.2.csv
benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=10000_epsilon=0.4.csv
benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=1000_epsilon=0.0.csv
benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=1000_epsilon=0.2.csv
benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=1000_epsilon=0.4.csv
benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=100_epsilon=0.0.csv
benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=100_epsilon=0.2.csv
benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=100_epsilon=0.4.csv
benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=10_epsilon=0.0.csv
benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=10_epsilon=0.2.csv
benchmarks/simulations/results/sampling_experiment/data/max_candidate_pedigrees=10_epsilon=0.4.csv
benchmarks/simulations/results/sampling_experiment/plots/degree_f1_heatmap.pdf
benchmarks/simulations/results/sampling_experiment/plots/relation_f1_heatmap.pdf
benchmarks/simulations/simulator/__init__.py
benchmarks/simulations/simulator/simulated_pedigree.py
examples/algorithm_diagram.svg
examples/nodes.csv
examples/relations.csv
examples/repare.sh
examples/outputs/corrected_input_relations.csv
examples/outputs/reconstructed_exact_relations.csv
examples/outputs/reconstructed_pedigree.pdf
src/repare/__init__.py
src/repare/main.py
src/repare/pedigree.py
src/repare/pedigree_reconstructor.py
src/repare.egg-info/PKG-INFO
src/repare.egg-info/SOURCES.txt
src/repare.egg-info/dependency_links.txt
src/repare.egg-info/entry_points.txt
src/repare.egg-info/requires.txt
src/repare.egg-info/top_level.txt