LICENSE
README.md
hapsolo_cli.py
pyproject.toml
HapSolo.egg-info/PKG-INFO
HapSolo.egg-info/SOURCES.txt
HapSolo.egg-info/dependency_links.txt
HapSolo.egg-info/entry_points.txt
HapSolo.egg-info/requires.txt
HapSolo.egg-info/top_level.txt
hapsolo/__init__.py
hapsolo/__main__.py
hapsolo/alignment.py
hapsolo/assembly.py
hapsolo/cost_formula.py
hapsolo/names.py
hapsolo/optimizers.py
hapsolo/preprocess.py
hapsolo/report.py
hapsolo/scoring.py
hapsolo/scoring_data.py
hapsolo/search.py
hapsolo/state.py
hapsolo/utils.py
tests/test_alignment_formats.py
tests/test_cost_formula.py
tests/test_edge_cases.py
tests/test_filtering_and_scoring.py
tests/test_hap_cache_atomic.py
tests/test_hapsolo_cli.py
tests/test_hapsolo_functions.py
tests/test_name_conversion.py
tests/test_optimizer.py
tests/test_preprocessfasta.py
tests/test_real_data_integration.py
tests/test_report.py
tests/test_score_dump_path.py
tests/test_search_orthologs.py