├── .gitignore ├── .idea ├── Liftoff.iml ├── deployment.xml ├── misc.xml ├── modules.xml ├── vcs.xml └── workspace.xml ├── .travis.yml ├── LICENSE.md ├── README.md ├── __init__.py ├── liftoff ├── __init__.py ├── align_features.py ├── aligned_seg.py ├── extract_features.py ├── feature_hierarchy.py ├── find_best_mapping.py ├── fix_overlapping_features.py ├── lift_features.py ├── liftoff_utils.py ├── liftover_types.py ├── merge_lifted_features.py ├── new_feature.py ├── polish.py ├── run_liftoff.py ├── tests │ ├── .gitignore │ ├── GCA_000146045.2_R64_genomic.fna.gz │ ├── GCA_000146045.2_R64_genomic.gff.gz │ ├── GCA_000146045.2_R64_to_GCA_000146045.2_R64_expected_advanced.gff │ ├── GCA_000146045.2_R64_to_GCA_000146045.2_R64_expected_basic.gff │ ├── __init__.py │ ├── chroms.txt │ ├── test_advanced.py │ ├── test_basic.py │ ├── unmapped_features_GCA_000146045.2_R64_expected_advanced.txt │ ├── unmapped_features_GCA_000146045.2_R64_expected_basic.txt │ └── unplaced.txt └── write_new_gff.py ├── 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