LICENSE
MANIFEST.in
README.md
lifton.yml
pyproject.toml
setup.py
lifton/__init__.py
lifton/align.py
lifton/annotation.py
lifton/annotation_validator.py
lifton/coreutils.py
lifton/exceptions.py
lifton/extract_sequence.py
lifton/get_id_fraction.py
lifton/gff3_validator.py
lifton/gffbase_adapter.py
lifton/intervals.py
lifton/lifton.py
lifton/lifton_class.py
lifton/lifton_utils.py
lifton/locus_pipeline.py
lifton/logger.py
lifton/miniprot_rescue.py
lifton/parallel.py
lifton/protein_maximization.py
lifton/run_evaluation.py
lifton/run_liftoff.py
lifton/run_miniprot.py
lifton/stats.py
lifton/variants.py
lifton/windowed_align.py
lifton/gffbase/LICENSE
lifton/gffbase/MIGRATION.md
lifton/gffbase/__init__.py
lifton/gffbase/_bins.py
lifton/gffbase/create_db.py
lifton/gffbase/dialect.py
lifton/gffbase/exceptions.py
lifton/gffbase/feature.py
lifton/gffbase/gffwriter.py
lifton/gffbase/helpers.py
lifton/gffbase/ingest.py
lifton/gffbase/interface.py
lifton/gffbase/iterators.py
lifton/gffbase/merge_criteria.py
lifton/gffbase/parser.py
lifton/gffbase/schema.py
lifton/gffbase/sqlite_export.py
lifton/gffbase/_pyfallback/__init__.py
lifton/gffbase/_pyfallback/attributes.py
lifton/gffbase/_pyfallback/parser.py
lifton/gffbase/_rust/Cargo.lock
lifton/gffbase/_rust/Cargo.toml
lifton/gffbase/_rust/src/attributes.rs
lifton/gffbase/_rust/src/dialect.rs
lifton/gffbase/_rust/src/escape.rs
lifton/gffbase/_rust/src/lib.rs
lifton/gffbase/_rust/src/parser.rs
lifton/gffbase/_rust/src/validate.rs
lifton/io/__init__.py
lifton/io/feature_serializer.py
lifton/io/gff3_validator.py
lifton/io/gff3_writer.py
lifton/io/ncbi_gff3_spec.py
lifton/liftoff/__init__.py
lifton/liftoff/align_features.py
lifton/liftoff/aligned_seg.py
lifton/liftoff/extract_features.py
lifton/liftoff/feature_hierarchy.py
lifton/liftoff/find_best_mapping.py
lifton/liftoff/fix_overlapping_features.py
lifton/liftoff/inmemory_emitter.py
lifton/liftoff/lift_features.py
lifton/liftoff/liftoff_main.py
lifton/liftoff/liftoff_utils.py
lifton/liftoff/liftover_types.py
lifton/liftoff/merge_lifted_features.py
lifton/liftoff/native_align.py
lifton/liftoff/new_feature.py
lifton/liftoff/polish.py
lifton/liftoff/write_new_gff.py
lifton/liftoff/tests/__init__.py
lifton/liftoff/tests/test_advanced.py
lifton/liftoff/tests/test_basic.py
lifton/native_bindings/__init__.py
lifton/native_bindings/minimap_facade.py
lifton/native_bindings/miniprot_facade.py
lifton/native_bindings/types.py