LICENSE
README.md
pyproject.toml
remag/__init__.py
remag/__main__.py
remag/cli.py
remag/clustering.py
remag/core.py
remag/features.py
remag/losses.py
remag/miniprot_utils.py
remag/models.py
remag/output.py
remag/rescue.py
remag/utils.py
remag.egg-info/PKG-INFO
remag.egg-info/SOURCES.txt
remag.egg-info/dependency_links.txt
remag.egg-info/entry_points.txt
remag.egg-info/requires.txt
remag.egg-info/top_level.txt
remag/db/refseq_db.faa.gz
remag/hyenadna_classifier/__init__.py
remag/hyenadna_classifier/hyenadna_model.py
remag/hyenadna_classifier/predictor.py
remag/hyenadna_classifier/standalone_tokenizer.py
remag/hyenadna_classifier/models/pytorch_model.bin.20251024
remag/hyenadna_classifier/models/pytorch_model.bin.20251116.4k
tests/test_cached_coverage_scaling.py
tests/test_cli_defaults.py
tests/test_clustering.py
tests/test_contig_names.py
tests/test_core.py
tests/test_coverage_inputs.py
tests/test_coverage_scaling.py
tests/test_cram_mapped_reads.py
tests/test_duplicate_fasta_ids.py
tests/test_exact_contig_names.py
tests/test_filter_batch_failures.py
tests/test_final_quality_statistics.py
tests/test_force.py
tests/test_force_symlinks.py
tests/test_gene_copy_counts.py
tests/test_hyenadna_batching.py
tests/test_hyenadna_filtering.py
tests/test_integration.py
tests/test_interval_contig_names.py
tests/test_issue_reproduction.py
tests/test_knn_self_neighbors.py
tests/test_lazy_imports.py
tests/test_losses.py
tests/test_miniprot_utils.py
tests/test_rescue_limits.py
tests/test_single_bin_rescue.py
tests/test_training_batches.py
tests/test_utils.py
tests/test_version.py
tests/test_zenodo_upload.py