MANIFEST.in
README.md
pyproject.toml
requirements-dev.txt
requirements-gpu.txt
requirements.txt
setup.py
strandweaver/__init__.py
strandweaver/cli.py
strandweaver/download.py
strandweaver/version.py
strandweaver.egg-info/PKG-INFO
strandweaver.egg-info/SOURCES.txt
strandweaver.egg-info/dependency_links.txt
strandweaver.egg-info/entry_points.txt
strandweaver.egg-info/not-zip-safe
strandweaver.egg-info/requires.txt
strandweaver.egg-info/top_level.txt
strandweaver/assembly_core/__init__.py
strandweaver/assembly_core/dbg_engine_module.py
strandweaver/assembly_core/edgewarden_module.py
strandweaver/assembly_core/haplotype_detangler_module.py
strandweaver/assembly_core/illumina_olc_contig_module.py
strandweaver/assembly_core/pathweaver_module.py
strandweaver/assembly_core/strandtether_module.py
strandweaver/assembly_core/string_graph_engine_module.py
strandweaver/assembly_core/svscribe_module.py
strandweaver/assembly_core/threadcompass_module.py
strandweaver/assembly_utils/__init__.py
strandweaver/assembly_utils/chromosome_classifier.py
strandweaver/assembly_utils/gap_filler.py
strandweaver/assembly_utils/gene_annotation.py
strandweaver/assembly_utils/graph_cleanup.py
strandweaver/assembly_utils/hic_graph_aligner.py
strandweaver/assembly_utils/iterative_polisher.py
strandweaver/assembly_utils/misassembly_detector.py
strandweaver/assembly_utils/qv_estimator.py
strandweaver/config/__init__.py
strandweaver/config/defaults.yaml
strandweaver/config/env_ml_training.yml
strandweaver/config/parser.py
strandweaver/config/schema.py
strandweaver/io_utils/__init__.py
strandweaver/io_utils/assembly_export.py
strandweaver/io_utils/io_core.py
strandweaver/io_utils/user_input.py
strandweaver/preprocessing/__init__.py
strandweaver/preprocessing/errorsmith_module.py
strandweaver/preprocessing/kmer_error_features.py
strandweaver/preprocessing/kweaver_module.py
strandweaver/preprocessing/read_classification_utility.py
strandweaver/preprocessing/read_error_profiling_utility.py
strandweaver/training/__init__.py
strandweaver/training/synthetic_data_generator.py
strandweaver/user_training/__init__.py
strandweaver/user_training/config_based_workflow.py
strandweaver/user_training/generate_sv_dense_data.py
strandweaver/user_training/generate_training_data.py
strandweaver/user_training/graph_training_data.py
strandweaver/user_training/patch_sv_injection.py
strandweaver/user_training/reextract_sv_features.py
strandweaver/user_training/reextract_sv_only.py
strandweaver/user_training/sv_detection.py
strandweaver/user_training/train_models.py
strandweaver/user_training/training_config.py
strandweaver/utils/__init__.py
strandweaver/utils/checkpoints.py
strandweaver/utils/hardware_management.py
strandweaver/utils/pipeline.py
strandweaver/utils/sequence_utils.py
tests/test_bubble_phasing.py
tests/test_cli.py
tests/test_e2e_pipeline.py
tests/test_edgewarden.py
tests/test_graph_training_data.py
tests/test_integration.py
tests/test_kweaver.py
tests/test_polisher_gap_filler.py
tests/test_qv_estimator.py
tests/test_read_classification.py
tests/test_sequence_utils.py
tests/test_train_models.py
tests/test_training_config.py
tests/test_ul_router.py