LICENSE
README.md
pyproject.toml
src/contigger/__init__.py
src/contigger/__main__.py
src/contigger/alignment_planning.py
src/contigger/benchmark.py
src/contigger/catalogue.py
src/contigger/cli.py
src/contigger/config.py
src/contigger/decision_policy.py
src/contigger/exceptions.py
src/contigger/fasta.py
src/contigger/graph.py
src/contigger/junction_benchmark.py
src/contigger/junction_remapping_benchmark.py
src/contigger/manifest.py
src/contigger/manifest_generator.py
src/contigger/merge.py
src/contigger/minimisers.py
src/contigger/models.py
src/contigger/outputs.py
src/contigger/path_planning.py
src/contigger/pipeline_benchmark.py
src/contigger/provenance.py
src/contigger/relationships.py
src/contigger/synthetic.py
src/contigger/textio.py
src/contigger.egg-info/PKG-INFO
src/contigger.egg-info/SOURCES.txt
src/contigger.egg-info/dependency_links.txt
src/contigger.egg-info/entry_points.txt
src/contigger.egg-info/requires.txt
src/contigger.egg-info/top_level.txt
src/contigger/aligners/__init__.py
src/contigger/aligners/base.py
src/contigger/aligners/minimap2.py
src/contigger/evidence/__init__.py
src/contigger/evidence/bam.py
src/contigger/evidence/base.py
src/contigger/evidence/junctions.py
src/contigger/utilities/__init__.py
src/contigger/utilities/sequences.py
src/contigger/utilities/subprocesses.py
tests/test_alignment_planning.py
tests/test_bam_evidence.py
tests/test_benchmark.py
tests/test_catalogue.py
tests/test_cli.py
tests/test_config.py
tests/test_decision_policy.py
tests/test_decision_policy_benchmark.py
tests/test_fasta.py
tests/test_graph.py
tests/test_graph_benchmark.py
tests/test_junction_benchmark.py
tests/test_junction_evidence.py
tests/test_junction_remapping_benchmark.py
tests/test_make_manifest.py
tests/test_manifest.py
tests/test_merge.py
tests/test_minimap2.py
tests/test_minimap2_integration.py
tests/test_minimisers.py
tests/test_paf.py
tests/test_path_planning.py
tests/test_path_planning_benchmark.py
tests/test_pipeline_benchmark.py
tests/test_relationships.py
tests/test_subprocesses.py
tests/test_synthetic.py