LICENSE
MANIFEST.in
README.md
pyproject.toml
docs/GFF4_single_file_spec.md
docs/GFF4_v0.1_spec.md
docs/GFF4_v0.3_spec.md
docs/MVP_scope.md
docs/gff4tools_cli.md
docs/publishing_gff4tools.md
docs/release_checklist.md
docs/release_checklist_gff4tools.md
docs/release_checklist_v0.2.md
docs/release_checklist_v0.3.md
docs/release_checklist_v0.4.md
docs/release_notes_gff4tools_v0.3.0rc1.md
docs/release_notes_gff4tools_v0.3.0rc2.md
docs/release_notes_gff4tools_v0.4.0.md
docs/release_notes_gff4tools_v0.4.0rc1.md
docs/release_notes_v0.1.md
docs/release_notes_v0.2.md
docs/release_notes_v0.3.md
docs/rfc_v0.5_store_and_indexed_pav.md
docs/roadmap.md
docs/tutorial_mvp.md
docs/superpowers/plans/2026-05-09-v04-release-to-v05-landing.md
examples/arabidopsis_ncbi_real/README.md
examples/arabidopsis_ncbi_real/accessions.tsv
examples/arabidopsis_ncbi_real/expected_pav_minimal.tsv
examples/arabidopsis_ncbi_real/region.toml
examples/arabidopsis_ncbi_real/region.yaml
examples/arabidopsis_public/README.md
examples/arabidopsis_public/arabidopsis_public.gfa
examples/arabidopsis_public/arabidopsis_public.gff3
examples/arabidopsis_public/path_map.tsv
examples/arabidopsis_public/source_metadata.json
examples/pav_multi_sample/README.md
examples/pav_multi_sample/path_map.tsv
examples/pav_multi_sample/pav_multi_sample.gfa
examples/pav_multi_sample/pav_multi_sample.gff3
examples/quinoa_cqu_real/README.md
examples/quinoa_cqu_real/dataset.toml
examples/quinoa_cqu_real/expected_gate.tsv
examples/quinoa_cqu_real/regions.tsv
examples/real_small/README.md
examples/real_small/path_map.tsv
examples/real_small/real_small.gfa
examples/real_small/real_small.gff3
examples/toy/README.md
examples/toy/expected_walks.tsv
examples/toy/path_map.tsv
examples/toy/toy.gfa
examples/toy/toy.gff3
gff4/__init__.py
gff4/cli.py
gff4/export.py
gff4/gfa.py
gff4/gfa_stream.py
gff4/gff3.py
gff4/graph_index.py
gff4/graph_subset.py
gff4/index.py
gff4/io.py
gff4/io_text.py
gff4/package.py
gff4/path_map.py
gff4/pav.py
gff4/projection.py
gff4/query.py
gff4/single_file.py
gff4/subset_validation.py
gff4/validator.py
gff4tools.egg-info/PKG-INFO
gff4tools.egg-info/SOURCES.txt
gff4tools.egg-info/dependency_links.txt
gff4tools.egg-info/entry_points.txt
gff4tools.egg-info/requires.txt
gff4tools.egg-info/top_level.txt
scripts/smoke_demos.sh
scripts/bench/run_command_benchmark.py
scripts/quinoa_realdata/00_audit_dataset.py
scripts/quinoa_realdata/01_inspect_gfa_wlines.py
scripts/quinoa_realdata/02_select_reference_locus.py
scripts/quinoa_realdata/02_select_regions.py
scripts/quinoa_realdata/03_subset_gfa_region.py
scripts/quinoa_realdata/04_prepare_reference_gff3.py
scripts/quinoa_realdata/05_build_gff4_quinoa_demo.sh
scripts/quinoa_realdata/06_assert_quinoa_demo.py
scripts/quinoa_realdata/07_assert_multi_region_gate.py
scripts/quinoa_realdata/08_assert_v04_benchmark.py
scripts/quinoa_realdata/run_quinoa_cqu_demo.sh
scripts/quinoa_realdata/run_quinoa_cqu_multi_region_demo.sh
scripts/quinoa_realdata/run_quinoa_cqu_v04_benchmark.sh
scripts/realdata/00_check_realdata_deps.py
scripts/realdata/01_fetch_ncbi_genomes.py
scripts/realdata/01_fetch_ncbi_genomes.sh
scripts/realdata/02_normalize_ncbi_package.py
scripts/realdata/02_prepare_col0_region.py
scripts/realdata/03_find_homologous_regions.sh
scripts/realdata/03_prepare_col0_region.py
scripts/realdata/04_extract_oriented_regions.py
scripts/realdata/04_find_homologous_regions.py
scripts/realdata/05_extract_oriented_regions.py
scripts/realdata/05_make_refanchored_gfa.py
scripts/realdata/06_build_gff4_demo.sh
scripts/realdata/06_make_refanchored_gfa.py
scripts/realdata/07_assert_arabidopsis_demo.py
scripts/realdata/07_build_gff4_demo.sh
scripts/realdata/08_assert_arabidopsis_demo.py
scripts/realdata/compare_gff3_roundtrip.py
scripts/realdata/run_arabidopsis_ncbi_demo.sh
tests/test_arabidopsis_public_demo_e2e.py
tests/test_benchmark_wrapper.py
tests/test_cli.py
tests/test_export.py
tests/test_export_gff3_cli.py
tests/test_gff3_projection.py
tests/test_gff4tools_cli.py
tests/test_package_schema.py
tests/test_packaging_release.py
tests/test_path_map.py
tests/test_projection.py
tests/test_query_cli.py
tests/test_real_small_demo_e2e.py
tests/test_realdata_scripts.py
tests/test_single_file_cli.py
tests/test_toy_demo_e2e.py
tests/test_v02_pav_cli.py
tests/test_v03_gfa_stream.py
tests/test_v03_graph_subset.py
tests/test_v03_index_cli.py
tests/test_v03_multi_region_assert.py
tests/test_v03_quinoa_scripts.py
tests/test_v03_region_selection.py
tests/test_v04_benchmark_assert.py
tests/test_validate_subset_discontinuity.py
tests/test_validator.py
tests/realdata_unit/test_local_gff3_rebase.py
tests/realdata_unit/test_paf_cigar_graph_builder.py
tests/realdata_unit/test_refanchored_gfa_builder.py