.gitignore
.pre-commit-config.yaml
.readthedocs.yaml
CHANGES.rst
LICENSE
MANIFEST.in
README.md
pyproject.toml
requirements.txt
setup.py
tox.ini
.attic/bicc_networkx.py
.attic/find_bubbles.py
.attic/graph.py
.attic/sort.py
.attic/.vcf_based_sorting_scripts/add-bubble-info.py
.attic/.vcf_based_sorting_scripts/bubble-sort.py
.github/workflows/ci.yml
docs/Makefile
docs/README.rst
docs/changes.rst
docs/conf.py
docs/develop.rst
docs/guide.rst
docs/index.rst
docs/installation.rst
docs/requirements.txt
docs/_static/bo_tags.png
docs/_static/no_tags.png
gaftools/.gitignore
gaftools/__init__.py
gaftools/__main__.py
gaftools/_version.py
gaftools/args.py
gaftools/conversion.py
gaftools/gaf.py
gaftools/gfa.py
gaftools/timer.py
gaftools/utils.py
gaftools.egg-info/PKG-INFO
gaftools.egg-info/SOURCES.txt
gaftools.egg-info/dependency_links.txt
gaftools.egg-info/entry_points.txt
gaftools.egg-info/requires.txt
gaftools.egg-info/top_level.txt
gaftools/cli/__init__.py
gaftools/cli/find_path.py
gaftools/cli/index.py
gaftools/cli/order_gfa.py
gaftools/cli/phase.py
gaftools/cli/realign.py
gaftools/cli/sort.py
gaftools/cli/stat.py
gaftools/cli/view.py
scripts/split_graph.sh
tests/test_extract_path.py
tests/test_find_path.py
tests/test_gaf.py
tests/test_gaf_gzipped.py
tests/test_gfa_class.py
tests/test_index.py
tests/test_parsegaf_tags.py
tests/test_run_ordergfa.py
tests/test_run_realign.py
tests/test_run_stat.py
tests/test_sort.py
tests/test_view.py
tests/data/alignments-graphaligner.gaf
tests/data/alignments-graphaligner.gaf.gz
tests/data/alignments-minigraph-reversed-reads-stable.gaf
tests/data/alignments-minigraph-reversed-reads-unstable.gaf
tests/data/alignments-minigraph-stable-conversioncheck-only-s2.gaf
tests/data/alignments-minigraph-stable-conversioncheck-only-s464827.gaf
tests/data/alignments-minigraph-stable-conversioncheck.gaf
tests/data/alignments-minigraph-stable-conversioncheck.gaf.gvi
tests/data/alignments-minigraph-stable-conversioncheck.gaf.gz
tests/data/alignments-minigraph-stable-conversioncheck.gaf.gz.gvi
tests/data/alignments-minigraph-stable.gaf
tests/data/alignments-minigraph-unstable-conversioncheck-only-s2.gaf
tests/data/alignments-minigraph-unstable-conversioncheck-only-s464827.gaf
tests/data/alignments-minigraph-unstable-conversioncheck.gaf
tests/data/alignments-minigraph-unstable-conversioncheck.gaf.gvi
tests/data/alignments-minigraph-unstable-conversioncheck.gaf.gz
tests/data/alignments-minigraph-unstable-conversioncheck.gaf.gz.gvi
tests/data/alignments-minigraph-unstable.gaf
tests/data/alignments-more-graphaligner.gaf
tests/data/alignments-more-graphaligner.gaf.gz
tests/data/find_path-input.txt
tests/data/find_path-output.fasta
tests/data/large-graph-chr1.gfa.gz
tests/data/reads-conversioncheck.fa
tests/data/reads-more.fa
tests/data/reads-reversed.fa
tests/data/reads.fa
tests/data/reads.fa.fai
tests/data/smallgraph-noseq.gfa
tests/data/smallgraph-ordered.gfa
tests/data/smallgraph.gfa
tests/data/smallgraph_withN.gfa
tests/data/test_GFA_class.gfa
tests/data/test_GFA_class_wrong_graph.gfa