├── .attic ├── .vcf_based_sorting_scripts │ ├── add-bubble-info.py │ └── bubble-sort.py ├── bicc_networkx.py ├── find_bubbles.py ├── graph.py └── sort.py ├── .github └── workflows │ └── ci.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── CHANGES.rst ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── README.rst ├── _static │ ├── bo_tags.png │ └── no_tags.png ├── changes.rst ├── conf.py ├── develop.rst ├── guide.rst ├── index.rst ├── installation.rst └── requirements.txt ├── gaftools ├── .gitignore ├── __init__.py ├── __main__.py ├── args.py ├── cli │ ├── __init__.py │ ├── find_path.py │ ├── gfa2rgfa.py │ ├── index.py │ ├── order_gfa.py │ ├── phase.py │ ├── realign.py │ ├── sort.py │ ├── stat.py │ └── view.py ├── conversion.py ├── gaf.py ├── gfa.py ├── timer.py └── utils.py ├── pyproject.toml ├── requirements.txt ├── scripts └── split_graph.sh ├── setup.py ├── tests ├── data │ ├── alignments-graphaligner.gaf │ ├── alignments-graphaligner.gaf.gz │ ├── alignments-minigraph-reversed-reads-stable.gaf │ ├── alignments-minigraph-reversed-reads-unstable.gaf │ ├── alignments-minigraph-stable-conversioncheck-only-s2.gaf │ ├── alignments-minigraph-stable-conversioncheck-only-s464827.gaf │ ├── alignments-minigraph-stable-conversioncheck.gaf │ ├── alignments-minigraph-stable-conversioncheck.gaf.gvi │ ├── alignments-minigraph-stable-conversioncheck.gaf.gz │ ├── alignments-minigraph-stable-conversioncheck.gaf.gz.gvi │ ├── alignments-minigraph-stable.gaf │ ├── alignments-minigraph-unstable-conversioncheck-only-s2.gaf │ ├── alignments-minigraph-unstable-conversioncheck-only-s464827.gaf │ ├── alignments-minigraph-unstable-conversioncheck.gaf │ ├── alignments-minigraph-unstable-conversioncheck.gaf.gvi │ ├── alignments-minigraph-unstable-conversioncheck.gaf.gz │ ├── alignments-minigraph-unstable-conversioncheck.gaf.gz.gvi │ ├── alignments-minigraph-unstable.gaf │ ├── alignments-more-graphaligner.gaf │ ├── alignments-more-graphaligner.gaf.gz │ ├── find_path-input.txt │ ├── find_path-output.fasta │ ├── graph-conversioncheck-assembly-BAR.1.fa │ ├── graph-conversioncheck-assembly-BAR.2.fa │ ├── graph-conversioncheck-assembly-BAZ.1.fa │ ├── graph-conversioncheck-assembly-BAZ.2.fa │ ├── graph-conversioncheck-assembly-FOO.1.fa │ ├── graph-conversioncheck-assembly-FOO.2.fa │ ├── graph-conversioncheck-assembly-REF.fa │ ├── graph-conversioncheck-gfa-invertednodes.gfa │ ├── graph-conversioncheck-gfa-partial-tagged.gfa │ ├── graph-conversioncheck-gfa-wrong-Wline-order.gfa │ ├── graph-conversioncheck-gfa.gfa │ ├── graph-conversioncheck-rgfa.gfa │ ├── graph-conversioncheck-samples.seqfile │ ├── large-graph-chr1.gfa.gz │ ├── reads-conversioncheck.fa │ ├── reads-more.fa │ ├── reads-reversed.fa │ ├── reads.fa │ ├── reads.fa.fai │ ├── smallgraph-noseq.gfa │ ├── smallgraph-ordered.gfa │ ├── smallgraph.gfa │ ├── smallgraph_withN.gfa │ ├── test_GFA_class.gfa │ └── test_GFA_class_wrong_graph.gfa ├── test_extract_path.py ├── test_find_path.py ├── test_gaf.py ├── test_gaf_gzipped.py ├── test_gfa2rgfa.py ├── test_gfa_class.py ├── test_index.py ├── test_parsegaf_tags.py ├── test_run_ordergfa.py ├── test_run_realign.py ├── test_run_stat.py ├── test_sort.py └── test_view.py └── tox.ini /.attic/.vcf_based_sorting_scripts/add-bubble-info.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/.attic/.vcf_based_sorting_scripts/add-bubble-info.py -------------------------------------------------------------------------------- /.attic/.vcf_based_sorting_scripts/bubble-sort.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/.attic/.vcf_based_sorting_scripts/bubble-sort.py -------------------------------------------------------------------------------- /.attic/bicc_networkx.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/.attic/bicc_networkx.py -------------------------------------------------------------------------------- /.attic/find_bubbles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/.attic/find_bubbles.py -------------------------------------------------------------------------------- /.attic/graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/.attic/graph.py -------------------------------------------------------------------------------- /.attic/sort.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/.attic/sort.py -------------------------------------------------------------------------------- /.github/workflows/ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/.github/workflows/ci.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /CHANGES.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/CHANGES.rst -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/MANIFEST.in -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/README.md -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/README.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/docs/README.rst -------------------------------------------------------------------------------- /docs/_static/bo_tags.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/docs/_static/bo_tags.png -------------------------------------------------------------------------------- /docs/_static/no_tags.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/docs/_static/no_tags.png -------------------------------------------------------------------------------- /docs/changes.rst: -------------------------------------------------------------------------------- 1 | .. _changes: 2 | 3 | .. include:: ../CHANGES.rst 4 | -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/develop.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/docs/develop.rst -------------------------------------------------------------------------------- /docs/guide.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/docs/guide.rst -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/docs/index.rst -------------------------------------------------------------------------------- /docs/installation.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/docs/installation.rst -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/docs/requirements.txt -------------------------------------------------------------------------------- /gaftools/.gitignore: -------------------------------------------------------------------------------- 1 | *.cpp 2 | *.cpython-*.so 3 | -------------------------------------------------------------------------------- /gaftools/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/gaftools/__init__.py -------------------------------------------------------------------------------- /gaftools/__main__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/gaftools/__main__.py -------------------------------------------------------------------------------- /gaftools/args.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/gaftools/args.py -------------------------------------------------------------------------------- /gaftools/cli/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/gaftools/cli/__init__.py -------------------------------------------------------------------------------- /gaftools/cli/find_path.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/gaftools/cli/find_path.py -------------------------------------------------------------------------------- /gaftools/cli/gfa2rgfa.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/gaftools/cli/gfa2rgfa.py -------------------------------------------------------------------------------- /gaftools/cli/index.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/gaftools/cli/index.py -------------------------------------------------------------------------------- /gaftools/cli/order_gfa.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/gaftools/cli/order_gfa.py -------------------------------------------------------------------------------- /gaftools/cli/phase.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/gaftools/cli/phase.py -------------------------------------------------------------------------------- /gaftools/cli/realign.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/gaftools/cli/realign.py -------------------------------------------------------------------------------- /gaftools/cli/sort.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/gaftools/cli/sort.py -------------------------------------------------------------------------------- /gaftools/cli/stat.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/gaftools/cli/stat.py -------------------------------------------------------------------------------- /gaftools/cli/view.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/gaftools/cli/view.py -------------------------------------------------------------------------------- /gaftools/conversion.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/gaftools/conversion.py -------------------------------------------------------------------------------- /gaftools/gaf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/gaftools/gaf.py -------------------------------------------------------------------------------- /gaftools/gfa.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/gaftools/gfa.py -------------------------------------------------------------------------------- /gaftools/timer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/gaftools/timer.py -------------------------------------------------------------------------------- /gaftools/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/gaftools/utils.py -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/pyproject.toml -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | pysam 2 | pywfa==0.5.1 3 | -------------------------------------------------------------------------------- /scripts/split_graph.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/scripts/split_graph.sh -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/setup.py -------------------------------------------------------------------------------- /tests/data/alignments-graphaligner.gaf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/alignments-graphaligner.gaf -------------------------------------------------------------------------------- /tests/data/alignments-graphaligner.gaf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/alignments-graphaligner.gaf.gz -------------------------------------------------------------------------------- /tests/data/alignments-minigraph-reversed-reads-stable.gaf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/alignments-minigraph-reversed-reads-stable.gaf -------------------------------------------------------------------------------- /tests/data/alignments-minigraph-reversed-reads-unstable.gaf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/alignments-minigraph-reversed-reads-unstable.gaf -------------------------------------------------------------------------------- /tests/data/alignments-minigraph-stable-conversioncheck-only-s2.gaf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/alignments-minigraph-stable-conversioncheck-only-s2.gaf -------------------------------------------------------------------------------- /tests/data/alignments-minigraph-stable-conversioncheck-only-s464827.gaf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/alignments-minigraph-stable-conversioncheck-only-s464827.gaf -------------------------------------------------------------------------------- /tests/data/alignments-minigraph-stable-conversioncheck.gaf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/alignments-minigraph-stable-conversioncheck.gaf -------------------------------------------------------------------------------- /tests/data/alignments-minigraph-stable-conversioncheck.gaf.gvi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/alignments-minigraph-stable-conversioncheck.gaf.gvi -------------------------------------------------------------------------------- /tests/data/alignments-minigraph-stable-conversioncheck.gaf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/alignments-minigraph-stable-conversioncheck.gaf.gz -------------------------------------------------------------------------------- /tests/data/alignments-minigraph-stable-conversioncheck.gaf.gz.gvi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/alignments-minigraph-stable-conversioncheck.gaf.gz.gvi -------------------------------------------------------------------------------- /tests/data/alignments-minigraph-stable.gaf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/alignments-minigraph-stable.gaf -------------------------------------------------------------------------------- /tests/data/alignments-minigraph-unstable-conversioncheck-only-s2.gaf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/alignments-minigraph-unstable-conversioncheck-only-s2.gaf -------------------------------------------------------------------------------- /tests/data/alignments-minigraph-unstable-conversioncheck-only-s464827.gaf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/alignments-minigraph-unstable-conversioncheck-only-s464827.gaf -------------------------------------------------------------------------------- /tests/data/alignments-minigraph-unstable-conversioncheck.gaf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/alignments-minigraph-unstable-conversioncheck.gaf -------------------------------------------------------------------------------- /tests/data/alignments-minigraph-unstable-conversioncheck.gaf.gvi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/alignments-minigraph-unstable-conversioncheck.gaf.gvi -------------------------------------------------------------------------------- /tests/data/alignments-minigraph-unstable-conversioncheck.gaf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/alignments-minigraph-unstable-conversioncheck.gaf.gz -------------------------------------------------------------------------------- /tests/data/alignments-minigraph-unstable-conversioncheck.gaf.gz.gvi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/alignments-minigraph-unstable-conversioncheck.gaf.gz.gvi -------------------------------------------------------------------------------- /tests/data/alignments-minigraph-unstable.gaf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/alignments-minigraph-unstable.gaf -------------------------------------------------------------------------------- /tests/data/alignments-more-graphaligner.gaf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/alignments-more-graphaligner.gaf -------------------------------------------------------------------------------- /tests/data/alignments-more-graphaligner.gaf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/alignments-more-graphaligner.gaf.gz -------------------------------------------------------------------------------- /tests/data/find_path-input.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/find_path-input.txt -------------------------------------------------------------------------------- /tests/data/find_path-output.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/find_path-output.fasta -------------------------------------------------------------------------------- /tests/data/graph-conversioncheck-assembly-BAR.1.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/graph-conversioncheck-assembly-BAR.1.fa -------------------------------------------------------------------------------- /tests/data/graph-conversioncheck-assembly-BAR.2.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/graph-conversioncheck-assembly-BAR.2.fa -------------------------------------------------------------------------------- /tests/data/graph-conversioncheck-assembly-BAZ.1.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/graph-conversioncheck-assembly-BAZ.1.fa -------------------------------------------------------------------------------- /tests/data/graph-conversioncheck-assembly-BAZ.2.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/graph-conversioncheck-assembly-BAZ.2.fa -------------------------------------------------------------------------------- /tests/data/graph-conversioncheck-assembly-FOO.1.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/graph-conversioncheck-assembly-FOO.1.fa -------------------------------------------------------------------------------- /tests/data/graph-conversioncheck-assembly-FOO.2.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/graph-conversioncheck-assembly-FOO.2.fa -------------------------------------------------------------------------------- /tests/data/graph-conversioncheck-assembly-REF.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/graph-conversioncheck-assembly-REF.fa -------------------------------------------------------------------------------- /tests/data/graph-conversioncheck-gfa-invertednodes.gfa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/graph-conversioncheck-gfa-invertednodes.gfa -------------------------------------------------------------------------------- /tests/data/graph-conversioncheck-gfa-partial-tagged.gfa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/graph-conversioncheck-gfa-partial-tagged.gfa -------------------------------------------------------------------------------- /tests/data/graph-conversioncheck-gfa-wrong-Wline-order.gfa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/graph-conversioncheck-gfa-wrong-Wline-order.gfa -------------------------------------------------------------------------------- /tests/data/graph-conversioncheck-gfa.gfa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/graph-conversioncheck-gfa.gfa -------------------------------------------------------------------------------- /tests/data/graph-conversioncheck-rgfa.gfa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/graph-conversioncheck-rgfa.gfa -------------------------------------------------------------------------------- /tests/data/graph-conversioncheck-samples.seqfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/graph-conversioncheck-samples.seqfile -------------------------------------------------------------------------------- /tests/data/large-graph-chr1.gfa.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/large-graph-chr1.gfa.gz -------------------------------------------------------------------------------- /tests/data/reads-conversioncheck.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/reads-conversioncheck.fa -------------------------------------------------------------------------------- /tests/data/reads-more.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/reads-more.fa -------------------------------------------------------------------------------- /tests/data/reads-reversed.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/reads-reversed.fa -------------------------------------------------------------------------------- /tests/data/reads.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/reads.fa -------------------------------------------------------------------------------- /tests/data/reads.fa.fai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/reads.fa.fai -------------------------------------------------------------------------------- /tests/data/smallgraph-noseq.gfa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/smallgraph-noseq.gfa -------------------------------------------------------------------------------- /tests/data/smallgraph-ordered.gfa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/smallgraph-ordered.gfa -------------------------------------------------------------------------------- /tests/data/smallgraph.gfa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/smallgraph.gfa -------------------------------------------------------------------------------- /tests/data/smallgraph_withN.gfa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/smallgraph_withN.gfa -------------------------------------------------------------------------------- /tests/data/test_GFA_class.gfa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/test_GFA_class.gfa -------------------------------------------------------------------------------- /tests/data/test_GFA_class_wrong_graph.gfa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/data/test_GFA_class_wrong_graph.gfa -------------------------------------------------------------------------------- /tests/test_extract_path.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/test_extract_path.py -------------------------------------------------------------------------------- /tests/test_find_path.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/test_find_path.py -------------------------------------------------------------------------------- /tests/test_gaf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/test_gaf.py -------------------------------------------------------------------------------- /tests/test_gaf_gzipped.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/test_gaf_gzipped.py -------------------------------------------------------------------------------- /tests/test_gfa2rgfa.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/test_gfa2rgfa.py -------------------------------------------------------------------------------- /tests/test_gfa_class.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/test_gfa_class.py -------------------------------------------------------------------------------- /tests/test_index.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/test_index.py -------------------------------------------------------------------------------- /tests/test_parsegaf_tags.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/test_parsegaf_tags.py -------------------------------------------------------------------------------- /tests/test_run_ordergfa.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/test_run_ordergfa.py -------------------------------------------------------------------------------- /tests/test_run_realign.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/test_run_realign.py -------------------------------------------------------------------------------- /tests/test_run_stat.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/test_run_stat.py -------------------------------------------------------------------------------- /tests/test_sort.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/test_sort.py -------------------------------------------------------------------------------- /tests/test_view.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tests/test_view.py -------------------------------------------------------------------------------- /tox.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marschall-lab/gaftools/HEAD/tox.ini --------------------------------------------------------------------------------