.gitignore
.gitlab-ci.yml
.readthedocs.yml
ContributionGuide.md
LICENSE
README.rst
bash_completion.sh
gratools_rice_analysis_commands.md
pyproject.toml
Contributors/contributorAgreementEntity.md
Contributors/contributorAgreementIndividual.md
GraTools.egg-info/PKG-INFO
GraTools.egg-info/SOURCES.txt
GraTools.egg-info/dependency_links.txt
GraTools.egg-info/entry_points.txt
GraTools.egg-info/requires.txt
GraTools.egg-info/top_level.txt
docs/Makefile
docs/requirements.txt
docs/source/conf.py
docs/source/gratools.rst
docs/source/index.rst
docs/source/module.rst
docs/source/modules.rst
docs/source/quick_start.rst
docs/source/_static/GraTools_logo.png
docs/source/_static/cirad_small.jpg
docs/source/_static/grasuite.png
docs/source/_static/ird_small.png
docs/source/_static/paneec_small.png
docs/source/_static/tree_data_test.png
docs/source/commands/core_dispensable_ratio.rst
docs/source/commands/depth_nodes_stat.rst
docs/source/commands/extract_subgraph.rst
docs/source/commands/get_fasta.rst
docs/source/commands/get_segment_by_depth.rst
docs/source/commands/gratools_all.rst
docs/source/commands/index.rst
docs/source/commands/list_chr.rst
docs/source/commands/list_samples.rst
docs/source/commands/shell_completion.rst
docs/source/commands/specific_groups_sample.rst
docs/source/commands/stats.rst
docs/source/dot_files/pan_graph.dot
docs/source/dot_files/pan_graph_sub.dot
docs/source/dot_files/pan_graph_sub_extract_subgraph_1.dot
docs/source/dot_files/pan_graph_sub_extract_subgraph_2.dot
docs/source/dot_files/sequences.dot
docs/source/dot_files/shared_segments_diagram.dot
docs/source/dot_files/specific_segments_diagram.dot
docs/source/dot_files/sub_sequences.dot
docs/source/png_files/core_dispensable_ratio_diagram.png
docs/source/png_files/get_segment_diagram_1.png
docs/source/png_files/get_segment_diagram_2.png
gratools/Graph.py
gratools/Gratools.py
gratools/__init__.py
gratools/_version.py
gratools/common_decorators.py
gratools/gfa_analysis.py
gratools/gfa_content_info.py
gratools/gfa_extract.py
gratools/logger_config.py
gratools/main.py
gratools/others_cmd.py
gratools/test_memory_profile.py
gratools/useful_function.py
gratools/containers/Dockerfile_test
gratools/tests/__init__.py
gratools/tests/all_test.py
gratools/tests/md5sum_tests/list_A.txt
gratools/tests/md5sum_tests/list_B.txt
gratools/tests/md5sum_tests/md5sum_core_dispensable_ratio.txt
gratools/tests/md5sum_tests/md5sum_depth_nodes_stat.txt
gratools/tests/md5sum_tests/md5sum_extract_subgraph_cg14_chr7_all.txt
gratools/tests/md5sum_tests/md5sum_extract_subgraph_cg14_chr7_all_fasta.txt
gratools/tests/md5sum_tests/md5sum_get_fasta_cg14_chr7_all.txt
gratools/tests/md5sum_tests/md5sum_get_segment_by_depth.txt
gratools/tests/md5sum_tests/md5sum_index.txt
gratools/tests/md5sum_tests/md5sum_list_chr.txt
gratools/tests/md5sum_tests/md5sum_list_chr_full.txt
gratools/tests/md5sum_tests/md5sum_list_samples.txt
gratools/tests/md5sum_tests/md5sum_specific_groups_sample.txt
gratools/tests/md5sum_tests/md5sum_stats.txt
manuscript/.gitkeep
scripts/get_seglen_frombam.py
scripts/print_venn_gratools.R
scripts/venn_gratools.py