├── .travis.yml ├── Cargo.toml ├── LICENSE ├── README.md ├── data ├── example_data │ ├── additional_input │ │ ├── edges.txt │ │ ├── mod_nodes.txt │ │ ├── mod_path.txt │ │ └── nodes.txt │ ├── gfa │ │ └── testGraph.gfa │ └── packs │ │ ├── 9986.1k.a1.a2.merge.pt │ │ ├── 9986.1k.node.a1.pt │ │ ├── 9986.1k.node.a2.pt │ │ ├── 9986.1k.pi │ │ ├── 9986.1k.seq.a1.pn │ │ ├── 9986.1k.seq.a1.pt │ │ ├── 9986.1k.seq.a3.pn │ │ ├── 9986.1k.seq.merge.pn │ │ ├── 9986.1k.seq.pc │ │ ├── 9986.1k.tail.2.header.txt │ │ ├── 9986.1k.tail.header.txt │ │ ├── 9986.1k.tail.seq.pc │ │ ├── 9986.1k.txt │ │ ├── 9986.compress.pc │ │ ├── realpath.compress.txt │ │ ├── realpath.plain.txt │ │ ├── realpath.pn.txt │ │ └── realpath.pt.txt └── output │ └── .gitkeep ├── doc └── plots │ └── gfa2bin_general_v1.png ├── scripts ├── manhattan.nearest.py ├── manhattan.nodes.py └── qq.py ├── src ├── core │ ├── bfile.rs │ ├── core.rs │ ├── helper.rs │ └── mod.rs ├── cov │ ├── cov_main.rs │ ├── mod.rs │ └── pack.rs ├── filter │ ├── filter_main.rs │ └── mod.rs ├── find │ ├── find_main.rs │ └── mod.rs ├── graph │ ├── graph_main.rs │ ├── mod.rs │ └── parser.rs ├── helper.rs ├── logging.rs ├── main.rs ├── merge │ ├── merge_main.rs │ └── mod.rs ├── nearest │ ├── mod.rs │ └── nearest_main.rs ├── remove │ ├── mod.rs │ └── remove_main.rs ├── split │ ├── mod.rs │ └── split_main.rs ├── subpath │ ├── mod.rs │ └── subpath_main.rs ├── view │ ├── mod.rs │ └── view_main.rs └── window │ ├── mod.rs │ └── window_main.rs ├── tests ├── cov_test.rs ├── filter_test.rs ├── find_test.rs ├── graph_test.rs ├── merge_split_test.rs ├── nearest_test.rs ├── remove_test.rs ├── subpath_test.rs └── view_test.rs └── workflows ├── config_template ├── config.yaml ├── packlist.csv ├── phenotypes.csv └── samples.csv ├── graph-gwas-pipeline ├── schemas └── config.schema.yaml ├── testdata ├── config │ ├── config.fastq.yaml │ ├── config.pack.yaml │ ├── phenotypes.csv │ ├── phenotypes2.csv │ ├── samples.csv │ └── testdata.kinship ├── fastq │ ├── 6909.1001G.PE.1.250k.fastq.gz │ ├── 6909.1001G.PE.2.250k.fastq.gz │ ├── 9741.1001G.PE.1.250k.fastq.gz │ └── 9741.1001G.PE.2.250k.fastq.gz ├── gemma │ └── mock.assoc.txt ├── graphs │ └── 2155413.gfa └── packs │ ├── 1001g_plus_pan.6909.pack │ ├── 1001g_plus_pan.9741.pack │ └── packlist.csv └── workflow ├── 00_validate_inputs ├── Snakefile └── scripts │ ├── check_graph.bash │ ├── validate_kinship_matrix.py │ └── validate_sample_names.py ├── 01_prepare_fasta_ref └── Snakefile ├── 02a_make_packs_align2fasta_ref └── Snakefile ├── 02b_make_packs_from_list └── Snakefile ├── 03_make_fambedbim └── Snakefile ├── 04_gwas ├── Snakefile └── scripts │ ├── create_phenotype_fam_file.py │ ├── manhattan.nearest.py │ ├── manhattan.nodes.py │ └── qq.py ├── Snakefile └── envs └── main.yaml /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MoinSebi/gfa2bin/HEAD/.travis.yml 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