├── .gitignore ├── .travis.yml ├── DockerFile ├── License.txt ├── README.md ├── TestGraphs ├── 1000.xml ├── 100000bp.xml ├── 10000bp.xml ├── 2000bp.xml ├── 30000bp.xml ├── 50000bp.xml ├── 5000bp.xml ├── 75000bp.xml ├── Docker command line.txt ├── H37Rv.fa ├── H37Rv1.fa ├── H37Rv2.fa ├── H37Rv_Rep_Two.fa ├── H37Rv_Reverse.fa ├── H37Rv_Reverse_With_SNP.fa ├── H37Rv_With_SNPS.fa ├── Inversion Graph Code.txt ├── Inversion with SNP graph.txt ├── Read and graph Info.txt ├── grid.edgelist ├── inversion.xml ├── kzn_2_pangenome.xml ├── mix_of_snps.xml ├── no_mutation.xml ├── one_deletion.xml ├── one_insertion.xml ├── one_sub.xml ├── sequences.txt └── test_kmer.xml ├── Tests.txt ├── __init__.py ├── gengraph.py ├── gengraphTool.py ├── gengraph_newfunctions.py ├── module_testing.py ├── requirements.txt ├── unitTest_Alignment.py └── unitTest_GG.py /.gitignore: -------------------------------------------------------------------------------- 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