├── .gitignore ├── Readme.md ├── __init__.py ├── benchmarking ├── Readme.md ├── all_mappers │ ├── chromosomes.txt │ ├── haplotypes.txt │ └── run.sh ├── analyse_variants_vs_reads_mapped.py ├── create_roc_plots.sh ├── find_rare_variants.py ├── hisat2_extract_snps_haplotypes_VCF.py ├── two_step_approach │ ├── chromosomes.txt │ ├── haplotypes.txt │ └── run.sh ├── two_step_approach_15x │ ├── chromosomes.txt │ ├── haplotypes.txt │ └── run.sh ├── two_step_approach_7.5x │ ├── chromosomes.txt │ ├── haplotypes.txt │ └── run.sh ├── two_step_approach_vg │ ├── chromosomes.txt │ ├── haplotypes.txt │ └── run.sh └── vg_sim_pos_compare.py ├── scripts ├── map_vg └── two_step_map ├── setup.py ├── tests └── hybridtesting.py └── two_step_graph_mapper ├── __init__.py ├── command_line_interface.py ├── coordinate_mappings.py ├── path_predicter.py ├── project_alignments.py └── util.py /.gitignore: -------------------------------------------------------------------------------- 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