├── .gitignore ├── .travis.yml ├── .travis └── install.sh ├── LICENSE ├── MANIFEST.in ├── README.md ├── conda_rck └── meta.yaml ├── docs ├── Adjacencies.md ├── AdjacencyGroups.md ├── Installation.md ├── README.md ├── Segments.md ├── Usage.md └── img │ └── RCK_Overview_vertical.png ├── rck ├── __init__.py ├── core │ ├── __init__.py │ ├── graph.py │ ├── ilp_gurobi.py │ ├── io.py │ ├── process.py │ └── structures.py ├── rck_run.py └── utils │ ├── __init__.py │ ├── adj │ ├── __init__.py │ ├── adjacency_group_inference.py │ ├── adjacency_group_process.py │ ├── adjacency_group_stats.py │ ├── analysis.py │ ├── convert.py │ ├── long_reads.py │ ├── main_chrs.txt │ ├── process.py │ ├── rck_adg_infer.py │ ├── rck_adg_process.py │ ├── rck_adg_stats.py │ ├── rck_adj_long_reads.py │ ├── rck_adj_process.py │ ├── rck_adj_rck2x.py │ ├── rck_adj_stats.py │ ├── rck_adj_x2rck.py │ └── stats.py │ ├── karyotype │ ├── __init__.py │ ├── analysis.py │ ├── rck_kar_graph.py │ └── rck_kar_stats.py │ ├── rck_input_refine.py │ └── scn │ ├── __init__.py │ ├── convert.py │ ├── process.py │ ├── rck_scnb.py │ ├── rck_scnt_process.py │ ├── rck_scnt_rck2x.py │ ├── rck_scnt_stats.py │ ├── rck_scnt_x2rck.py │ └── stats.py ├── setup.cfg ├── setup.py └── tests ├── __init__.py ├── test_graph.py └── test_structures.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aganezov/RCK/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aganezov/RCK/HEAD/.travis.yml -------------------------------------------------------------------------------- /.travis/install.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/aganezov/RCK/HEAD/.travis/install.sh 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