├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── demos └── demo-A12.sh ├── doc └── decifer.png ├── man └── man-decifer.md ├── scripts ├── README.md ├── best.seg.ucn ├── cn_states.txt ├── input_from_varscan │ ├── README.md │ └── create_input.ipynb └── vcf_2_decifer.py ├── setup.py ├── src └── decifer │ ├── __init__.py │ ├── __main__.py │ ├── config.py │ ├── coordinate_ascent.py │ ├── cpp │ ├── CMakeLists.txt │ ├── arg_parser.cpp │ ├── arg_parser.h │ ├── basematrix.cpp │ ├── basematrix.h │ ├── beta_distribution.hpp │ ├── generatestatetreesmain.cpp │ ├── mergestatetreesmain.cpp │ ├── readmatrix.cpp │ ├── readmatrix.h │ ├── solver.cpp │ ├── solver.h │ ├── stategraph.cpp │ ├── stategraph.h │ ├── statetree.cpp │ ├── statetree.h │ ├── utils.cpp │ └── utils.h │ ├── fileio.py │ ├── generator.py │ ├── mutation.py │ ├── new_coordinate_ascent.py │ ├── parse_args.py │ ├── process_input.py │ ├── progress_bar.py │ └── state_trees.txt ├── test.png └── test ├── data ├── PDAC │ ├── decifer_input.tsv │ └── purity.tsv ├── decifer_Outliers_output.tsv ├── decifer_clusterCIs.tsv ├── decifer_input.tsv ├── decifer_model_selection.tsv ├── decifer_output.tsv ├── generate_true_output.sh ├── purity.tsv ├── segfile.tsv └── snpfile.tsv ├── decifer_Outliers_output.tsv ├── decifer_clusterCIs.tsv ├── decifer_model_selection.tsv ├── decifer_output.tsv ├── plot_results.ipynb ├── test.png └── test_end2end.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphael-group/decifer/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raphael-group/decifer/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 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