├── .gitignore ├── .hgignore ├── LICENSE.md ├── MANIFEST.in ├── README.md ├── conda └── recipe │ └── meta.yaml ├── doc ├── model.pdf └── model.tm ├── examples └── mixing │ ├── ibbmm.yaml │ ├── ibmm.yaml │ ├── igmm.yaml │ ├── pyclone_beta_binomial.yaml │ ├── pyclone_binomial.yaml │ ├── tsv │ ├── README.txt │ ├── SRR385938.tsv │ ├── SRR385939.tsv │ ├── SRR385940.tsv │ └── SRR385941.tsv │ └── yaml │ └── parental_copy_number │ ├── SRR385938.yaml │ ├── SRR385939.yaml │ ├── SRR385940.yaml │ └── SRR385941.yaml ├── pyclone ├── __init__.py ├── cli.py ├── config.py ├── math_utils.py ├── multi_sample.py ├── paths.py ├── post_process │ ├── __init__.py │ ├── clusters.py │ ├── loci.py │ └── plot │ │ ├── __init__.py │ │ ├── _scatter.py │ │ ├── clusters.py │ │ ├── defaults.py │ │ ├── loci.py │ │ └── utils.py ├── pyclone_beta_binomial.py ├── pyclone_binomial.py ├── run.py ├── sampler.py ├── test │ ├── __init__.py │ └── profile_pyclone.py ├── trace.py └── utils.py └── setup.py /.gitignore: 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