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            "License :: OSI Approved :: MIT License",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "inheritance models for mendelian diseases\n-----------------------------------------\n\n[![Build Status](https://travis-ci.org/brentp/inheritance.svg?branch=master)](https://travis-ci.org/brentp/inheritance)\n\nThis module is a general-purpose framework for evaluating if a family exihibits, for example, and autosomal dominant pattern.\nThe logic for this was tuned in [gemini](https://github.com/arq5x/gemini) but we make it available here as a more general purpose library to encourage:\n1. community driven improvements\n2. use outside of gemini\n3. more comprehensive testing\n\nFinding variants that match autosomal dominance in a trio, for example is very simple to find,\nhowever, after considering multiple generations, arbitrary family sizes, depth cutoffs, and unknown\ngenotypes and phenotypes to support to real-world datasets it becomes tedious and error-prone.\n\nSupported inheritance tests\n===========================\n\n+ autosomal dominant\n+ autosomal recessive\n+ de novo\n+ X-linked dominant, recessive, and de novo\n+ compound heterozygote\n+ mendelian violation\n\nUsage\n=====\n\nFor now, the use is via api only. Users can look at the tests to see how to use. Most functions have a signature like:\n\n```Python\n auto_dom(self, min_depth=0, gt_ll=False, strict=True, only_affected=True)\n```\n\nwhere the arguments enforce a minimum depth, a maximum genotype likelihood, strictness (mostly related to parent-offspring requirements)\nand wether to allow unaffecteds to have the variant (or be homozygous alt).\n\nToDo\n====\n1. add support for X-linked soon.\n2. add a simple example of running on a VCF+PED\n3. code coverage\n4. code documentation\n\nTesting\n=======\n\nTests can be run as:\n\n```\nnosetests --with-coverage -x --with-doctest --cover-package inheritance\n```\n\nOverview\n========\n\nthe generic code is in `inheritance/inheritance.py` and a specific implementation that we use in gemini is in `inheritance/pyeval.py`.\nTo make this available for a new resource, for example to `bcftools` we would look at the implementation of Filter in `inheritance/pyval.py`\nand make the generated strings match those expected by `bcftools`.",
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