Metadata-Version: 2.1
Name: AlphaPeel
Version: 1.1.1
Summary: Multilocus and hybrid peeling
Author: Andrew Whalen
Author-email: Andrew Whalen <awhalen@roslin.ed.ac.uk>
License: Copyright (C) 2020 University of Edinburgh
        
        Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
        
Project-URL: Homepage, https://github.com/AlphaGenes/AlphaPeel
Project-URL: Bug Tracker, https://github.com/AlphaGenes/AlphaPeel/issues
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Description-Content-Type: text/markdown

# AlphaPeel

AlphaPeel is a software package for calling, phasing, and imputing genotype and sequence data in pedigree populations. This program implements single locus peeling, multi locus peeling, and hybrid peeling. A complete description of these methods is given in <a href="https://gsejournal.biomedcentral.com/articles/10.1186/s12711-018-0438-2">Hybrid peeling for fast and accurate calling, phasing, and imputation with sequence data of any coverage in pedigrees, Genetics Selection Evolution</a>.

## User guide

See `docs/source/index.rst` or PDF in the ZIP file in this repository.

## Conditions of use

AlphaPeel is part of a suite of software that our group has developed. It is fully and freely available for all use under the MIT License.

## Suggested Citation

Whalen, A, Ros-Freixedes, R, Wilson, DL, Gorjanc, G, Hickey, JM. (2018). Hybrid peeling for fast and accurate calling, phasing, and imputation with sequence data of any coverage in pedigrees. Genetics Selection Evolution; doi: <a href="https://doi.org/10.1186/s12711-018-0438-2"> https://doi.org/10.1186/s12711-018-0438-2</a>

## Requirements

* Python 3
* NumPy
* Numba

## Installation

    wget https://github.com/AlphaGenes/AlphaPeel/raw/main/AlphaPeel.zip
    unzip AlphaPeel.zip
    pip install AlphaPeel/AlphaPeel*.whl

## Build instructions

Run the following to build the Python wheel and user guide. You will need an installation of [Sphinx](https://www.sphinx-doc.org) and [LaTex](https://www.latex-project.org/get) to build the user guide.

    git clone --recurse-submodules https://github.com/AlphaGenes/AlphaPeel.git
    cd AlphaPeel
    
    mamba create -n AlphaPeel
    mamba activate AlphaPeel
    mamba install python=3.9
    pip install sphinx
    ./build_pipeline.sh
    pip install --force-reinstall dist/AlphaPeel*.whl
    
    cd example; ./runScript.sh

The wheel can be found in `dist/` and PDF of the user guide at `docs/build/latex/alphaplantimpute2.pdf`
