orthanq

Uncerainty aware haplotype quantification using a Bayesian model that is based on collecting evidences from Varlociraptor.

Orthanq is under active development.

Installation

Orthanq is available as a Bioconda package and can be installed via:

mamba install orthanq

Haplotype quantification & HLA typing

Docs: https://orthanq.github.io/docs/index.html

Building for development and manual installation

The easiest way to build Orthanq is via Conda/Mamba. First, create the environment given by the environment.yml in this repository.

mamba env create -n orthanq-dev -f environment.yml

Second, activate the environment with

mamba activate orthanq-dev

Third, build Orthanq via

HDF5_DIR=$CONDA_PREFIX RUSTFLAGS='-L $CONDA_PREFIX/include' cargo build

Fourth, conda lib location is set via

export LD_LIBRARY_PATH=$CONDA_PREFIX/lib

Last, Orthanq can be built with:

cargo build    

or

cargo build --release