relate_lib

C++ library containing functions for parsing/dumping Relate output files

Leo Speidel
Department of Statistics, University of Oxford, Oxford, UK

Requirements

C++11 and cmake version 3.1.

Installation

Clone/fork from this github repository to a local directory. Then execute

cd PATH_TO_RELATE_LIB/
mkdir build
cd build
cmake ..
make

Documentation

Conversion from tskit format

relate_lib/bin/Convert --mode ConvertFromTreeSequence \
              --anc example.anc.gz \
              --mut example.mut.gz \
              -i example

Conversion to tskit format

relate_lib/bin/Convert --mode ConvertToTreeSequence \
              --anc example.anc.gz \
              --mut example.mut.gz \
              -o example

Thanks to Nathaniel S. Pope, you can now also specify an argument that compresses these Relate-converted tree sequences by assigning the same age to nodes with identical descendant sets across adjacent trees.

relate_lib/bin/Convert --mode ConvertToTreeSequence \
              --compress \
              --anc example.anc.gz \
              --mut example.mut.gz \
              -o example

C++ library

Please see ./include/example/Example.cpp for example code and ./example/example.sh for examples and how to run them.