#!/bin/bash
if [ ! -f cluster ]; then
  echo
  echo "Download ibd-cluster program: cluster"
  echo
  wget https://faculty.washington.edu/browning/ibd-cluster.jar
fi

if [ ! -f ibd-cluster.test.vcf.gz ]; then
    echo
    echo "Download test VCF file: ibd-cluster.test.vcf.gz"
    echo
    wget https://raw.githubusercontent.com/browning-lab/ibd-cluster/master/test/ibd-cluster.test.vcf.gz
fi

if [ ! -f ibd-cluster.test.map ]; then
    echo
    echo "Download genetic map: ibd-cluster.test.map"
    echo
    wget https://raw.githubusercontent.com/browning-lab/ibd-cluster/master/test/ibd-cluster.test.map
fi

echo
echo "Run ibd-cluster analysis of test data"
echo
java -Xmx4g -jar ibd-cluster.jar gt=ibd-cluster.test.vcf.gz map=ibd-cluster.test.map out=ibd-cluster.test