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

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

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

echo
echo "Run hap-ibd analysis of test data"
echo
java -jar hap-ibd.jar gt=target.truth.vcf.gz map=target.map out=hap-ibd.out