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

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

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

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

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

echo
echo "Run ibd-ends analysis of hap-ibd output"
echo "======================================="
echo
java -jar ibd-ends.jar gt=phased.vcf.gz map=genetic.map ibd=hap-ibd.out.ibd.gz out=ibd-ends.out quantiles=0.5,0.95