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

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

if [ ! -f outgroup.ids ]; then
    echo
    echo "Download outgroup sample identifers: outgroup.ids"
    echo
    wget https://raw.githubusercontent.com/browning-lab/sprime/master/test/outgroup.ids
fi

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

echo
echo "Run sprime analysis of test data"
echo
java -jar sprime.jar gt=three.segments.vcf.gz outgroup=outgroup.ids map=three.segments.map out=sprime.out