#!/bin/sh -e
# http://dep.debian.net/deps/dep8/
# Autopkgtest: Test if beagle run analysis correctly
# Author: Dylan Aïssi <bob.dybian@gmail.com>
# Last-Update: 2016-06-17

pkg=beagle
if [ "$ADTTMP" = "" ] ; then
  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
fi
cd $ADTTMP
cp -a /usr/share/doc/${pkg}/examples/* $ADTTMP

BEAGLE_TEST='java -jar /usr/share/beagle/beagle.jar'

# Generate necessary files
zcat test.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.vcf.gz
zcat test.vcf.gz | cut -f1-9,191-200 | gzip > target.vcf.gz
java -jar /usr/share/beagle/bref.jar ref.vcf.gz

# Beagle with gt argument
$BEAGLE_TEST gt=test.vcf.gz out=out.gt

# Beagle with gl argument
$BEAGLE_TEST gl=test.vcf.gz out=out.gl

# Beagle with ref argument
$BEAGLE_TEST ref=ref.vcf.gz gt=target.vcf.gz out=out.ref

# Beagle with bref argument
$BEAGLE_TEST ref=ref.bref gt=target.vcf.gz out=out.bref

rm -f $ADTTMP/*
