#!/bin/bash
set -e

pkg="bwa-mem2"

if [ "$AUTOPKGTEST_TMP" = "" ] ; then
  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
fi

cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP

cd $AUTOPKGTEST_TMP

bwa-mem2 index ref.fa
bwa-mem2 mem ref.fa reads.fq > aln-se.sam 
bwa-mem2 mem ref.fa read1.fq read2.fq > aln-pe.sam 

echo "PASS"
