#!/bin/bash
set -e

pkg="bwa"

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 index ref.fa
bwa mem ref.fa reads.fq > aln-se.sam 
bwa mem ref.fa read1.fq read2.fq > aln-pe.sam 
bwa aln ref.fa read1.fq > aln_sa.sai
bwa samse ref.fa aln_sa.sai read1.fq > aln-se.sam
bwa aln ref.fa read2.fq > aln_sa2.sai
bwa sampe ref.fa aln_sa.sai aln_sa2.sai read1.fq read2.fq > aln-pe.sam
bwa bwasw ref.fa reads.fq > aln.sam

echo "PASS"
