#!/bin/bash
set -e

pkg="maq"

if [ "$AUTOPKGTEST_TMP" = "" ] ; then
  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi

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

cd $AUTOPKGTEST_TMP
find . -name "*.gz" -exec gunzip \{\} \;

echo '---Fasta2bfa Test---'
/usr/bin/maq fasta2bfa test.fa test.bfa
echo '---Fastaq2bfq Test---'
/usr/bin/maq fastq2bfq test.fastq part1.bfq
/usr/bin/maq fastq2bfq test.fastq part2.bfq
echo '---Map Test---'
/usr/bin/maq map part1.map test.fa part1.bfq
/usr/bin/maq map part2.map test.fa  part2.bfq
echo '---Mapmerge Test---'
/usr/bin/maq mapmerge aln.map part1.map part2.map
echo '---Assemble Test---'
/usr/bin/maq assemble cns.cns test.fa aln.map
