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#!/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
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