#!/bin/sh

set -e
pkg=`dpkg-parsechangelog | sed -n 's/^Source: //p'`
examplesdir=/usr/share/doc/$pkg/examples
WORKDIR=$(mktemp -d)
cd $WORKDIR
for file in reference/lambda_virus.fa.gz reads/reads_1.fq.gz 
do
	extracted=`echo $file | awk -F/ '{print $NF}'`
        zcat $examplesdir/$file >${extracted%.gz}
done

bowtie2-build lambda_virus.fa lambda_virus >/dev/null 2>&1 
bowtie2 -x lambda_virus -U reads_1.fq -S eg1.sam >/dev/null 2>&1
