#!/bin/bash
set -e

pkg=gasic

export LC_ALL=C.UTF-8
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}"

gunzip -r *

cd genomes

bowtie-build dwv.fasta dwv.fasta
bowtie-build vdv1.fasta vdv1.fasta             
bowtie-build vdv1dwv9.fasta vdv1dwv9.fasta
bowtie-build vdv1dwv5.fasta vdv1dwv5.fasta

cd ..

run_mappers names reads/SRR059298_subset.fastq -i ./genomes/%s.fasta -o ./SAM/mapped_%s.sam -m bowtie
