#!/bin/bash
set -e

pkg=vsearch

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

cd "${AUTOPKGTEST_TMP}"
gunzip -r *

function compare_cksum()
{
	# $1: file whose md5sum needs to be tested
	# $2: expected checksum
	if [ "$(cat $1 | md5sum | awk '{print $1}')" != "$2" ]
	then
		echo "Checksums do not match"
		exit 1
	fi

}

echo 'Test 1'
vsearch --cluster_fast BioMarKs50k.fsa --id 0.97 --centroids test1.out
compare_cksum test1.out f83633b2f3d9891122056f62b7f4d863
echo 'PASS'
echo

echo 'Test 2'
vsearch --usearch_global query.fsa --db BioMarKs50k.fsa --id 0.9 --alnout test2.out
(tail -n +3 test2.out) > test2_.out
compare_cksum test2_.out a84f0fe81dfac71bef52eb715bfb9404
echo 'PASS'

