#!/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 *

echo 'Test 1'
vsearch --cluster_fast BioMarKs50k.fsa --id 0.97 --centroids test1.out
diff -u test1.out test1-expected.out 
echo 'PASS'
echo

echo 'Test 2'
vsearch --usearch_global query.fsa --db BioMarKs50k.fsa --id 0.9 --alnout test2.out
diff -u <(tail -n +3 test2.out) <(tail -n +3 test2-expected.out)
echo 'PASS'

