#!/bin/bash
set -e

CUR_DIR=`pwd`
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

cd "${AUTOPKGTEST_TMP}"
cp ${CUR_DIR}/debian/tests/test.fastq .
cat test.fastq | gzip > test.fastq.gz
mkdir subdir
cp test.fastq test.fastq.gz subdir

echo "Test recursive directory descent and dedup"
catfishq --log debug --recursive --dedup --out catfishq.dedup.test.out .

# with dedup, the output should match the input
diff -q catfishq.dedup.test.out test.fastq

echo "PASS"
