#!/bin/bash
set -e

pkg=tiddit
CUR_DIR=`pwd`

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 ${CUR_DIR}/debian/tests/data/* -a "${AUTOPKGTEST_TMP}"

cd "${AUTOPKGTEST_TMP}"
gunzip -r *
cat normal.sam | samtools view -Sb - > normal.bam
cat tumor.sam | samtools view -Sb - > tumor.bam

echo 'Test 1'
TIDDIT.py --sv --p_ratio 0.10 --bam tumor.bam -o test1 --ref ref.fa
echo 'PASS'

echo 'Test 2'
TIDDIT.py --sv --bam normal.bam -o test2 --ref ref.fa
echo 'PASS'

