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#!/bin/bash
set -e
pkg=delly
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
cp -a ${CUR_DIR}/example/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
echo -e "\e[93m\e[1mRunning Tests\e[0m"
echo -e "\e[93m\e[1mTest 1\e[0m"
delly call -o sr.bcf -g ref.fa sr.bam
echo -e "\e[93m\e[1mTest 2\e[0m"
delly lr -g ref.fa lr.bam -o lr.vcf
echo -e "\e[93m\e[1mTest 3\e[0m"
delly cnv -g ref.fa -m map.fa.gz sr.bam -o cnv.vcf
if [[ -f sr.bcf ]] && [[ -f lr.vcf ]] && [[ -f cnv.vcf ]]
then
echo -e "\e[92m\e[1mPASS\e[0m"
else
echo -e "\e[1;31mFAILED!"
fi
|
