#!/usr/bin/env bash

function unpack_test_data() {

t=test_data.tar.gz

if [ ! -f $t ]; then

echo "Error: file $t not found!"

exit 1

fi

echo "..unpacking test data.."

echo

tar -xzf $t

if [ ! -f test_data/human-chr19_P.gff ]; then

echo "Error: invalid test data archive?"

exit 1

fi

/bin/rm -f test_data.tar.gz

}

#if [ ! -f test_data/human-chr19_P.gff ]; then

if [ -f test_data.tar.gz ]; then

#extract the tarball and rename the directory

echo "..Using existing ./test_data.tar.gz"

unpack_test_data

else

echo "..Downloading test data.."

#use curl to fetch the tarball from a specific github release or branch

curl -sLJO https://github.com/gpertea/stringtie/raw/test_data/test_data.tar.gz

unpack_test_data

fi

# fi

cd test_data

# array element format:

#

arrins=("short_reads" "short_reads_and_superreads" "long_reads" "long_reads")

arrparms=("" "" "-L" "-L -G human-chr19_P.gff")

arrout=("short_reads" "short_reads_and_superreads" "long_reads" "long_reads_guided")

arrmsg=("Short reads" "Short reads and super-reads" \

"Long reads" "Long reads with annotation guides")

for i in ${!arrmsg[@]}; do

fout="${arrout[$i]}.out.gtf"

/bin/rm -f $fout

fcmp="${arrout[$i]}.out_expected.gtf"

if [ ! -f $fcmp ]; then

echo "Error: file $fcmp does not exist! Re-download test data."

exit 1

fi

n=$i

((n++))

echo "Test ${n}: ${arrmsg[$i]}"

fin=${arrins[$i]}.bam

../stringtie ${arrparms[$i]} -o $fout $fin

if [ ! -f $fout ]; then

echo "Error: file $fout not created! Failed running stringtie on $fin"

exit 1

fi

if diff -q -I '^#' $fout $fcmp &>/dev/null; then

echo " OK."

else

echo "Error: test failed, output $fout different than expected ($fcmp)!"

exit 1

fi

done