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|
#!/bin/bash
set -ex
pkg=stringtie
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 "${AUTOPKGTEST_TMP}"
gunzip -r *
for f in *.sam; do
outfile=${f::-4}.bam
cat $f | samtools view -Sb - > $outfile
done
arrins=("short_reads" "short_reads_and_superreads" "long_reads" "long_reads" \
"mix_short mix_long" "mix_short mix_long")
arrparms=("" "" "-L" "-L -G human-chr19_P.gff" "--mix" "--mix -G mix_guides.gff")
arrout=("short_reads" "short_reads_and_superreads" "long_reads" "long_reads_guided" \
"mix_reads" "mix_reads_guided")
arrmsg=("Short reads" "Short reads and super-reads" "Long reads" \
"Long reads with annotation guides" "Mixed reads" "Mixed reads with annotation guides")
for i in ${!arrmsg[@]}; do
fout="${arrout[$i]}.out.gtf"
/bin/rm -f $fout
fcmp="${arrout[$i]}.out_expected.gtf"
n=$i
echo $n
n=$((n+1))
echo "Test ${n}: ${arrmsg[$i]}"
fin=${arrins[$i]}.bam
if [[ ${arrins[$i]} =~ ^mix ]]; then
ins=( ${arrins[$i]} )
fin="${ins[0]}.bam ${ins[1]}.bam"
fi
echo ${arrparms[$i]} $fout $fin
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
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