Don't use external expr for arithmetic

The external expr command exits with a non-zero exit status, if the
expression evaluates to zero. This is in conflict with the -e setting
of this script.

Bash can do arithmetic by itself with $(( and )) which doesn't have this
complexity, so use that instead.

Adapting_new_script_for_computing_cluster.sh

@@ -148,10 +148,10 @@ execute() {
 	map=$(grep -Po '[0-9, /.]*% overall alignment rate' $id.mappingStats.txt | grep -Po '[0-9,/.]*')
 	mapFrac=$(printf "%.4f" $(echo $map / 100 | bc -l))
 	dedup=$(printf "%.4f" $(grep -Po 'Unknown Library.*' dedup/${id}_dedupMetric.txt | awk '{print $10}'))
-	filtered=$(expr $(samtools view -c dedup/${id}_dedup.bam) / 2)
-	fripReads=$(expr $(bedtools intersect -a dedup/${id}_dedup.bam -b dedup_peaks/${id}_peaks.narrowPeak -u -ubam | samtools view -c) / 2)
+	filtered=$(( $(samtools view -c dedup/${id}_dedup.bam) / 2 ))
+	fripReads=$(( $(bedtools intersect -a dedup/${id}_dedup.bam -b dedup_peaks/${id}_peaks.narrowPeak -u -ubam | samtools view -c) / 2 ))
 	FRiP=$(printf "%.4f" $(echo $fripReads / $filtered | bc -l))
-	peaks=$(expr $(wc -l <"dedup_peaks/${id}_peaks.narrowPeak") - 1)
+	peaks=$(( $(wc -l <"dedup_peaks/${id}_peaks.narrowPeak") - 1 ))
 	echo -e "$id\t$fragments\t$filtered\t$mapFrac\t$dedup\t$FRiP\t$peaks" >> cnt_gata_qc_metrics.txt
 
 	# Here I have no idea how to transfer this