this should fix the 1 off count of footprins discrepacy

The input file $data might still have or have not the header, thus it is checked.
The file "filtered_flagged.bed" however has no header, thus no check needs to be made.

bin/1.2_filter_motifs/compareBed.sh

@@ -276,20 +276,18 @@ first_line=`sed -n 1p $data | sed "s/$/\tcontains_maxpos\tsequence/"`
 if [[ ${first_line:0:1} == "#" ]]
 then
 	echo "$first_line" > $output
-	# add some final values to the log file
+	# add initial number of footprints to the log file
 	fp_initial=`cat $data | wc -l`
 	fp_initial=`expr $fp_initial - 1`
-	fp_final=`cat "$workdir"/filtered_flagged.bed | wc -l`
-	fp_final=`expr $fp_final - 1`
 	echo $fp_initial | sed 's/^/initial number of footprints: /g' >> "$workdir"/compareBed.stats
-	echo $fp_final | sed 's/^/number of footprints after subtract: /g' >> "$workdir"/compareBed.stats
 else
 	# output will be overwritten if it exists
 	rm -f $output
-	# add some final values to the log file
+	# add initial number of footprints to the log file
 	cat $data | wc -l | sed 's/^/initial number of footprints: /g' >> "$workdir"/compareBed.stats
-	cat "$workdir"/filtered_flagged.bed | wc -l | sed 's/^/number of footprints after subtract: /g' >> "$workdir"/compareBed.stats
 fi
+# add number of footprints after filtering to the log file
+cat "$workdir"/filtered_flagged.bed | wc -l | sed 's/^/number of footprints after subtract: /g' >> "$workdir"/compareBed.stats
 
 # add fasta sequences to bed and create fasta file
 out_fasta=`echo $output | sed "s|.bed$|.fasta|g"`