the max_pos is the index, and so add always 1 after calculating it. O…

…therwise it could be 0 as index

bin/1.1_footprint_extraction/footprints_extraction.py

@@ -143,6 +143,8 @@ def save_footprint(footprint_count, footprint_scores, peak_footprints, chromosom
 		else:
 			max_pos = first_max_pos
 
+		max_pos = max_pos + 1 #as the index of an array starts with 0
+
 		#calculate the score for the current footprint as mean of all scores from the bigwig file
 		footprint_score = np.mean(footprint_scores)
 
@@ -527,6 +529,10 @@ def write_to_bed_file(all_footprints, sorted_output_file_name):
 
 	#write each footprint line for line to the output file
 	for footprint in all_footprints:
+		#if footprint[1]['start'] >= footprint[1]['end']:
+		#	print(footprint)
+		#if footprint[1]['max_pos'] == 0:
+		#	print(footprint)
 		output_file.write('\t'.join([footprint[1]['chromosom'], str(footprint[1]['start']), str(footprint[1]['end']), footprint[0], str(round(footprint[1]['score'], 6)), '.', str(footprint[1]['len']), str(footprint[1]['max_pos']), ';'.join(footprint[1]['bonus'])]) + '\n')
 
 	output_file.close()