Merge branch 'master' into dev

CLAM/preprocessor.py

@@ -116,6 +116,7 @@ def filter_bam_multihits(filename, max_tags, max_hits, out_dir, read_tagger_meth
 			if read_tag==-1:
 				continue
 			read.tags += [('RT', read_tag)] ## add the tag
+
 			tagged_read = pysam.AlignedSegment()
 			tagged_read.query_name = read.query_name
 			tagged_read.query_sequence = 'N'
@@ -239,17 +240,17 @@ def filter_bam_maxtags(obam_fn, ibam_fn, max_tags=1):
 				last_pos = read.positions[0]
 				stack = [read]
 				for new_alignment in new_alignment_list:
-					new_alignment.query_sequence = '*'
-					new_alignment.query_qualities = '0'
+					#new_alignment.query_sequence = '*'
+					#new_alignment.query_qualities = '0'
 					_ = obam.write(new_alignment)
 			else:
 				stack.append(read)
 		new_alignment_list, collapse_dict = collapse_stack(stack, collapse_dict, max_tags)
 		output_counter += len(new_alignment_list)
 		last_pos = read.positions[0]
 		for new_alignment in new_alignment_list:
-			new_alignment.query_sequence = '*'
-			new_alignment.query_qualities = '0'
+			#new_alignment.query_sequence = '*'
+			#new_alignment.query_qualities = '0'
 			_ = obam.write(new_alignment)
 	ibam.close()
 	obam.close()