trimSoftClippedReads

bioinform · Nov 26, 2017 · 6198b63 · 6198b63
1 parent 6c2e5d4
commit 6198b63
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/utilities/trimSoftClippedReads.py b/utilities/trimSoftClippedReads.py
@@ -26,7 +26,8 @@
 
                 front_num = int( front_clipped.groups()[0] )
                 back_num  = int( back_clipped.groups()[0] )
-
+                read_i.cigarstring = re.sub(r'^[0-9]+S|[0-9]+S$', '', read_i.cigarstring)
+
                 qual_i = read_i.qual[front_num::][:-back_num]
 
                 read_i.seq = read_i.seq[front_num::][:-back_num]
@@ -76,7 +77,7 @@
         if read_i.has_tag('MC'):
             mate_cigar = read_i.get_tag('MC')
             if 'S' in mate_cigar:
-                new_cigar = re.sub(r'[0-9]+S', '', mate_cigar)
+                new_cigar = re.sub(r'^[0-9]+S|[0-9]+S$', '', mate_cigar)
                 read_i.set_tag(tag='MC', value=new_cigar, value_type='Z', replace=True)
 
         bamout.write(read_i)