Fix #231 Allow N's in bam output (Try 2)

pinellolab · Jul 14, 2022 · b0b7d41 · b0b7d41
1 parent c460b3e
commit b0b7d41
Showing 1 changed file with 7 additions and 6 deletions.
diff --git a/CRISPResso2/CRISPRessoShared.py b/CRISPResso2/CRISPRessoShared.py
@@ -278,12 +278,13 @@ def slugify(value): #adapted from the Django project
 
 
 CIGAR_LOOKUP = {
-    ('A', 'A'): 'M', ('A', 'C'): 'M', ('A', 'T'): 'M', ('A', 'G'): 'M',
-    ('C', 'A'): 'M', ('C', 'C'): 'M', ('C', 'T'): 'M', ('C', 'G'): 'M',
-    ('T', 'A'): 'M', ('T', 'C'): 'M', ('T', 'T'): 'M', ('T', 'G'): 'M',
-    ('G', 'A'): 'M', ('G', 'C'): 'M', ('G', 'T'): 'M', ('G', 'G'): 'M',
-    ('A', '-'): 'I', ('T', '-'): 'I', ('C', '-'): 'I', ('G', '-'): 'I',
-    ('-', 'A'): 'D', ('-', 'T'): 'D', ('-', 'C'): 'D', ('-', 'G'): 'D',
+    ('A', 'A'): 'M', ('A', 'C'): 'M', ('A', 'T'): 'M', ('A', 'G'): 'M', ('A', 'N'): 'M',
+    ('C', 'A'): 'M', ('C', 'C'): 'M', ('C', 'T'): 'M', ('C', 'G'): 'M', ('C', 'N'): 'M',
+    ('T', 'A'): 'M', ('T', 'C'): 'M', ('T', 'T'): 'M', ('T', 'G'): 'M', ('T', 'N'): 'M',
+    ('G', 'A'): 'M', ('G', 'C'): 'M', ('G', 'T'): 'M', ('G', 'G'): 'M', ('G', 'N'): 'M',
+    ('N', 'A'): 'M', ('N', 'C'): 'M', ('N', 'T'): 'M', ('N', 'G'): 'M', ('N', 'N'): 'M',
+    ('A', '-'): 'I', ('T', '-'): 'I', ('C', '-'): 'I', ('G', '-'): 'I', ('N', '-'): 'I',
+    ('-', 'A'): 'D', ('-', 'T'): 'D', ('-', 'C'): 'D', ('-', 'G'): 'D', ('-', 'N'): 'D',
     }
 
 cigarUnexplodePattern = re.compile(r'((\w)\2{0,})')