Remove multi-mapping reads

akikuno · Mar 25, 2024 · d00bea8 · d00bea8
1 parent 9d55830
commit d00bea8
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/src/DAJIN2/core/preprocess/mapping.py b/src/DAJIN2/core/preprocess/mapping.py
@@ -43,6 +43,10 @@ def to_sam(
             query_seq = QUERY_SEQ.upper()
             query_qual = QUERY_QUAL
 
+            # Skip multi-mapping reads
+            if hit.mapq == 0:
+                continue
+
             # Report flag
             if hit.is_primary:
                 flag = 0 if hit.strand == 1 else 16