Final dragen standardizer cleanup

broadinstitute · Jan 21, 2025 · f4b502f · f4b502f
1 parent 266734e
commit f4b502f
Showing 1 changed file with 5 additions and 6 deletions.
diff --git a/src/svtk/svtk/standardize/std_dragen.py b/src/svtk/svtk/standardize/std_dragen.py
@@ -75,18 +75,17 @@ def standardize_info(self, std_rec, raw_rec):
         5. Define ALGORITHMS.
         """
 
-        # Update SVTYPE
+        # Retrieve record data
         svtype = raw_rec.info['SVTYPE']
-
-        # Check INV
         isInv3, isInv5, matePos = checkInversion(raw_rec)
         if isInv3 or isInv5:
             svtype = 'INV'
 
-        # Check TANDEM DUP
-        if 'DUPSVLEN' in raw_rec.info:
-            svtype = 'DUP'
+        # Convert INS to DUP for tandem duplications
+        # if 'DUPSVLEN' in raw_rec.info:
+            # svtype = 'DUP'
 
+        # Update SVTYPE
         std_rec.info['SVTYPE'] = svtype
 
         # Update ID