Updated standardizer to mark inversions

broadinstitute · Jan 9, 2025 · 395d519 · 395d519
1 parent 9079a3b
commit 395d519
Showing 1 changed file with 13 additions and 8 deletions.
diff --git a/src/svtk/svtk/standardize/std_dragen.py b/src/svtk/svtk/standardize/std_dragen.py
@@ -98,8 +98,20 @@ def standardize_info(self, std_rec, raw_rec):
         std_rec.info['CHR2'] = chrB
         std_rec.stop = posB
 
+        # Update INV
+        isInv3, isInv5, matePos = checkInversion(raw_rec)
+        if isInv3 or isInv5:
+            std_rec.stop = matePos
+            std_rec.info['SVTYPE'] = 'INV'
+            std_rec.info['SVLEN'] = matePos - std_rec.pos
+
         # Update STRANDS
-        if svtype == 'BND':
+        if svtype == 'INV':
+            if isInv3:
+                strands = '++'
+            else:
+                strands = '--'
+        elif svtype == 'BND':
             strands = parse_bnd_strands(raw_rec.alts[0])
         elif svtype == 'DEL':
             strands = '+-'
@@ -129,13 +141,6 @@ def standardize_info(self, std_rec, raw_rec):
         # Update ALGORITHMS
         std_rec.info['ALGORITHMS'] = ['dragen']
 
-        # Update INV
-        isInv3, isInv5, matePos = checkInversion(raw_rec)
-        if isInv3 or isInv5:
-            std_rec.stop = matePos
-            std_rec.info['SVTYPE'] = 'INV'
-            std_rec.info['SVLEN'] = matePos - std_rec.pos
-
         return std_rec
 
     def standardize_alts(self, std_rec, raw_rec):