Retain gt and gq vals in dragen std

Author: kjaisingh

src/svtk/svtk/standardize/std_dragen.py

@@ -151,6 +151,25 @@ def standardize_info(self, std_rec, raw_rec):
 
         return std_rec
 
+    def standardize_format(self, std_rec, raw_rec):
+        """
+        Retain GT and GQ. 
+        """
+
+        for sample, std_sample in zip(raw_rec.samples, self.std_sample_names):
+            gt = raw_rec.samples[sample]['GT']
+            gq = raw_rec.samples[sample]['GQ']
+            if self.call_null_sites:
+                if gt == (None, None):
+                    gt = (0, 1)
+                if gt == (None,):
+                    gt = (1,)
+            
+            std_rec.samples[std_sample]['GT'] = gt
+            std_rec.samples[std_sample]['GQ'] = gq
+
+        return std_rec
+
     def standardize_alts(self, std_rec, raw_rec):
         """
         Standardize Dragen ALT field.

src/svtk/svtk/standardize/std_dragen_cnv.py

@@ -73,26 +73,7 @@ def standardize_info(self, std_rec, raw_rec):
         std_rec.qual = raw_rec.qual
 
         return std_rec
-
-    def standardize_alts(self, std_rec, raw_rec):
-        """
-        Standardize Dragen CNV ALT field.
-
-        Replace with N and SVTYPE.
-        """
-
-        # Set ALT to SVTYPE tag
-        svtype = std_rec.info['SVTYPE']
-        simple_alt = f'<{svtype}>'
-        std_rec.alts = (simple_alt, )
-
-        # Set REF to null
-        stop = std_rec.stop
-        std_rec.ref = 'N'
-        std_rec.stop = stop
-
-        return std_rec
-
+    
     def standardize_format(self, std_rec, raw_rec):
         """
         Parse ./1 GTs for DUPs into 1/1.
@@ -118,3 +99,22 @@ def standardize_format(self, std_rec, raw_rec):
                 std_rec.samples[std_sample][source] = 0
 
         return std_rec
+
+    def standardize_alts(self, std_rec, raw_rec):
+        """
+        Standardize Dragen CNV ALT field.
+
+        Replace with N and SVTYPE.
+        """
+
+        # Set ALT to SVTYPE tag
+        svtype = std_rec.info['SVTYPE']
+        simple_alt = f'<{svtype}>'
+        std_rec.alts = (simple_alt, )
+
+        # Set REF to null
+        stop = std_rec.stop
+        std_rec.ref = 'N'
+        std_rec.stop = stop
+
+        return std_rec