check_reference_allele was erroring if chr value not found

MRCIEU · Feb 9, 2021 · f974475 · f974475
1 parent e1867b9
commit f974475
Showing 1 changed file with 9 additions and 5 deletions.
diff --git a/gwas.py b/gwas.py
@@ -44,11 +44,15 @@ def reverse_sign(self):
             self.alt_freq = None
 
     def check_reference_allele(self, fasta):
-        assert self.ref == fasta.fetch(
-            reference=self.chrom,
-            start=self.pos - 1,
-            end=self.pos + len(self.ref) - 1
-        ).upper()
+        try:
+            x = fasta.fetch(
+                reference=self.chrom,
+                start=self.pos - 1,
+                end=self.pos + len(self.ref) - 1
+            ).upper()
+        except:
+            assert 1 == 2
+        assert self.ref == x
 
     def normalise(self, fasta, padding=100):
         # TODO handle padding edge cases