handling for if no reference provided and reference_seq not in GVF

Author: khetherin

convert_gvf_to_vcf/convertGVFtoVCF.py

@@ -516,7 +516,11 @@ def get_ref(self):
         if "Reference_seq" in self.vcf_value.keys():
             return self.vcf_value["Reference_seq"] # attributes:reference_seq
         else:
-            reference_allele = extract_reference_allele(self.assembly, self.chrom, self.pos)
+            if self.assembly:
+                reference_allele = extract_reference_allele(self.assembly, self.chrom, self.pos)
+            else:
+                print("WARNING: No reference provided. Placeholder inserted for Reference allele.")
+                reference_allele = "."
             return reference_allele
 
     def __str__(self):