From 7bebc6a579b5bc62ab6fc6b9c1d3c4133d4ff982 Mon Sep 17 00:00:00 2001
From: Uma Paila <udp3f@eservices.virginia.edu>
Date: Mon, 7 Oct 2013 16:39:55 -0400
Subject: [PATCH] add VEP format for version 73

---
 gemini/gemini_load_chunk.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/gemini/gemini_load_chunk.py b/gemini/gemini_load_chunk.py
index 8b08a26a..e132e951 100755
--- a/gemini/gemini_load_chunk.py
+++ b/gemini/gemini_load_chunk.py
@@ -171,10 +171,14 @@ def _is_proper_vep_input(self):
         Test whether the VCF header meets expectations for
         proper execution of VEP for use with Gemini.
         """
+        #support versions >2.4<73
         format = "Consequence|Codons|Amino_acids|Gene|HGNC|Feature|EXON|PolyPhen|SIFT".upper()
+        #support version 73
+        format73 = "Consequence|Codons|Amino_acids|Gene|SYMBOL|Feature|EXON|PolyPhen|SIFT".upper()
 
         if 'CSQ' in self.vcf_reader.infos and \
-                format in str(self.vcf_reader.infos['CSQ']).upper():
+                (format in str(self.vcf_reader.infos['CSQ']).upper() or \
+                format73 in str(self.vcf_reader.infos['CSQ']).upper()):
             return True
         return False