Merge pull request #184 from oncokb/update-sv

Support additional SV headers

Author: zhx828

AnnotatorCore.py

@@ -196,9 +196,9 @@ def setsampleidsfileterfile(f):
                           GC_VAR_ALLELE_1_HEADER, GC_VAR_ALLELE_2_HEADER]
 
 # columns for structural variant annotation
-SV_GENEA_HEADER = ['SITE1_GENE', 'GENEA', 'GENE1']
-SV_GENEB_HEADER = ['SITE2_GENE', 'GENEB', 'GENE2']
-SV_TYPE_HEADER = ['SV_CLASS_NAME', 'SV_TYPE']
+SV_GENEA_HEADER = ['SITE1_GENE', 'GENEA', 'GENE1', 'SITE1_HUGO_SYMBOL']
+SV_GENEB_HEADER = ['SITE2_GENE', 'GENEB', 'GENE2', 'SITE2_HUGO_SYMBOL']
+SV_TYPE_HEADER = ['SV_CLASS_NAME', 'SV_TYPE', 'CLASS']
 SV_TYPES = ['DELETION', 'TRANSLOCATION', 'DUPLICATION', 'INSERTION', 'INVERSION', 'FUSION', 'UNKNOWN']
 
 UNKNOWN = 'UNKNOWN'