From 5b8199ede44de44941cc516ad69829bce23b586c Mon Sep 17 00:00:00 2001
From: Craig Bielski <bielskic@s01.cbio.private>
Date: Fri, 6 May 2016 10:46:27 -0400
Subject: [PATCH] quick fix

---
 filter_ffpe.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/filter_ffpe.R b/filter_ffpe.R
index 97a5e66..4c8b4b1 100755
--- a/filter_ffpe.R
+++ b/filter_ffpe.R
@@ -23,8 +23,8 @@ add_mut_tri <- function(maf) {
   ### reverse complement Ref_Tri if ref is either G or A
   maf[Variant_Type == "SNP",
       Ref_Tri := ifelse(Reference_Allele %in% c('G', 'A'),
-                        revc(Ref_Tri),
-                        Ref_Tri)]
+                        revc(TriNuc),
+                        TriNuc)]
   ### reverse complement Tumor_Seq_Allele2 if ref is either G or A
   Tumor_Seq_Allele2_CT <- maf[Variant_Type == "SNP",
                               ifelse(Reference_Allele %in% c('G', 'A'),