From 7e2e3eb29d9b8cd616458b332f77bd89ac5179e3 Mon Sep 17 00:00:00 2001
From: Shifu Chen <chen@haplox.com>
Date: Sun, 22 Oct 2017 09:06:35 +0800
Subject: [PATCH] fix VCF indel position issue

---
 src/mutation.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/mutation.cpp b/src/mutation.cpp
index 8fe0e65..b3e89ea 100644
--- a/src/mutation.cpp
+++ b/src/mutation.cpp
@@ -252,7 +252,7 @@ vector<Mutation> Mutation::parseVcf(string vcfFile, string refFile) {
             ss<<cds<<"_";
         ss<<chrom<<"_"<<v.pos<<"_"<<v.ref<<">"<<v.alt;
         string name = ss.str();
-        string left = ref[chrom].substr(v.pos-25-v.ref.length(), 25);
+        string left = ref[chrom].substr(v.pos-25-1, 25);
         str2upper(left);
         string center = v.alt;
         string right = ref[chrom].substr(v.pos+v.ref.length()-1, 25);