From 472f20cdb06dae796a8008d9f76485abc2cb66e7 Mon Sep 17 00:00:00 2001
From: Jia-Xing Yue <yjx1217@users.noreply.github.com>
Date: Fri, 12 Jul 2019 11:07:30 +0200
Subject: [PATCH] enhanced robustnesss

---
 vcf2model.pl | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/vcf2model.pl b/vcf2model.pl
index 93aa8f6..5e54ca8 100755
--- a/vcf2model.pl
+++ b/vcf2model.pl
@@ -8,7 +8,7 @@
 #  script: vcf2model.pl
 #  author: Jia-Xing Yue (GitHub ID: yjx1217)
 #  version: 1.0.0
-#  last edited: 2019.04.08
+#  last edited: 2019.07.12
 #  description: vcf2model.pl will characterize mutational profile for SNPs and INDELs
 #               based on user-provided vcf file.
 ##############################################################
@@ -141,7 +141,11 @@
   foreach my $alt_allele (@base) {
 	  if ($ref_allele ne $alt_allele) {
 	    if ($total_snp_count > 0) {
-		    $snp{$ref_allele}{$alt_allele}{'freq'} = $snp{$ref_allele}{$alt_allele}{'count'}/$total_snp_count;
+		    if (not exists $snp{$ref_allele}{$alt_allele}{'count'}) {
+		      $snp{$ref_allele}{$alt_allele}{'freq'} = 0;
+		    } else {
+		      $snp{$ref_allele}{$alt_allele}{'freq'} = $snp{$ref_allele}{$alt_allele}{'count'}/$total_snp_count;
+		    }
 		    print $snp_model_output_fh "$ref_allele->$alt_allele\t$snp{$ref_allele}{$alt_allele}{'freq'}\n";
 	    } else {
 		    print "!!! Warning! total_snp_count = 0! Set the frequency of $ref_allele->$alt_allele substitution as NA!\n";