don't bail on nucleotide check errors

print an error message and keep going

1 files changed, 1 insertions, 1 deletions

diff --git a/varscan2codon.pl b/varscan2codon.pl
index e45da77..6352a24 100755
--- a/varscan2codon.pl
+++ b/varscan2codon.pl
@@ -57,7 +57,7 @@ while (<$variants>) {
     # verify the nucleotide at $start is what's expected from the csv.
     my $check_nt = substr $genome, $start+$protein_start+$offset, 1;
     if ($check_nt ne $orig_nt) {
-        die "$name: nucleotide at position $pos is $check_nt, but expected $orig_nt.\n";
+        print STDERR "warning: $name (line $.): nucleotide at position $pos is $check_nt, but expected $orig_nt.\n";
     }
 
     my $codon = substr $genome, $start+$protein_start, 3;