From 337f04c364a2c291a4df23c31f5aff4070d08b47 Mon Sep 17 00:00:00 2001
From: Brian Cully <bjc@spork.org>
Date: Fri, 19 Jan 2024 20:33:00 -0500
Subject: don't bail on nucleotide check errors

print an error message and keep going
---
 varscan2codon.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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;
-- 
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