From a0b19de6a07da91037787bac900453693147e0e4 Mon Sep 17 00:00:00 2001
From: Brian Cully <bjc@kublai.com>
Date: Mon, 12 Dec 2022 10:06:30 -0500
Subject: crash out early if codon lookup fails

---
 varscan2codon.pl | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/varscan2codon.pl b/varscan2codon.pl
index 8cd36c6..71d880f 100755
--- a/varscan2codon.pl
+++ b/varscan2codon.pl
@@ -61,6 +61,8 @@ while (<$variants>) {
     }
 
     my $codon = substr $genome, $start+$protein_start, 3;
+    die "$. - couldn't find amino acid for codon '$codon'\n" unless ($codon2aa{$codon});
+
     my $orig_aa = $aa2letter{$codon2aa{$codon}};
     substr $codon, $offset, 1, $new_nt;
     my $new_aa = $aa2letter{$codon2aa{$codon}};
-- 
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