From c0c8775cb79412d515d43c7f1dc0db95b7f795a9 Mon Sep 17 00:00:00 2001
From: Brian Cully <bjc@kublai.com>
Date: Mon, 12 Dec 2022 10:05:42 -0500
Subject: strip newlines in input before codon lookup

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

diff --git a/varscan2codon.pl b/varscan2codon.pl
index e0eaaf8..8cd36c6 100755
--- a/varscan2codon.pl
+++ b/varscan2codon.pl
@@ -33,6 +33,7 @@ my $variants = IO::File->new($ARGV[2])
     or die "Couldn't open $ARGV[1] for reading: $!\n";
 my $name = 'unnamed-change';
 while (<$variants>) {
+    chomp;
     my ($name_maybe, $ref, $pos, $orig_nt, $new_nt) = split /,/;
     $name = $name_maybe if length($name_maybe) > 0;
 
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