As mentioned before, you're invoking the subroutine (it's invoked during  GetOptions() processing) before the array is initialized. Eg.:

c:\@Work\Perl\monks>perl -wMstrict -le
"S('before');
 ;;
 my @ra = qw(A C T G);
 ;;
 S('after');
 ;;
 sub S { print qq{$_[0] initialization: [@ra] }; }
"
before initialization: []
after initialization: [A C T G]
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