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#!/usr/bin/env perl

...
    $filtered[$_][0] //= 'undef';
    printf $fmt, $_, @{$filtered[$_]};
}

*** Original:
0: undef column2 column3
...
0: 1     column2 column3
1: 12    column2 column3
2: 100   column2 column3

use warnings;
...
...
    # all warnings except XYZ in effect here
}
# all warnings in effect here