You could simplify you code a bit. For example: send_output could look something like

sub send_output{
    my ($out,$show_line,$show_file_name, $file_name,$line_count, $data
+) = @_;
    chomp($data); #strp end of line's to avoid double spacing.
    my $line;
  
    $line = "$file_name," if $show_file_name;
    $line .= "$line_count," if $show_line;
    $line .= $data;
    push @output,$line;
}
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