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  1. or download this
    [module1]

...
$;Chromosome$; = 
;;use --v for verbose summary
$;OTHER_ARGS$; = --v
  2. or download this
    [module1]

...
 $;Chromosome$; = "USER_INPUT_CHR.txt"
 ;;use --v for verbose summary
 $;OTHER_ARGS$; = --v
  3. or download this
    my ($template_name, $Prefix, $Seq1File,$Seq2File,$Align_Reference,$Chr
+omosome_list,$Reference,$KnownSites ) = @ARGV;

...
}
close $out_fh;
}