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  1. or download this
    my %file1;
while(<INPUT1>){
    chomp;
...
}
print "Processed $. lines from $ARGV[0] file\n";
close(INPUT1);
  2. or download this
    while(<INPUT2>){
    chomp;
    my @current_line  = split /\t/;
...
}

close (INPUT2);
  3. or download this
        # eliminate unqualified lines early
    next unless $current_line[2] ==1 && $current_line[3] >= 3;