$file1 = $ARGV[0];

%hashfreq = ();
$freq = 0;
$geneold = "NA";
open(INPUTR,"<$file1") || die "Can't open \$file1 for reading.\n";
while($line=<INPUTR>){
    chomp $line;
    @toks = split(/\t/, $line);
    $gene = $toks[1];
    if ($gene =~ /^$geneold$/){
        if ($toks[0] >= $numold){
            $freq = $toks[0];
            print $toks[0]."\t".$numold."\t".$freq."\t".$gene."\n";
        } else {
            $freq = $numold;
        }
        $hashfreq{$toks[0]} = $freq;
    } else {
        $hashfreq{$toks[1]} = $toks[0];
    }
    $numold = $toks[0];
    $geneold = $toks[1];
}
close(INPUTR);

open(OUTD1,">output.txt");
open(INPUTR,"<$file1") || die "Can't open \$file1 for reading.\n";
while($line=<INPUTR>){
    chomp $line;
    @toks = split(/\t/, $line);
    $idgene = $toks[1];
    if (exists $hashfreq{$idgene}){
        print OUTD1 $line."\t".$hashfreq{$idgene}."\n";
        print $line."\t".$hashfreq{$idgene}."\n";
    }
}