unless (@ARGV == 3) {
    print "Use as follows: perl program.pl in1.file in2.file output.file\n";
    die;
}

my $in1 = $ARGV[0];
my $in2 = $ARGV[1];
my $fout = $ARGV[2];

open ONE, $in1;
open TWO, $in2;
open foutname, ">$fout";

my %hash1;
my @hit;    

while (<ONE>){
    	chomp;
    	my @hit = split(/\t/, $_);
	#start them as "0" for "no duplicates"
    	$hash1{$hit[0]}=0;
	}
close ONE;

my @col;

while (<TWO>){
    	chomp;
    	my @col = split(/\t/, $_);
	#increment the counter if %hash1 has what we're 	looking for.
	++$hash1{$col[0]} if(exists($hash1{$col[0]}));
	}

my @dups = grep { $hash1{$_} > 0 } keys %hash1;
for my $k (@dups) {
	print foutname "$k\t$hash1{$k}\n";
	}
 
close TWO;
close foutname;