file 1 (test)
chr1    30
chr2    20
chr2    50
chr3    80

file 2 (reference)
chr1    40
chr1    50
chr2    60
chr2    80
chr3    100

##</code><code>##

output
chr1    10
chr2    40
chr2    10
chr3    20

##</code><code>##

 #!/usr/bin/env perl
use strict;
use warnings;

my ( @cols, $p1, $p2, $p3, $p4, @sec, @cols2 );

@ARGV or die "No input file specified";

open my $first , '<',$ARGV[0] or die "Unable to open input file: $!";
open my $second,'<', $ARGV[1] or die "Unable to open input file: $!";

print scalar <$first>;
<$second>; #...throw away first line...
while (<$first>) {
    @cols = split /\s+/;
    $p1   = $cols[0];
    $p2   = $cols[1];
    #print $p1;
    while (<$second>) {
        @cols2 = split /\s+/;
        $p3   = $cols2[0];
        $p4   = $cols2[1];
      
        if ($p3 eq $p1) {
            print "yes";
        }
    }
}