Intersect two hash tables in Perl

intersect.pl

#!/usr/bin/env perl

use strict;
use warnings;
use Getopt::Long;

my $fileA = undef;
my $fileB = undef;
my $result = GetOptions("fileA=s" => \$fileA, "fileB=s" => \$fileB);

sub convert_file_into_ht {
    my ($fn) = @_;
    open(my $fh, '<:encoding(UTF-8)', $fn) or die "$!\n";
    my $line = <$fh>;
    my $ht = undef;
    while(<$fh>) {
        chomp;
        my ($location, $position) = split("\t", $_);
        if (! exists $ht->{$location}) {
            $ht->{$location} = [];
        }
        push(@{$ht->{$location}}, int($position));
    }
    close($fh);
    return \%{$ht};
}

my $aRef = convert_file_into_ht($fileA);
my $bRef = convert_file_into_ht($fileB);

print("LOCATION\tPOSITION\n");
foreach my $key (keys %{$aRef}) {
    my $aVals = $aRef->{$key};
    if (exists $bRef->{$key}) {
        my $bVals = $bRef->{$key};
        my $intersection = undef;
        for (@{$aVals}) {
            if ($_ ~~ @{$bVals}) {
                push(@{$intersection}, $_);
            }
        }
        if (defined $intersection) {
            for (@{$intersection}) {
                print("$key\t$_\n");
            }
        }
    }
}

Usage:

$ intersect.pl --fileA="A.txt" --fileB="B.txt" > answer.txt