#!/usr/bin/perl

use warnings;
use strict;

my $usage = "merge_bed.pl <input1> <input2> <output>";
my $input_1 = shift or die $usage;
my $input_2 = shift or die $usage;
my $output = shift or die $usage;

open my $in1, "<", "$input_1" or die "Cannot open $input_1: $!\n";
open my $in2, "<", "$input_2" or die "Cannot open $input_2: $!\n";
open my $out, ">", "$output" or die "Cannot open $output: $!\n";

my %bed_files = (); 

while ( <$in1> ) {
    chomp;
    my ($chrom, $start, $end, undef, undef, $strand) = split "\t";
    $bed_files{$chrom}{$start}[0] = $end; # you can save multiple values as an array, so both the end and strand and anything else you want
    $bed_files{$chrom}{$start}[1] = $strand;
}

while ( <$in2> ) {
    chomp;
    my ($chrom, $start, $end, undef, undef, $strand) = split "\t";
    $bed_files{$chrom}{$start}[0] = $end;
    $bed_files{$chrom}{$start}[1] = $strand;
}

for my $chrom (sort keys %bed_files) {
    for my $start (sort {$a <=> $b} keys %{$bed_files[$chrom}}) {
        # print out the results sorted by chromosome (or scaffold) and start site
        print $out "$chrom\t$start\t$bed_files{$chrom}{$start}[0]\t$bed_files{$chrom}{$start}[1]\n";
    }
}

close $in1;
close $in2;
close $out;
exit;