chr1	100	159	0
chr1	200	260	0
chr1	500	750	0
chr3	450	700	0
chr4	100	300	0
chr7	350	600	0
chr9	100	125	0
chr11	679	687	0
chr24	100	200	0
chr24	300	400	0

##</code><code>##

chr1	104	104	0	0	+
chr1	145	145	0	0	+
chr1	205	205	0	0	+
chr1	600	600	0	0	+
chr3	500	500	0	0	+
chr4	150	150	0	0	+
chr4	175	175	0	0	+
chr7	400	400	0	0	+
chr7	550	550	0	0	+
chr9	100	100	0	0	+
chr11	680	680	0	0	+
chr11	681	681	0	0	+
chr24	105	105	0	0	+
chr24	110	110	0	0	+
chr24	350	350	0	0	+

##</code><code>##

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

my $region = 'testReg.txt';
my $position = 'testPos.txt';
my $writeOut = '>>testOut.txt';

open(R,$region) or die "error reading file";
open(OUT,$writeOut) or die "error writing to the file ";
open(P, $position) or die "error reading file ";

my $rline; 
my $pline; 

while ($rline=<R>) {	
	chomp($rline);
	my @r_arr=split("\t",$rline);
		
		chomp($r_arr[0]);
		my @rID = split("r",$r_arr[0]);
		$r_arr[0] = $rID[1]; #this removes the "chr" portion of the first element and leaves number
		#i.e. instead of [0] -> "chr24"; [0] -> "24"

	while($pline=<P>) {			
			if(!$rline) {
				last;
			} #end if
		
		chomp($pline);
		my @p_arr=split("\t",$pline);
		
			chomp($p_arr[0]);
			my @pID = split("r",$p_arr[0]);
			$p_arr[0] = $pID[1];
		
			if($p_arr[1]>$r_arr[2]) {
			  $rline=<R>; 
			  redo;
			} #end if
		
			else {				
			      if($p_arr[0] == $r_arr[0] && $p_arr[1] >= $r_arr[1] && $p_arr[1] <= $r_arr[2]) {
					#NOTE: [0] element in each array now corresponds to chr number
					# r[1] is start of region and r[2] is end of region
					# p[1] is the position of the base pair
					shift(@p_arr);
					print (OUT "chr$r_arr[0]\t$r_arr[1]\t$r_arr[2]\t$r_arr[3]\t"); 
                    	print OUT join ("\t", @p_arr), "\n"; 
                    	#essentially I'm joining the two files with matching lines
                    	#w/ columns separated by tab
			       } #end if
			} #end else		
	} # end while <P>	
} #end while <R>
close R;
close P;
close OUT;

##</code><code>##

chr1	100	159	0	104	104	0	0	+
chr1	100	159	0	145	145	0	0	+

##</code><code>##

chr1	100	159	0	chr1	104	104	0	0	+
chr1	100	159	0	chr1	145	145	0	0	+
chr1	200	260	0	chr1	205	205	0	0	+
chr1	500	750	0	chr1	600	600	0	0	+
chr3	450	700	0	chr3	500	500	0	0	+
chr4	100	300	0	chr4	150	150	0	0	+
chr4	100	300	0	chr4	175	175	0	0	+
chr7	350	600	0	chr7	400	400	0	0	+
chr7	350	600	0	chr7	550	550	0	0	+
chr9	100	125	0	chr9	100	100	0	0	+
chr11	679	687	0	chr11	680	680	0	0	+
chr11	679	687	0	chr11	681	681	0	0	+
chr22	100	200	0	chr22	105	105	0	0	+
chr22	100	200	0	chr22	110	110	0	0	+
chr22	300	400	0	chr22	350	350	0	0	+