# perl Overlaps.pl STR.txt IQ_meta_242loci.txt > Output.xls

open (IN2,"$ARGV[1]");
while (<IN2>){
	chomp;@lines=split ("\t",$_);
	$Start=int($lines[1]/1000);$End=int($lines[2]/1000);
	foreach $n($Start..$End){
		$ChrPos="$lines[0] $n";
		$leadSNP{$ChrPos}=$lines[4];
	}	
}
close (IN2);

open (IN1,"$ARGV[0]");
while (<IN1>){
	chomp;@lines=split ("\t",$_);$Result=0;
	$Start=int($lines[1]/1000);$End=int($lines[2]/1000);
	HERE:foreach $n($Start..$End){
		$ChrPos="$lines[0] $n";
		$Leader=$leadSNP{$ChrPos};
		if (defined($Leader)){
			print "$Leader\t$_\n";$Result=1;last HERE;
		}	
	}
	if ($Result==0){
		print "NotFound\t$_\n";
	}			
}
close (IN1);