#!/usr/bin/perl
#use warnings; 
#use strict;
#use Data::Dumper;

my $file1 = $ARGV[0];
open($infile1,$file1);
my $file2 = $ARGV[1];
open($infile2,$file2);

my %file2_hash;

while (my $line = <$infile2>)
{
   next if $line =~ /^\s*$/;   #skip blank lines (a common infile goof)
   
   my ($key, $value1, $value2) = split /\s+/, $line; # use better "names" I have
                                           # no idea of what a chr col means
   $file2_hash{"$key:$value1:$value2"} = 1;
}
close $infile2;

while (my $line = <$infile1>)
{
   chomp $line;  #so that output with E or M can be on same line
   next if $line =~ /^\s*$/;   #skip blank lines (a common infile goof)
   
   my ($chr, $value1) = split /\s+/,$line;
   
   if (exists $file2_hash{"$chr:$value1"} or exists $file2_hash{"$chr:$value2"} )
   {
      print "$line\tE\n";  # match exists with file 1
   }
   else
   {
      print "$line\tM\n";  # match does NOT exist with file 1
   }
}