################################################################
# Read the first file, break the first col to its components   #
# Expand the last two last numbers e.g. (591_592) plus/minus 8 #      
# Make a hash of multiple value for each key                   #
# Print the numner of lines read and put into a variable       #
################################################################

my %file1=();
while(<INPUT1>){
         chomp;
         (my $id, my $number) = split("\t", $_);

          if ($id=~ m/^(CLS_S3_Contig[0-9]+)([-]?)([0-9]+)([_]?)([0-9]+)$/i) {

              my $matched_id=$id; # breaks the CLS_Contig1000_200-202 to its componenents
                                  # and expands the second col plus minus 8 
                  for (my $i=$3-8;$i<$5+8;$i++){
              print join ("\t", $1, $i), "\n";
              push (@{$file1{$1}}, $i); #make a hash of array
        }
   }
}

           # Count the numnber of lines minus header line
           
           my $counter_1 = `wc -l < $ARGV[0]`;
           die "wc failed: $?"
           if $?;
           chomp($counter_1);
           my $counter = $counter_1 -1; #First file has a header row 
           print "$counter lines read from  $ARGV[0] file\n";

close(INPUT1);


###########################################################
#                    Reading the Second file              #
###########################################################

print "Reading the 2nd file\n";
print "It may take a while, please wait...\n";
print "-----------------------------------\n";



while(<INPUT2>){
         chomp;
         my @current_line  = split /\t/;

        foreach my $key (sort keys %file1){
                 foreach my $position1 (@{$file1{$key}}){
            if ($current_line[0] eq $key) {
              if ($current_line[1] == $position1) {
                  if ($current_line[2] ==1) {
                      if ($current_line[3] >= 3) {

          print join ("\t", $current_line[0],$current_line[1],$current_line[2],$current_line[3], "***",$key, $position1), "\n";
                   }
                }
              }
           }
        }
    }
}

close (INPUT2);