#!/usr/bin/perl -w
use strict;

while (<DATA>)
{
   next if /^\s*$/;  #skip blank lines
   my ($input, $CIGAR) = split;
   my $ref = $input; #working copy of $input
   
   my (@edit_cmd) = $CIGAR =~ m/\d+\w/g;
   
   my $curr_pos = 0;
   my $total_len =0;
   
   foreach my $cmd (@edit_cmd)
   { 
      if    (my ($M) = $cmd =~ m/(\d+)M/)
      {
         $curr_pos += $M;
         $total_len+= $M;      
      }
   
      elsif (my ($I) = $CIGAR =~ m/(\d+)I/)
      {
         substr($ref,$curr_pos,$I,'');     #delete $I characters
         $total_len -= $I  
      }
   
      elsif (my ($D) = $CIGAR =~ m/(\d+)D/)
      {
         substr($ref,$curr_pos,0,"X" x $D);  #insert $D X's
         $total_len += $D;
         $curr_pos  += $D;
      }  
   }
   
   $ref = substr($ref,0,$total_len); #truncate ?????
   
   print "INPUT = $input   CIGAR = $CIGAR\n";
   print "REF   = $ref\n\n";
   
}

=prints
INPUT = CGAATTAATGGGAATTG   CIGAR = 8M2I7M
REF   = CGAATTAAGGAAT

INPUT = CGAATTAATGGGAATTG   CIGAR = 2M2I2M3D10M
REF   = CGTTTGGGAA

INPUT = CGAATTAATGGGA   CIGAR = 8M2D7M
REF   = CGAATTAAXXTGGGA
=cut

__DATA__
CGAATTAATGGGAATTG 8M2I7M
CGAATTAATGGGAATTG 2M2I2M3D10M
CGAATTAATGGGA     8M2D7M