#!/bin/perl --

$num = 1;
$grp = 0;

while(<>){
   chomp;
   split(/\t+/);
   if (/^\s*$/){
   } elsif (/^G/){
      print "G\t$grp\t$_[2]\t$_[3]\t$_[4]\t$_[5]\t$_[6]\n";
      $grp++;
   } elsif (/^M/){
      $_[6] =~ s/-//g;
      print "M\t$num\t$_[2]\t$_[3]\t$_[4]\t$_[5]\t$_[6]\n";
      $num++;
   } else {
      print "$_\n";
   }
}


syntax highlighted by Code2HTML, v. 0.9.1