Arg [1]    : ref to list of slices  
Arg [2]    : int maxlength of sub slices  
Arg [3]    : int overlap length (optional)  Example    : my $sub_slices = split_Slices($slices,$maxlen,$overlap)  Description: splits a slice into smaller slices   Returntype : ref to list of slices  
Exceptions : maxlen <1 or overlap < 0

sub split_Slices {
  my ($slice_big,$max_length,$overlap)=@_;

  if(!defined($max_length) or $max_length < 1){
    throw("maxlength needs to be set and > 0");
  }

  if(!defined($overlap)){
    $overlap = 0;
  }
  elsif($overlap < 0){
    throw("negative overlaps not allowed");
  }

  my @out=();

  foreach my $slice (@$slice_big){

    my $start = $slice->start;
    my $end;
    my $multiple;
    my $number;
    my $length = $slice->length;

    if($max_length && ($length > $overlap)) {
      #No seq region may be longer than max_length but we want to make      
#them all similar size so that the last one isn't much shorter.      
#Divide the seq_region into the largest equal pieces that are shorter      
#than max_length
      #calculate number of slices to create      
$number = ($length-$overlap) / ($max_length-$overlap);      
$number = ceil($number); 
#round up to int
      #calculate length of created slices      
$multiple = $length / $number;      
$multiple   = floor($multiple); #round down to int    } else {
      #just one slice of the whole seq_region      
$number = 1;
      $multiple = $length;
    }

    my $i;
    for(my $i=0; $i < $number; $i++) {
      $end = $start + $multiple + $overlap;

      #any remainder gets added to the last slice of the seq_region      $end = $slice->end if($i == $number-1);
      push @out, Bio::EnsEMBL::Slice->new
        (-START             => $start,
         -END               => $end,
         -STRAND            => 1,
         -SEQ_REGION_NAME   => $slice->seq_region_name,
         -SEQ_REGION_LENGTH => $slice->seq_region_length,
         -COORD_SYSTEM      => $slice->coord_system,
         -ADAPTOR           => $slice->adaptor);
      $start += $multiple + 1;
    }
  }

  return\@ out;
}



1;
}