=head1 LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2019] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

=cut


=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.

=head1 NAME

Bio::EnsEMBL::Compara::RunnableDB::PairAligner::UcscChainFactory

=head1 DESCRIPTION

Effectively splits a UCSC chain file into smaller bits by using a seek position and the number of lines to be read, to allow for parallel processing 

=cut

package Bio::EnsEMBL::Compara::RunnableDB::PairAligner::UcscChainFactory;

use strict;
use warnings;

use base ('Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable');


############################################################

=head2 fetch_input

    Title   :   fetch_input
    Usage   :   $self->fetch_input
    Returns :   nothing
    Args    :   none

=cut

sub fetch_input {
  my( $self) = @_; 

  #Read at least this many lines to the next chain
  my $step = $self->param('step');

  #Open Ucsc chain file
  open(FILE, $self->param('chain_file')) or die ("Unable to open " . $self->param('chain_file'));

  my $seek_positions;
  my $prev_pos = 0;
  my $line_num = 1;
  
  my $first_chain = 1;

  #
  #Read through UCSC chain file. Store the position of the first chain tag 
  #(prev_pos) and read $step lines and store the number of lines until you
  #reach the next chain tag ($line_num-1)
  #
  while (<FILE>) {
      my $curr_pos = tell(FILE); #current position in file
      if (/chain /) {
	  if ($first_chain || $line_num >= $step) {
	      my $pos_line;
	      %$pos_line = ('pos' => $prev_pos,
			    'line' => $line_num-1);
	      push @$seek_positions, $pos_line;
	      $line_num = 1;
	      $first_chain = 0;
	  }
      }
      $prev_pos = $curr_pos; 
      $line_num++;
  }

  #Store last position
  my $pos_line;
  %$pos_line = ('pos' => $prev_pos,
		'line' => $line_num-1);
  push @$seek_positions, $pos_line;
  
  close FILE;

  for (my $index = 0;  $index < (@$seek_positions-1); $index++) {
      my $seek_pos = $seek_positions->[$index]->{pos};
      my $num_lines = $seek_positions->[$index+1]->{line};

      my $output_id = "{seek_offset=>" . $seek_pos . ",num_lines=>" .  $num_lines . "}";
      $self->dataflow_output_id($output_id, 2);
  }
}

1;