#!/usr/bin/env ruby

# Copyright (C) 2007-2013 Martin A. Hansen.

# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.

# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.

# http://www.gnu.org/copyleft/gpl.html

# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# This program is part of the Biopieces framework (www.biopieces.org).

# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Split joined pair-end sequences in the stream.

# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

require 'maasha/biopieces'
require 'maasha/seq'
require 'pp'

options = Biopieces.options_parse(ARGV)

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  input.each_record do |record|
    if record[:SEQ_NAME] and record[:SEQ] and record[:SEQ_LEN_LEFT] and record[:SEQ_LEN_RIGHT]
      entry = Seq.new_bp(record)

      len_left  = record[:SEQ_LEN_LEFT].to_i
      len_right = record[:SEQ_LEN_RIGHT].to_i

      unless len_left + len_right == entry.length
        raise "SEQ_LEN_LEFT + SEQ_LEN_RIGHT != SEQ_LEN #{len_left} + #{len_right} != #{entry.length}"
      end

      entry1 = entry.subseq(0, len_left)
      entry2 = entry.subseq(len_left)

      if entry.seq_name =~ /^[^ ]+ \d:/
        entry2.seq_name.sub!(/ \d:/, " 2:")
      elsif entry.seq_name =~ /^.+\/\d$/
        entry2.seq_name[-1] = "2"
      else
        raise "Could not match sequence name: #{entry.seq_name}"
      end

      output.puts entry1.to_bp
      output.puts entry2.to_bp
    else
      output.puts record
    end
  end
end


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


__END__