#!/usr/bin/env ruby

# Copyright (C) 2007-2012 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Order records with pair end sequence data.

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

require 'maasha/biopieces'
require 'pp'

options = Biopieces.options_parse(ARGV)

hash = {}

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  input.each_record do |record|
    if record[:SEQ_NAME]
      seq_name = record[:SEQ_NAME]

      case seq_name
      when /^(.+)\/(\d)$/   # Illumina 1.5
        name = $1.to_sym
        pair = $2.to_i
        type = 15
      when /^(.+) (\d):/    # Illumina 1.8
        name = $1.to_sym
        pair = $2.to_i
        type = 18
      else
        $stderr.puts "WARNING: Unmatched sequence name: #{record[:SEQ_NAME]}"
      end

      if hash[name]
        if pair == 1
          output.puts({:SEQ_NAME => seq_name})
          output.puts({:SEQ_NAME => (type == 15) ? seq_name.sub(/\d$/, '2') : seq_name.sub(/ \d:/, ' 2:')})
        else
          output.puts({:SEQ_NAME => (type == 15) ? seq_name.sub(/\d$/, '1') : seq_name.sub(/ \d:/, ' 1:')})
          output.puts({:SEQ_NAME => seq_name})
        end
      else
        hash[name] = true
      end
    end
  end
end


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


__END__