#!/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)

hash1 = {}
hash2 = {}

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  input.each_record do |record|
    if record[:SEQ_NAME]
      case record[:SEQ_NAME]
      when /^(.+)\/(\d)$/   # Illumina 1.5
        name = $1.to_sym
        pair = $2.to_i
      when /^(.+) (\d):/    # Illumina 1.8
        name = $1.to_sym
        pair = $2.to_i
      else
        $stderr.puts "WARNING: Unmatched sequence name: #{record[:SEQ_NAME]}"
      end

      if pair == 1
        if hash2[name]
          record[:ORDER]      = "paired"
          hash2[name][:ORDER] = "paired"
          output.puts record
          output.puts hash2[name]

          hash2.delete(name)
        else
          hash1[name] = record
        end
      elsif pair == 2
        if hash1[name]
          hash1[name][:ORDER] = "paired"
          record[:ORDER]      = "paired"
          output.puts hash1[name]
          output.puts record

          hash1.delete(name)
        else
          hash2[name] = record
        end
      end
    end
  end

  hash1.each_value do |record|
    record[:ORDER] = "orphan 1"
    output.puts record
  end

  hash2.each_value do |record|
    record[:ORDER] = "orphan 2"
    output.puts record
  end
end


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


__END__