#!/usr/bin/env ruby

# Copyright (C) 2007-2011 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 so SEQ_NAME/1 and SEQ_NAME/2 are in the order.

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


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]
      name = record[:SEQ_NAME][0 ... -2].to_sym
      pair = record[:SEQ_NAME][-1].to_i

      if pair == 1
        if hash2.has_key? name
          output.puts record
          output.puts hash2[name]

          hash2.delete(name)
        else
          hash1[name] = record
        end
      elsif pair == 2
        if hash1.has_key? name
          output.puts hash1[name]
          output.puts record

          hash1.delete(name)
        else
          hash2[name] = record
        end
      else
        $stderr.puts "WARNING: Badly formatted name: #{record[:SEQ_NAME]}" if options[:verbose]
      end
    end
  end
end

if options[:verbose]
  $stderr.puts "Unmatched names with /1: #{hash1.size}"
  $stderr.puts "Unmatched names with /2: #{hash2.size}"
end


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


__END__