#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Merge pair-end sequences in the stream.

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

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

def names_match(entry1, entry2)
  if entry1.seq_name =~ /^([^ ]+) \d:/
    name1 = $1
  elsif entry1.seq_name =~ /^(.+)\/\d$/
    name1 = $1
  else
    raise "Could not match sequence name: #{entry1.seq_name}"
  end

  if entry2.seq_name =~ /^([^ ]+) \d:/
    name2 = $1
  elsif entry2.seq_name =~ /^(.+)\/\d$/
    name2 = $1
  else
    raise "Could not match sequence name: #{entry2.seq_name}"
  end

  name1 == name2
end

options = Biopieces.options_parse(ARGV)

entry1 = nil
entry2 = nil

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  input.each_record do |record|
    if record[:SEQ_NAME] and record[:SEQ]
      if entry1.nil?
         entry1 = Seq.new_bp(record)
      elsif entry2.nil?
        entry2 = Seq.new_bp(record)
      end

      if entry1 and entry2
        if names_match(entry1, entry2)
          seq_len_left  = entry1.length
          seq_len_right = entry2.length

          entry1 << entry2

          new_record = entry1.to_bp
          new_record[:SEQ_LEN_LEFT]  = seq_len_left
          new_record[:SEQ_LEN_RIGHT] = seq_len_right
          output.puts new_record
        else
          raise "name mismatch: #{entry1.seq_name} != #{entry2.seq_name}"
        end

        entry1 = nil
        entry2 = nil
      end
    else
      output.puts record
    end
  end
end


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


__END__