#!/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 'gdbm'
require 'pp'

ILLUMINA15 = 15
ILLUMINA18 = 18

options = Biopieces.options_parse(ARGV)

tmpdir  = Biopieces.mktmpdir
#tmpdir  = "Sletmig"
tmpfile = File.join(tmpdir, "data.gdbm")

db = GDBM.new(tmpfile)

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  input.each_record do |record|
    if record[:SEQ_NAME]
      db[record[:SEQ_NAME]] = Marshal.dump(record)
    else
      output.puts record
    end
  end

  skip = {}

  db.keys.each do |seq_name|
    next if skip[seq_name]

    case seq_name
    when /^(.+)\/(\d)$/   # Illumina 1.5
      type = ILLUMINA15
      name = $1
      pair = $2.to_i
    when /^(.+) (\d):/    # Illumina 1.8
      type = ILLUMINA18
      name = $1.to_sym
      pair = $2.to_i
    else
      $stderr.puts "WARNING: Unmatched sequence name: #{record[:SEQ_NAME]}"
    end

    pair2 = (pair == 1) ? 2 : 1

    if type == ILLUMINA15
      seq_name2 = "#{name}/#{pair2}"
    else
      seq_name2 = seq_name.sub(/^(.+) \d:/, "#{$1} #{pair2}:")
    end

    record1 = Marshal.load(db[seq_name])
    record2 = db[seq_name2]
    record2 = Marshal.load(record2) unless record2.nil?

    if record2.nil?
      record1[:ORDER] = "orphan#{pair}"
      output.puts record1
    else
      record1[:ORDER] = "paired"
      record2[:ORDER] = "paired"

      output.puts record1
      output.puts record2

      skip[seq_name2] = true
    end
  end
end

db.close

FileUtils.remove_entry_secure(tmpfile, true)

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


__END__