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

# Assemble ordered overlapping pair-end sequences in the stream.

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

require 'maasha/biopieces'
require 'maasha/fastq'
require 'pp'

casts = []
casts << {:long=>'overlap', :short=>'o', :type=>'uint', :mandatory=>false, :default=>1, :allowed=>nil, :disallowed=>"0"}

options = Biopieces.options_parse(ARGV, casts)

tmpdir   = Biopieces.mktmpdir
file_in1 = File.join(tmpdir, "in1.fq")
file_in2 = File.join(tmpdir, "in2.fq")
file_out = File.join(tmpdir, "out.fq")

io_in1 = Fastq.open(file_in1, 'w')
io_in2 = Fastq.open(file_in2, 'w')

name1  = ""
name2  = ""
entry1 = ""
entry2 = ""

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  input.each_record do |record|
    if record[:SEQ_NAME] and record[:SEQ] and record[:SCORES]
      entry = Seq.new_bp(record)

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

      if pair == 1
        name1  = name.dup
        entry1 = entry.dup
      else
        name2  = name.dup
        entry2 = entry.dup
      end

      if name1 != nil and name1 == name2
        io_in1.puts entry1.to_fastq
        io_in2.puts entry2.to_fastq
      end
    end
  end

  io_in1.close
  io_in2.close

  cmd = "pandaseq"
  cmd << " -6"
  cmd << " -F"
  cmd << " -B"
  cmd << " -N"
  cmd << " -o #{options[:overlap]}"
  cmd << " -f #{file_in1}"
  cmd << " -r #{file_in2}"
  cmd << " > #{file_out}"
  cmd << " 2> /dev/null" unless options[:verbose]

  $stderr.puts cmd if options[:verbose]

  system(cmd)

  raise RunTimeError "Error: command failed: #{cmd}" unless $?.success?

  Fastq.open(file_out) do |ios|
    ios.each do |entry|
      output.puts entry.convert_scores!('illumina18', 'illumina15').to_bp
    end
  end
end


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


__END__