#!/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/seq'
require 'maasha/seq/assemble'
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

casts = []
casts << {:long=>'mismatches',  :short=>'m', :type=>'uint', :mandatory=>false, :default=>5,   :allowed=>nil, :disallowed=>nil}
casts << {:long=>'overlap_min', :short=>'o', :type=>'uint', :mandatory=>false, :default=>1,   :allowed=>nil, :disallowed=>"0"}
casts << {:long=>'overlap_max', :short=>'p', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>"0"}

options = Biopieces.options_parse(ARGV, casts)

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] and record[:SCORES]
      if entry1.nil?
        entry1 = Seq.new_bp(record)
      elsif entry2.nil?
        entry2 = Seq.new_bp(record)
      end

      if entry1 and
         entry2 and
         entry1.length >= options[:overlap_min] and
         entry2.length >= options[:overlap_min]

        if names_match(entry1, entry2)
          entry2.type = :dna
          entry2.reverse!.complement!

          merged = Assemble.pair(
            entry1,
            entry2,
            mismatches_max:options[:mismatches],
            overlap_min:options[:overlap_min],
            overlap_max:options[:overlap_max]
          )

          if merged
            new_record = merged.to_bp

            if merged.seq_name =~ /overlap=(\d+):hamming=(\d+)$/
              new_record[:OVERLAP_LEN]  = $1
              new_record[:HAMMING_DIST] = $2
            end

            output.puts new_record
          end
        else
          raise "name mismatch: #{entry1.seq_name} != #{entry2.seq_name}"
        end

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


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


__END__