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

# Read FASTQ entries from one or more files.

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

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

MAX_TEST = 1_000

allowed_enc = 'auto,base_33,base_64'

casts = []
casts << {:long=>'data_in',  :short=>'i', :type=>'files!', :mandatory=>false, :default=>nil,    :allowed=>nil,         :disallowed=>nil}
casts << {:long=>'data_in2', :short=>'j', :type=>'files!', :mandatory=>false, :default=>nil,    :allowed=>nil,         :disallowed=>nil}
casts << {:long=>'num',      :short=>'n', :type=>'uint',   :mandatory=>false, :default=>nil,    :allowed=>nil,         :disallowed=>'0'}
casts << {:long=>'encoding', :short=>'e', :type=>'string', :mandatory=>false, :default=>'auto', :allowed=>allowed_enc, :disallowed=>nil}

options = Biopieces.options_parse(ARGV, casts)

encoding = options[:encoding].to_sym

num  = 0
last = false

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  unless options[:data_in] and options[:data_in].first == '-'
    input.each_record do |record|
      output.puts record
    end
  end

  if options[:data_in] and options[:data_in2]
    raise "data_in files differ" if options[:data_in].size != options[:data_in2].size

    (0 ... options[:data_in].size).each do |i|
      file1 = options[:data_in][i]
      file2 = options[:data_in2][i]

      io1 = Fastq.open(file1, 'r')
      io2 = Fastq.open(file2, 'r')

      while entry1 = io1.get_entry and entry2 = io2.get_entry
        if encoding == :auto
          if entry1.qual_base33? or entry2.qual_base33?
            encoding = :base_33
          elsif entry1.qual_base64? or entry2.qual_base64?
            encoding = :base_64
          else
            raise SeqError, "Could not auto-detect quality score encoding"
          end
        end

        entry1.qual_convert!(encoding, :base_33)
        entry2.qual_convert!(encoding, :base_33)
        entry1.qual_coerce!(:base_33)
        entry2.qual_coerce!(:base_33)

        if num < MAX_TEST
          raise SeqError, "Quality score outside valid range" unless entry1.qual_valid?(:base_33)
          raise SeqError, "Quality score outside valid range" unless entry2.qual_valid?(:base_33)
        end

        output.puts entry1.to_bp
        output.puts entry2.to_bp

        num += 2

        if options[:num] and num >= options[:num]
          last = true
          break
        end
      end

      io1.close
      io2.close

      break if last
    end
  elsif options[:data_in]
    options[:data_in].each do |file|
      Fastq.open(file, 'r') do |fastq|
        fastq.each do |entry|
          if encoding == :auto
            if entry.qual_base33?
              encoding = :base_33
            elsif entry.qual_base64?
              encoding = :base_64
            else
              raise SeqError, "Could not auto-detect quality score encoding"
            end
          end

          entry.qual_convert!(encoding, :base_33)
          entry.qual_coerce!(:base_33)

          if num < MAX_TEST
            raise SeqError, "Quality score outside valid range" unless entry.qual_valid?(:base_33)
          end

          output.puts entry.to_bp
          num += 1

          if options[:num] == num
            last = true
            break
          end
        end
      end

      break if last
    end
  end
end


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


__END__