#!/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'

allowed_enc = 'auto,sanger,solexa,illumina1.3,illumina1.5,illumina1.8'

casts = []
casts << {:long=>'data_in',  :short=>'i', :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)

num   = 0
first = true
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]
    options[:data_in].each do |file|
      encoding = options[:encoding].downcase.delete('.')

      Fastq.open(file, mode='r') do |fastq|
        fastq.each do |entry|
          if encoding == 'auto'
            if entry.qual_base33? # sanger or illumina18
              encoding = 'illumina18'
            elsif entry.qual_base64? # solexa or illumina13 or illumina15
              encoding = 'illumina13'
            else
              raise SeqError, "Could not auto-detect quality score encoding"
            end
          end

          entry.convert_scores!(encoding, 'illumina13')

          if first
#            raise SeqError, "Quality score outside valid range" unless entry.qual_valid?('illumina13')
            first = false
          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__