#!/usr/bin/env ruby

# Copyright (C) 2007-2010 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Convert ASCII encoded quality scores in stream to a semi-colon seperated string of decimal values.

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


require 'biopieces'

# Expading class Hash with possibly evil monkey patch.
class Hash
  # Method to convert scores from ASCII encode string to
  # a semi-colon seperated string of decimal values.
  def scores2dec!(base)
    if self.has_key? :SCORES
      self[:SCORES].gsub! /./ do |score|
        score = (score.ord - base).to_s + ";"
      end

      self[:SCORES].chomp! ";"
    end

    self
  end
end

casts = []
casts << {:long=>'base', :short=>'b', :type=>'uint', :mandatory=>false, :default=>64, :allowed=>"33,59,64", :disallowed=>nil}

bp = Biopieces.new

options = bp.parse(ARGV, casts)

bp.each_record do |record|
  bp.puts record.scores2dec!(options[:base])
end


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


__END__