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

# Soft mask sequences in the stream based on quality scores.

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


require 'maasha/biopieces'

ILLUMINA_BASE = 64

# Expading class Hash with possibly evil monkey patch.
class Hash
  # Soft masks sequence residues where the corresponding quality score
  # is below a given cutoff.
  def mask_seq!(cutoff)
    if self.has_key? :SEQ and self.has_key? :SCORES
      seq    = self[:SEQ].upcase
      scores = self[:SCORES]
      i      = 0

      scores.each_char do |score|
        seq[i] = seq[i].downcase if score.ord - ILLUMINA_BASE < cutoff
        i += 1
      end

      self[:SEQ] = seq
    end

    self
  end
end

casts = []
casts << {:long=>'cutoff', :short=>'c', :type=>'int', :mandatory=>false, :default=>20, :allowed=>nil, :disallowed=>nil}

options = Biopieces.options_parse(ARGV, casts)

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  input.each_record do |record|
    output.puts record.mask_seq!(options[:cutoff])
  end
end


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


__END__