#!/usr/bin/env ruby

# Copyright (C) 2007-2012 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Trim sequence ends removing residues with a low quality score.

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

require 'maasha/biopieces'
require 'maasha/seq'
require 'pp'

casts = []
casts << {:long=>'min_qual', :short=>'m', :type=>'uint',   :mandatory=>true, :default=>20,     :allowed=>nil,               :disallowed=>'0'}
casts << {:long=>'min_len',  :short=>'l', :type=>'uint',   :mandatory=>true, :default=>3,      :allowed=>nil,               :disallowed=>'0'}
casts << {:long=>'trim',     :short=>'t', :type=>'string', :mandatory=>true, :default=>'both', :allowed=>'left,right,both', :disallowed=>nil}

options = Biopieces.options_parse(ARGV, casts)

trim = options[:trim].to_sym

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  input.each_record do |record|
    if record[:SEQ] and record[:SCORES]
      entry = Seq.new_bp(record)

      case trim
      when :both  then entry.quality_trim!(options[:min_qual], options[:min_len])
      when :left  then entry.quality_trim_left!(options[:min_qual], options[:min_len])
      when :right then entry.quality_trim_right!(options[:min_qual], options[:min_len])
      end

      record.merge! entry.to_bp
    end

    output.puts record
  end
end


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


__END__