#!/usr/bin/env ruby

# Copyright (C) 2007-2011 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Remove adaptors or parts thereof from sequences in the stream.

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


require 'biopieces'
require 'seq'
require 'profile'

casts = []
casts << {:long=>'adaptor',    :short=>'r', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'mismatches', :short=>'m', :type=>'uint',   :mandatory=>false, :default=>20,  :allowed=>nil, :disallowed=>nil}
casts << {:long=>'insertions', :short=>'i', :type=>'uint',   :mandatory=>false, :default=>10,  :allowed=>nil, :disallowed=>nil}
casts << {:long=>'deletions',  :short=>'d', :type=>'uint',   :mandatory=>false, :default=>10,  :allowed=>nil, :disallowed=>nil}

bp = Biopieces.new

options = bp.parse(ARGV, casts)

bp.each_record do |record|
  if record.has_key? :SEQ
    entry = Seq.new(record[:SEQ_NAME], record[:SEQ], record[:TYPE], record[:SCORES])

    if match = entry.adaptor_find(options[:adaptor], options[:mismatches], options[:insertions], options[:deletions])
      record[:POS] = match.pos
    end
  end

  bp.puts record
end


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


__END__