#!/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 primers from sequences in the stream.

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


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

include BackTrack

casts = []
casts << {:long=>'forward',    :short=>'f', :type=>'string', :mandatory=>true,  :default=>nil, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'reverse',    :short=>'r', :type=>'string', :mandatory=>true,  :default=>nil, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'mismatches', :short=>'m', :type=>'uint',   :mandatory=>false, :default=>2,   :allowed=>nil, :disallowed=>nil}
casts << {:long=>'insertions', :short=>'i', :type=>'uint',   :mandatory=>false, :default=>1,   :allowed=>nil, :disallowed=>nil}
casts << {:long=>'deletions',  :short=>'d', :type=>'uint',   :mandatory=>false, :default=>1,   :allowed=>nil, :disallowed=>nil}

options = Biopieces.options_parse(ARGV, casts)

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  input.each do |record|
    if record[:SEQ]
      forward = false
      reverse = false
      entry = Seq.new_bp(record)

      entry.patscan(options[:forward].to_s,
                  max_mismatches: options[:mismatches],
                  max_insertions: options[:insertions],
                  max_deletions:  options[:deletions]) do |match|
        record[:FORWARD_POS] = match.pos
        record[:FORWARD_LEN] = match.length
        pos = match.pos + match.length
        len = entry.length - pos
        entry = entry[pos ... pos + len] if len > 0
        forward = true
        break
      end

      entry.patscan(options[:reverse].to_s,
                  max_mismatches: options[:mismatches],
                  max_insertions: options[:insertions],
                  max_deletions:  options[:deletions]) do |match|
        record[:REVERSE_POS] = match.pos
        record[:REVERSE_LEN] = match.length
        pos = 0
        len = match.pos

        if len == 0
          entry.seq  = ""
          entry.qual = "" if entry.qual
        else
          entry = entry[pos ... pos + len]
        end 

        reverse = true
        break
      end

      if forward or reverse
        record.merge!(entry.to_bp)
      end

      output.puts record
    else
      output.puts record
    end
  end
end

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

__END__