#!/usr/bin/env ruby

# Copyright (C) 2007-2013 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Find homopolymers in sequences in the stream.

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


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

class Seq; include Homopolymer; end

casts = []
casts << {:long=>'min',     :short=>'m', :type=>'uint', :mandatory=>false, :default=>1,   :allowed=>nil, :disallowed=>"0"}
casts << {:long=>'limit',   :short=>'l', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>"0"}
casts << {:long=>'longest', :short=>'L', :type=>'flag', :mandatory=>false, :default=>nil, :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|
    if record[:SEQ]
      seq = Seq.new(seq: record[:SEQ])

      longest = Seq::Homopolymer.new("", 0, 0)
      got_one = false
      count   = 0

      seq.each_homopolymer(options[:min]) do |h|
        got_one = true

        record[:HOMOPOL_PAT] = h.pattern
        record[:HOMOPOL_LEN] = h.length
        record[:HOMOPOL_POS] = h.pos

        if options[:longest]
          longest = h.length > longest.length ? h : longest
        else
          output.puts record

          count += 1

          break if options[:limit] and options[:limit] == count
        end
      end

      if options[:longest]
        if longest.length > options[:min]
          record[:HOMOPOL_PAT] = longest.pattern
          record[:HOMOPOL_LEN] = longest.length
          record[:HOMOPOL_POS] = longest.pos
        end

        output.puts record
      elsif not got_one
        output.puts record
      end
    else
      output.puts record
    end
  end
end


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


__END__