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

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

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

require 'maasha/biopieces'
require 'pp'

casts = []
casts << {:long=>'min',  :short=>'m', :type=>'uint',   :mandatory=>true, :default=>15,     :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)

ILLUMINA_BASE = 64

regex_left  = Regexp.new("^[#{(ILLUMINA_BASE).chr}-#{(ILLUMINA_BASE + options[:min]).chr}]+")
regex_right = Regexp.new("[#{(ILLUMINA_BASE).chr}-#{(ILLUMINA_BASE + options[:min]).chr}]+$")

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  input.each_record do |record|
    if record.has_key? :SEQ and record.has_key? :SCORES
      case options[:trim]
      when /both/
        record[:SCORES].match(regex_right) do |m|
          record[:SEQ]       = record[:SEQ][0 ... record[:SEQ].length - m.to_s.length]
          record[:SCORES]    = $`
          record[:SEQ_LEN]   = record[:SEQ].length
          record[:TRIM_LEFT] = m.to_s.length
        end
        record[:SCORES].match(regex_left) do |m|
          record[:SEQ]        = record[:SEQ][m.to_s.length ... record[:SEQ].length]
          record[:SCORES]     = $'
          record[:SEQ_LEN]    = record[:SEQ].length
          record[:TRIM_RIGHT] = $'.length - 1
        end
      when /left/
        record[:SCORES].match(regex_left) do |m|
          record[:SEQ]       = record[:SEQ][m.to_s.length ... record[:SEQ].length]
          record[:SCORES]    = $'
          record[:SEQ_LEN]   = record[:SEQ].length
          record[:TRIM_LEFT] = m.to_s.length
        end
      when /right/
        record[:SCORES].match(regex_right) do |m|
          record[:SEQ]        = record[:SEQ][0 ... record[:SEQ].length - m.to_s.length]
          record[:SCORES]     = $`
          record[:SEQ_LEN]    = record[:SEQ].length
          record[:TRIM_RIGHT] = $`.length - 1
        end
      end
    end

    output.puts record
  end
end


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


__END__