#!/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 columns with indels only from aligned sequences in the stream.

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

require 'maasha/biopieces'
require 'narray'
require 'pp'

options      = Biopieces.options_parse(ARGV)
tmpdir       = Biopieces.mktmpdir
file_records = File.join(tmpdir, "data.stream")
na_mask      = false
count        = 0

Biopieces.open(options[:stream_in], file_records) do |input, output|
  input.each do |record|
    if record[:SEQ]
      na_mask = NArray.int(record[:SEQ].length) unless na_mask
      na_seq  = NArray.to_na(record[:SEQ], "byte")
      na_mask += na_seq.eq('-'.ord) 
      na_mask += na_seq.eq('.'.ord) 
      na_mask += na_seq.eq('_'.ord) 
      na_mask += na_seq.eq('~'.ord) 

      count += 1
    end

    output.puts record
  end
end

na_mask = na_mask.ne count

sum = na_mask.sum

Biopieces.open(file_records, options[:stream_out]) do |input, output|
  input.each do |record|
    if sum > 0 and record[:SEQ]
      na_seq           = NArray.to_na(record[:SEQ], "byte")
      record[:SEQ]     = na_seq[na_mask].to_s
      record[:SEQ_LEN] = record[:SEQ].length
    end

    output.puts record
  end
end

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


__END__