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

# Run bowtie2 to map sequences in the stream.

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

require 'maasha/biopieces'
require 'maasha/fasta'
require 'maasha/sam'

casts = []
casts << {:long=>'index_name', :short=>'i', :type=>'string', :mandatory=>true,  :default=>nil,      :allowed=>nil,             :disallowed=>nil}
casts << {:long=>'type',       :short=>'t', :type=>'string', :mandatory=>false, :default=>"single", :allowed=>"single,paired", :disallowed=>nil}
casts << {:long=>'cpus',       :short=>'c', :type=>'uint',   :mandatory=>false, :default=>1,        :allowed=>nil,             :disallowed=>"0"}

options = Biopieces.options_parse(ARGV, casts)

tmp_dir  = Biopieces.mktmpdir
in_file  = File.join(tmp_dir, "in.fna")
in1_file = File.join(tmp_dir, "in1.fna")
in2_file = File.join(tmp_dir, "in2.fna")
out_file = File.join(tmp_dir, "out.sam")

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  if options[:type] == "single"
    Fasta.open(in_file, 'w') do |fasta_io|
      input.each_record do |record|
        output.puts record

        if record[:SEQ_NAME] and record[:SEQ]
          fasta_io.puts Seq.new_bp(record).to_fasta
        end
      end
    end
  else
    Fasta.open(in1_file, 'w') do |fasta1_io|
      Fasta.open(in2_file, 'w') do |fasta2_io|
        input.each_record do |record|
          output.puts record

          if record[:SEQ_NAME] and record[:SEQ]
            case record[:SEQ_NAME]
            when /\/1$/ then fasta1_io.puts Seq.new_bp(record).to_fasta
            when / 1:/  then fasta1_io.puts Seq.new_bp(record).to_fasta
            when /\/2$/ then fasta2_io.puts Seq.new_bp(record).to_fasta
            when / 2:/  then fasta2_io.puts Seq.new_bp(record).to_fasta
            else
              raise "Error: could not identify paired read in: #{record[:SEQ_NAME]}"
            end
          end
        end
      end
    end
  end

  cmd = []
  cmd << "bowtie2"
  cmd << "-f"
  cmd << "--quiet" unless options[:verbose]
  cmd << "--threads #{options[:cpus]}"
  cmd << "-x #{options[:index_name]}"

  if options[:type] == "single"
    cmd << "-U #{in_file}"
  else
    cmd << "-1 #{in1_file}"
    cmd << "-2 #{in2_file}"
  end

  cmd << "-S #{out_file}"

  c = cmd.join(" ")

  $stderr.puts c if options[:verbose]

  system(c)

  raise "Error: executing #{c}" unless $?.success?

  Sam.open(out_file, 'r') do |sam_io|
    sam_io.each do |entry|
      output.puts Sam.to_bp(entry)
    end
  end
end


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


__END__