#!/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 SNPs in records of SAM type in the stream.

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


require 'maasha/biopieces'
require 'pp'

casts = []
casts << {:long=>'coverage', :short=>'c', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}

options = Biopieces.options_parse(ARGV, casts)

snp_hash = Hash.new { |hash, key| hash[key] = Hash.new { |h, k| h[k] = Hash.new(0) } }
cov_hash = Hash.new { |hash, key| hash[key] = Hash.new(0) }

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  input.each_record do |record|
    output.puts record

    if record[:ALIGN] and
       record[:S_ID]  and
       record[:S_BEG] and
       record[:ALIGN] != '.'

       record[:ALIGN].split(',').each do |snp|
         pos, event = snp.split(':')

         pos = pos.to_i + record[:S_BEG].to_i

         snp_hash[record[:S_ID].to_sym][pos][event.to_sym] += 1
       end
    end

    if options[:coverage] and 
       record[:S_ID]      and
       record[:S_BEG]     and
       record[:S_END]
      (record[:S_BEG].to_i .. record[:S_END].to_i).each do |i|
        cov_hash[record[:S_ID].to_sym][i] += 1
      end
    end
  end

  snp_hash.each_pair do |s_id, pos_hash|
    new_record = {}
    new_record[:REC_TYPE] = 'SNP'
    new_record[:S_ID]     = s_id

    pos_hash.each_pair do |pos, event_hash|
      new_record[:POS]      = pos
      new_record[:COVERAGE] = cov_hash[s_id][pos] if options[:coverage]

      event_hash.each_pair do |event, count|
        new_record[:EVENT]     = event
        new_record[:SNP_COUNT] = count

        before, after = event.to_s.split('>')

        if before == '-'
          type = 'INSERTION'
        elsif after == '-'
          type = 'DELETION'
        else
          type = 'MISMATCH'
        end

         new_record[:TYPE] = type
      end

      output.puts new_record
    end
  end
end

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


__END__