3 # Copyright (C) 2007-2013 Martin A. Hansen.
5 # This program is free software; you can redistribute it and/or
6 # modify it under the terms of the GNU General Public License
7 # as published by the Free Software Foundation; either version 2
8 # of the License, or (at your option) any later version.
10 # This program is distributed in the hope that it will be useful,
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 # GNU General Public License for more details.
15 # You should have received a copy of the GNU General Public License
16 # along with this program; if not, write to the Free Software
17 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
19 # http://www.gnu.org/copyleft/gpl.html
21 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
23 # This program is part of the Biopieces framework (www.biopieces.org).
25 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
27 # Find paired end orphan in records with sequence data.
29 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
31 require 'maasha/biopieces'
34 options = Biopieces.options_parse(ARGV)
37 def self.name_match?(name1, name2)
40 name1[0 .. -3 ] == name2[0 .. -3] # Solexa and Illumina <= 1.5 version names
42 name1.split(" ").first == name2.split(" ").first # Illumina > 1.5 version names
49 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
50 input.each_record do |record|
55 if Illumina.name_match?(records.first[:SEQ_NAME], records.last[:SEQ_NAME])
56 records.first[:TYPE] = "paired"
57 records.last[:TYPE] = "paired"
59 output.puts records.first
60 output.puts records.last
64 records.first[:TYPE] = "orphan"
65 output.puts records.first
73 records.each do |record|
74 record[:TYPE] = "orphan"
80 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<