1 # Copyright (C) 2007-2011 Martin A. Hansen.
3 # This program is free software; you can redistribute it and/or
4 # modify it under the terms of the GNU General Public License
5 # as published by the Free Software Foundation; either version 2
6 # of the License, or (at your option) any later version.
8 # This program is distributed in the hope that it will be useful,
9 # but WITHOUT ANY WARRANTY; without even the implied warranty of
10 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
11 # GNU General Public License for more details.
13 # You should have received a copy of the GNU General Public License
14 # along with this program; if not, write to the Free Software
15 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
17 # http://www.gnu.org/copyleft/gpl.html
19 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
21 # This software is part of the Biopieces framework (www.biopieces.org).
23 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
26 require 'maasha/filesys'
28 # Error class for all exceptions to do with FASTQ.
29 class FastqError < StandardError; end
32 # Method to get the next FASTQ entry form an ios and return this
33 # as a Seq object. If no entry is found or eof then nil is returned.
36 seq_name = @io.gets.chomp!
38 qual_name = @io.gets.chomp!
39 qual = @io.gets.chomp!
42 entry.type = @type.nil? ? nil : @type.downcase
44 entry.seq_name = seq_name[1 .. seq_name.length]
53 # TODO - this should be some custom to_s method instead.
55 if record[:SEQ_NAME] and record[:SEQ] and record[:SCORES]
56 @io.print "@#{record[:SEQ_NAME]}\n"
57 @io.print "#{record[:SEQ]}\n"
59 @io.print "#{record[:SCORES]}\n"