--- /dev/null
+#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Assemble ordered overlapping pair-end sequences in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/biopieces'
+require 'maasha/fastq'
+require 'pp'
+
+casts = []
+casts << {:long=>'overlap', :short=>'o', :type=>'uint', :mandatory=>false, :default=>1, :allowed=>nil, :disallowed=>"0"}
+
+options = Biopieces.options_parse(ARGV, casts)
+
+tmpdir = Biopieces.mktmpdir
+file_in1 = File.join(tmpdir, "in1.fq")
+file_in2 = File.join(tmpdir, "in2.fq")
+file_out = File.join(tmpdir, "out.fq")
+
+io_in1 = Fastq.open(file_in1, 'w')
+io_in2 = Fastq.open(file_in2, 'w')
+
+name1 = ""
+name2 = ""
+entry1 = ""
+entry2 = ""
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+ input.each_record do |record|
+ if record[:SEQ_NAME] and record[:SEQ] and record[:SCORES]
+ entry = Seq.new_bp(record)
+
+ case entry.seq_name
+ when /^(.+)\/(\d)$/ # Illumina 1.5
+ name = $1
+ pair = $2.to_i
+ type = 15
+ when /^(.+) (\d):/ # Illumina 1.8
+ name = $1
+ pair = $2.to_i
+ type = 18
+ else
+ $stderr.puts "WARNING: Unmatched sequence name: #{entry.seq_name}"
+ end
+
+ if pair == 1
+ name1 = name.dup
+ entry1 = entry.dup
+ else
+ name2 = name.dup
+ entry2 = entry.dup
+ end
+
+ if name1 != nil and name1 == name2
+ io_in1.puts entry1.to_fastq
+ io_in2.puts entry2.to_fastq
+ end
+ end
+ end
+
+ io_in1.close
+ io_in2.close
+
+ cmd = "pandaseq"
+ cmd << " -6"
+ cmd << " -F"
+ cmd << " -B"
+ cmd << " -N"
+ cmd << " -o #{options[:overlap]}"
+ cmd << " -f #{file_in1}"
+ cmd << " -r #{file_in2}"
+ cmd << " > #{file_out}"
+ cmd << " 2> /dev/null" unless options[:verbose]
+
+ $stderr.puts cmd if options[:verbose]
+
+ system(cmd)
+
+ raise RunTimeError "Error: command failed: #{cmd}" unless $?.success?
+
+ Fastq.open(file_out) do |ios|
+ ios.each do |entry|
+ output.puts entry.convert_scores!('illumina18', 'illumina15').to_bp
+ end
+ end
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__