removing order_pairs2 and order_pairs3

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1985 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/order_pairs2 b/bp_bin/order_pairs2
deleted file mode 100755 (executable)
index 6eb247e..0000000
--- a/bp_bin/order_pairs2
+++ /dev/null
@@ -1,107 +0,0 @@
-#!/usr/bin/env ruby
-
-# Copyright (C) 2007-2012 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Order records with pair end sequence data.
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'maasha/biopieces'
-require 'gdbm'
-require 'pp'
-
-ILLUMINA15 = 15
-ILLUMINA18 = 18
-
-options = Biopieces.options_parse(ARGV)
-
-tmpdir  = Biopieces.mktmpdir
-#tmpdir  = "Sletmig"
-tmpfile = File.join(tmpdir, "data.gdbm")
-
-db = GDBM.new(tmpfile)
-
-Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
-  input.each_record do |record|
-    if record[:SEQ_NAME]
-      db[record[:SEQ_NAME]] = Marshal.dump(record)
-    else
-      output.puts record
-    end
-  end
-
-  skip = {}
-
-  db.keys.each do |seq_name|
-    next if skip[seq_name]
-
-    case seq_name
-    when /^(.+)\/(\d)$/   # Illumina 1.5
-      type = ILLUMINA15
-      name = $1
-      pair = $2.to_i
-    when /^(.+) (\d):/    # Illumina 1.8
-      type = ILLUMINA18
-      name = $1.to_sym
-      pair = $2.to_i
-    else
-      $stderr.puts "WARNING: Unmatched sequence name: #{record[:SEQ_NAME]}"
-    end
-
-    pair2 = (pair == 1) ? 2 : 1
-
-    if type == ILLUMINA15
-      seq_name2 = "#{name}/#{pair2}"
-    else
-      seq_name2 = seq_name.sub(/^(.+) \d:/, "#{$1} #{pair2}:")
-    end
-
-    record1 = Marshal.load(db[seq_name])
-    record2 = db[seq_name2]
-    record2 = Marshal.load(record2) unless record2.nil?
-
-    if record2.nil?
-      record1[:ORDER] = "orphan#{pair}"
-      output.puts record1
-    else
-      record1[:ORDER] = "paired"
-      record2[:ORDER] = "paired"
-
-      output.puts record1
-      output.puts record2
-
-      skip[seq_name2] = true
-    end
-  end
-end
-
-db.close
-
-FileUtils.remove_entry_secure(tmpfile, true)
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-__END__

diff --git a/bp_bin/order_pairs3 b/bp_bin/order_pairs3
deleted file mode 100755 (executable)
index 6a943c0..0000000
--- a/bp_bin/order_pairs3
+++ /dev/null
@@ -1,176 +0,0 @@
-#!/usr/bin/env ruby
-
-# Copyright (C) 2007-2012 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Order records with pair end sequence data.
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-require 'pp'
-require 'maasha/biopieces'
-
-def files_merge(file_in1, file_in2)
-  file_out = "#{file_in1}.merge"
-
-  in1, out1 = Biopieces.open(file_in1, file_out)
-  in2, out2 = Biopieces.open(file_in2)
-
-  record1 = in1.get_entry
-  record2 = in2.get_entry
-
-  while 1
-    if record1 and record2
-      if record1[:SEQ_NAME] < record2[:SEQ_NAME]
-        out1.puts record1
-        record1 = in1.get_entry
-      else
-        out1.puts record2
-        record2 = in2.get_entry
-      end
-    elsif record1
-      out1.puts record1
-      record1 = in1.get_entry
-    elsif record2
-      out1.puts record2
-      record2 = in2.get_entry
-    else
-      break
-    end
-  end
-
-  File.rename(file_out, file_in1)
-  File.delete(file_in2)
-end
-
-casts = []
-casts << {:long=>'block_size', :short=>'b', :type=>'uint', :mandatory=>false, :default=>100_000_000, :allowed=>nil, :disallowed=>'0'}
-
-options = Biopieces.options_parse(ARGV, casts)
-tmpdir  = Biopieces.mktmpdir
-
-Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
-  block = []
-  file_count = 0
-  block_size = 0
-
-  input.each do |record|
-    block << record
-
-    block_size += record.to_s.size
-
-    if block_size >= options[:block_size]
-      block.sort_by! { |r| r[:SEQ_NAME] }
-
-      tmpfile = File.join(tmpdir, "#{file_count}.stream")
-
-      $stderr.puts "Writing tmp file #{tmpfile}" if options[:verbose]
-      Biopieces.open(nil, tmpfile) do |tmpin, tmpout|
-        block.each { |r| tmpout.puts r }
-      end
-
-      block       = []
-      block_size  = 0
-      file_count += 1
-    end
-  end
-
-  block.sort_by! { |r| r[:SEQ_NAME] }
-
-  tmpfile = File.join(tmpdir, "#{file_count}.stream")
-
-  $stderr.puts "Writing tmp file #{tmpfile}" if options[:verbose]
-  Biopieces.open(nil, tmpfile) do |tmpin, tmpout|
-    block.each { |r| tmpout.puts r }
-  end
-end
-
-while files = Dir.glob(File.join(tmpdir, "*.stream")) and files.size > 1
-  0.step(files.size - 2, 2) do |i|
-    $stderr.puts "Merging files #{files[i]} #{files[i + 1]}" if options[:verbose]
-    files_merge(files[i], files[i + 1])
-  end
-end
-
-Biopieces.open(File.join(tmpdir, "0.stream"), options[:stream_out]) do |input, output|
-  record1 = input.get_entry
-
-  while record2 = input.get_entry
-    case record1[:SEQ_NAME]
-    when /^(.+)\/(\d)$/   # Illumina 1.5
-      name1 = $1
-      pair1 = $2.to_i
-    when /^(.+) (\d):/    # Illumina 1.8
-      name1 = $1
-      pair1 = $2.to_i
-    else
-      $stderr.puts "WARNING: Unmatched sequence name: #{record1[:SEQ_NAME]}"
-    end
-
-    case record2[:SEQ_NAME]
-    when /^(.+)\/(\d)$/   # Illumina 1.5
-      name2 = $1
-      pair2 = $2.to_i
-    when /^(.+) (\d):/    # Illumina 1.8
-      name2 = $1
-      pair2 = $2.to_i
-    else
-      $stderr.puts "WARNING: Unmatched sequence name: #{record2[:SEQ_NAME]}"
-    end
-
-    if name1 == name2 and (pair1 - pair2).abs == 1
-      record1[:ORDER] = "paired"
-      record2[:ORDER] = "paired"
-      output.puts record1
-      output.puts record2
-      record1 = input.get_entry
-    else
-      record1[:ORDER] = "orphan #{pair1}"
-      output.puts record1
-      record1 = record2
-    end
-  end
-
-  if record1
-    case record1[:SEQ_NAME]
-    when /^(.+)\/(\d)$/   # Illumina 1.5
-      name1 = $1
-      pair1 = $2.to_i
-    when /^(.+) (\d):/    # Illumina 1.8
-      name1 = $1
-      pair1 = $2.to_i
-    else
-      $stderr.puts "WARNING: Unmatched sequence name: #{record1[:SEQ_NAME]}"
-    end
-
-    record1[:ORDER] = "orphan #{pair1}"
-    output.puts record1
-  end
-end
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-__END__