From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 25 Oct 2011 14:52:19 +0000 (+0000)
Subject: added find_barcodes biopiece
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=a271a3dec9077d8306cdf0e30196f994927eb7c5;p=biopieces.git

added find_barcodes biopiece

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1599 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/find_barcodes b/bp_bin/find_barcodes
new file mode 100755
index 0000000..aedea09
--- /dev/null
+++ b/bp_bin/find_barcodes
@@ -0,0 +1,337 @@
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2011 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 barcodes in sequences in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/biopieces'
+require 'maasha/bits'
+require 'pp'
+
+# Hard coded Roche Genome Sequencing MIDs
+GSMID_HASH = {
+  ACGAGTGCGT: "MID1",
+  TCTCTATGCG: "MID10",
+  TAGACTGCAC: "MID100",
+  TAGCGCGCGC: "MID101",
+  TAGCTCTATC: "MID102",
+  TATAGACATC: "MID103",
+  TATGATACGC: "MID104",
+  TCACTCATAC: "MID105",
+  TCATCGAGTC: "MID106",
+  TCGAGCTCTC: "MID107",
+  TCGCAGACAC: "MID108",
+  TCTGTCTCGC: "MID109",
+  TGATACGTCT: "MID11",
+  TGAGTGACGC: "MID110",
+  TGATGTGTAC: "MID111",
+  TGCTATAGAC: "MID112",
+  TGCTCGCTAC: "MID113",
+  ACGTGCAGCG: "MID114",
+  ACTCACAGAG: "MID115",
+  AGACTCAGCG: "MID116",
+  AGAGAGTGTG: "MID117",
+  AGCTATCGCG: "MID118",
+  AGTCTGACTG: "MID119",
+  TACTGAGCTA: "MID12",
+  AGTGAGCTCG: "MID120",
+  ATAGCTCTCG: "MID121",
+  ATCACGTGCG: "MID122",
+  ATCGTAGCAG: "MID123",
+  ATCGTCTGTG: "MID124",
+  ATGTACGATG: "MID125",
+  ATGTGTCTAG: "MID126",
+  CACACGATAG: "MID127",
+  CACTCGCACG: "MID128",
+  CAGACGTCTG: "MID129",
+  CATAGTAGTG: "MID13",
+  CAGTACTGCG: "MID130",
+  CGACAGCGAG: "MID131",
+  CGATCTGTCG: "MID132",
+  CGCGTGCTAG: "MID133",
+  CGCTCGAGTG: "MID134",
+  CGTGATGACG: "MID135",
+  CTATGTACAG: "MID136",
+  CTCGATATAG: "MID137",
+  CTCGCACGCG: "MID138",
+  CTGCGTCACG: "MID139",
+  CGAGAGATAC: "MID14",
+  CTGTGCGTCG: "MID140",
+  TAGCATACTG: "MID141",
+  TATACATGTG: "MID142",
+  TATCACTCAG: "MID143",
+  TATCTGATAG: "MID144",
+  TCGTGACATG: "MID145",
+  TCTGATCGAG: "MID146",
+  TGACATCTCG: "MID147",
+  TGAGCTAGAG: "MID148",
+  TGATAGAGCG: "MID149",
+  ATACGACGTA: "MID15",
+  TGCGTGTGCG: "MID150",
+  TGCTAGTCAG: "MID151",
+  TGTATCACAG: "MID152",
+  TGTGCGCGTG: "MID153",
+  TCACGTACTA: "MID16",
+  CGTCTAGTAC: "MID17",
+  TCTACGTAGC: "MID18",
+  TGTACTACTC: "MID19",
+  ACGCTCGACA: "MID2",
+  ACGACTACAG: "MID20",
+  CGTAGACTAG: "MID21",
+  TACGAGTATG: "MID22",
+  TACTCTCGTG: "MID23",
+  TAGAGACGAG: "MID24",
+  TCGTCGCTCG: "MID25",
+  ACATACGCGT: "MID26",
+  ACGCGAGTAT: "MID27",
+  ACTACTATGT: "MID28",
+  ACTGTACAGT: "MID29",
+  AGACGCACTC: "MID3",
+  AGACTATACT: "MID30",
+  AGCGTCGTCT: "MID31",
+  AGTACGCTAT: "MID32",
+  ATAGAGTACT: "MID33",
+  CACGCTACGT: "MID34",
+  CAGTAGACGT: "MID35",
+  CGACGTGACT: "MID36",
+  TACACACACT: "MID37",
+  TACACGTGAT: "MID38",
+  TACAGATCGT: "MID39",
+  AGCACTGTAG: "MID4",
+  TACGCTGTCT: "MID40",
+  TAGTGTAGAT: "MID41",
+  TCGATCACGT: "MID42",
+  TCGCACTAGT: "MID43",
+  TCTAGCGACT: "MID44",
+  TCTATACTAT: "MID45",
+  TGACGTATGT: "MID46",
+  TGTGAGTAGT: "MID47",
+  ACAGTATATA: "MID48",
+  ACGCGATCGA: "MID49",
+  ATCAGACACG: "MID5",
+  ACTAGCAGTA: "MID50",
+  AGCTCACGTA: "MID51",
+  AGTATACATA: "MID52",
+  AGTCGAGAGA: "MID53",
+  AGTGCTACGA: "MID54",
+  CGATCGTATA: "MID55",
+  CGCAGTACGA: "MID56",
+  CGCGTATACA: "MID57",
+  CGTACAGTCA: "MID58",
+  CGTACTCAGA: "MID59",
+  ATATCGCGAG: "MID6",
+  CTACGCTCTA: "MID60",
+  CTATAGCGTA: "MID61",
+  TACGTCATCA: "MID62",
+  TAGTCGCATA: "MID63",
+  TATATATACA: "MID64",
+  TATGCTAGTA: "MID65",
+  TCACGCGAGA: "MID66",
+  TCGATAGTGA: "MID67",
+  TCGCTGCGTA: "MID68",
+  TCTGACGTCA: "MID69",
+  CGTGTCTCTA: "MID7",
+  TGAGTCAGTA: "MID70",
+  TGTAGTGTGA: "MID71",
+  TGTCACACGA: "MID72",
+  TGTCGTCGCA: "MID73",
+  ACACATACGC: "MID74",
+  ACAGTCGTGC: "MID75",
+  ACATGACGAC: "MID76",
+  ACGACAGCTC: "MID77",
+  ACGTCTCATC: "MID78",
+  ACTCATCTAC: "MID79",
+  CTCGCGTGTC: "MID8",
+  ACTCGCGCAC: "MID80",
+  AGAGCGTCAC: "MID81",
+  AGCGACTAGC: "MID82",
+  AGTAGTGATC: "MID83",
+  AGTGACACAC: "MID84",
+  AGTGTATGTC: "MID85",
+  ATAGATAGAC: "MID86",
+  ATATAGTCGC: "MID87",
+  ATCTACTGAC: "MID88",
+  CACGTAGATC: "MID89",
+  TAGTATCAGC: "MID9",
+  CACGTGTCGC: "MID90",
+  CATACTCTAC: "MID91",
+  CGACACTATC: "MID92",
+  CGAGACGCGC: "MID93",
+  CGTATGCGAC: "MID94",
+  CGTCGATCTC: "MID95",
+  CTACGACTGC: "MID96",
+  CTAGTCACTC: "MID97",
+  CTCTACGCTC: "MID98",
+  CTGTACATAC: "MID99",
+}
+
+# Hard coded Roche Rapid Labrary MIDs
+RLMID_HASH = {
+  ACACGACGACT: "RL1",
+  ACACGTAGTAT: "RL2",
+  ACACTACTCGT: "RL3",
+  ACGACACGTAT: "RL4",
+  ACGAGTAGACT: "RL5",
+  ACGCGTCTAGT: "RL6",
+  ACGTACACACT: "RL7",
+  ACGTACTGTGT: "RL8",
+  ACGTAGATCGT: "RL9",
+  ACTACGTCTCT: "RL10",
+  ACTATACGAGT: "RL11",
+  ACTCGCGTCGT: "RL12" 
+}
+
+class BarCodeFinderError < StandardError; end
+
+class BarCodeFinder
+  def initialize(pos, max_mismatches)
+    @pos            = pos
+    @max_mismatches = max_mismatches
+    @barcode_hash   = {}
+    @barcode_sizes  = []
+  end
+
+  def parse_barcodes(file)
+    length = 0
+    hash   = {}
+
+    File.open(file, "r") do |ios|
+      while not ios.eof?
+        name, barcode = ios.readline.chomp.split(/\s+/)
+
+        if length > 0
+          raise BarCodeFinderError, "Uneven barcode length detected" if length != barcode.length
+        else
+          length = barcode.length
+        end
+
+        hash[barcode.upcase.to_sym] = name
+      end
+    end
+
+    load_barcodes(hash)
+  end
+
+  def load_barcodes(hash)
+    @barcode_sizes << hash.keys.first.to_s.size
+
+    @barcode_hash.merge!(hash)
+  end
+
+  def find_barcode(seq)
+    raise BarCodeFinderError, "No barcodes to find" if @barcode_hash.empty?
+
+    @barcode_sizes.each do |size|
+      hamming_dist = 0
+      barcode      = seq[@pos ... @pos + size].upcase.to_sym
+
+      if @barcode_hash.has_key? barcode
+        return BarCode.new(barcode, @barcode_hash[barcode], @pos, size, hamming_dist)
+      elsif @max_mismatches > 0
+        @barcode_hash.each_key do |key|
+          if key.to_s.length == barcode.to_s.size
+            hamming_dist = barcode.to_s.hamming_distance(key.to_s)
+
+            if hamming_dist <= @max_mismatches
+              return BarCode.new(key, @barcode_hash[key], @pos, size, hamming_dist)
+            end
+          end
+        end
+      end
+    end
+
+    nil
+  end
+
+  private
+
+  # Class to hold a BacCode object.
+  class BarCode
+    attr_accessor :barcode, :name, :pos, :len, :mismatches
+
+    def initialize(barcode, name, pos, len, mismatches)
+      @barcode    = barcode
+      @name       = name
+      @pos        = pos
+      @len        = len
+      @mismatches = mismatches
+    end
+
+    def to_hash
+      hash = {}
+      hash[:BARCODE]            = @barcode
+      hash[:BARCODE_NAME]       = @name
+      hash[:BARCODE_POS]        = @pos
+      hash[:BARCODE_LEN]        = @len
+      hash[:BARCODE_MISMATCHES] = @mismatches
+      hash
+    end
+
+    def start
+      @pos + @len
+    end
+  end
+end
+
+casts = []
+casts << {:long=>'barcodes_in', :short=>'b', :type=>'file!', :mandatory=>false, :default=>nil, :allowed=>nil,     :disallowed=>nil}
+casts << {:long=>'pos',         :short=>'p', :type=>'uint',  :mandatory=>false, :default=>0,   :allowed=>nil,     :disallowed=>nil}
+casts << {:long=>'mismatches',  :short=>'m', :type=>'uint',  :mandatory=>false, :default=>0,   :allowed=>"0,1,2", :disallowed=>nil}
+casts << {:long=>'gsmids',      :short=>'g', :type=>'flag',  :mandatory=>false, :default=>nil, :allowed=>nil,     :disallowed=>nil}
+casts << {:long=>'rlmids',      :short=>'r', :type=>'flag',  :mandatory=>false, :default=>nil, :allowed=>nil,     :disallowed=>nil}
+casts << {:long=>'remove',      :short=>'R', :type=>'flag',  :mandatory=>false, :default=>nil, :allowed=>nil,     :disallowed=>nil}
+
+options = Biopieces.options_parse(ARGV, casts)
+
+bc_finder = BarCodeFinder.new(options[:pos], options[:mismatches])
+bc_finder.parse_barcodes(options[:barcodes_in]) if options[:barcodes_in]
+bc_finder.load_barcodes(GSMID_HASH)             if options[:gsmids]
+bc_finder.load_barcodes(RLMID_HASH)             if options[:rlmids]
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each_record do |record|
+    if record.has_key? :SEQ
+      if barcode = bc_finder.find_barcode(record[:SEQ])
+        record.merge!(barcode.to_hash)
+
+        if options[:remove]
+          record[:SEQ]     = record[:SEQ][barcode.start .. -1]
+          record[:SCORES]  = record[:SCORES][barcode.start .. -1] if record[:SCORES]
+          record[:SEQ_LEN] = record[:SEQ].length
+        end
+      end
+    end
+
+    output.puts record
+  end
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
diff --git a/bp_test/in/find_barcodes.in.1 b/bp_test/in/find_barcodes.in.1
new file mode 100644
index 0000000..1a74b61
--- /dev/null
+++ b/bp_test/in/find_barcodes.in.1
@@ -0,0 +1,48 @@
+SEQ_NAME: test_gs
+SEQ: ACGAGTGCGT
+SEQ_LEN: 10
+---
+SEQ_NAME: test_rl
+SEQ: ACACGACGACT
+SEQ_LEN: 11
+---
+SEQ_NAME: test_Il
+SEQ: ATCACG
+SEQ_LEN: 6
+---
+SEQ_NAME: test_gs_4p
+SEQ: atcgACGAGTGCGT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p
+SEQ: atcgACACGACGACT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p
+SEQ: atcgATCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_1mm
+SEQ: atcgAgGAGTGCGT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p_1mm
+SEQ: atcgAgACGACGACT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p_1mm
+SEQ: atcgAaCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_2mm
+SEQ: atcgAgGAGTGCcT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p_2mm
+SEQ: atcgAgACGACGAgT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p_2mm
+SEQ: atcgAaCAgG
+SEQ_LEN: 10
+---
diff --git a/bp_test/in/find_barcodes.in.2 b/bp_test/in/find_barcodes.in.2
new file mode 100644
index 0000000..2e88d2f
--- /dev/null
+++ b/bp_test/in/find_barcodes.in.2
@@ -0,0 +1 @@
+Index_1  ATCACG
diff --git a/bp_test/out/find_barcodes.out.1 b/bp_test/out/find_barcodes.out.1
new file mode 100644
index 0000000..dfa125e
--- /dev/null
+++ b/bp_test/out/find_barcodes.out.1
@@ -0,0 +1,53 @@
+SEQ_NAME: test_gs
+SEQ: ACGAGTGCGT
+SEQ_LEN: 10
+---
+SEQ_NAME: test_rl
+SEQ: ACACGACGACT
+SEQ_LEN: 11
+BARCODE: ACACGACGACT
+BARCODE_NAME: RL1
+BARCODE_POS: 0
+BARCODE_LEN: 11
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_Il
+SEQ: ATCACG
+SEQ_LEN: 6
+---
+SEQ_NAME: test_gs_4p
+SEQ: atcgACGAGTGCGT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p
+SEQ: atcgACACGACGACT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p
+SEQ: atcgATCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_1mm
+SEQ: atcgAgGAGTGCGT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p_1mm
+SEQ: atcgAgACGACGACT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p_1mm
+SEQ: atcgAaCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_2mm
+SEQ: atcgAgGAGTGCcT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p_2mm
+SEQ: atcgAgACGACGAgT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p_2mm
+SEQ: atcgAaCAgG
+SEQ_LEN: 10
+---
diff --git a/bp_test/out/find_barcodes.out.10 b/bp_test/out/find_barcodes.out.10
new file mode 100644
index 0000000..5d1912a
--- /dev/null
+++ b/bp_test/out/find_barcodes.out.10
@@ -0,0 +1,63 @@
+SEQ_NAME: test_gs
+SEQ: ACGAGTGCGT
+SEQ_LEN: 10
+---
+SEQ_NAME: test_rl
+SEQ: ACACGACGACT
+SEQ_LEN: 11
+---
+SEQ_NAME: test_Il
+SEQ: ATCACG
+SEQ_LEN: 6
+---
+SEQ_NAME: test_gs_4p
+SEQ: atcgACGAGTGCGT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p
+SEQ: atcgACACGACGACT
+SEQ_LEN: 15
+BARCODE: ACACGACGACT
+BARCODE_NAME: RL1
+BARCODE_POS: 4
+BARCODE_LEN: 11
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_Il_4p
+SEQ: atcgATCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_1mm
+SEQ: atcgAgGAGTGCGT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p_1mm
+SEQ: atcgAgACGACGACT
+SEQ_LEN: 15
+BARCODE: ACACGACGACT
+BARCODE_NAME: RL1
+BARCODE_POS: 4
+BARCODE_LEN: 11
+BARCODE_MISMATCHES: 1
+---
+SEQ_NAME: test_Il_4p_1mm
+SEQ: atcgAaCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_2mm
+SEQ: atcgAgGAGTGCcT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p_2mm
+SEQ: atcgAgACGACGAgT
+SEQ_LEN: 15
+BARCODE: ACACGACGACT
+BARCODE_NAME: RL1
+BARCODE_POS: 4
+BARCODE_LEN: 11
+BARCODE_MISMATCHES: 2
+---
+SEQ_NAME: test_Il_4p_2mm
+SEQ: atcgAaCAgG
+SEQ_LEN: 10
+---
diff --git a/bp_test/out/find_barcodes.out.11 b/bp_test/out/find_barcodes.out.11
new file mode 100644
index 0000000..392dd2b
--- /dev/null
+++ b/bp_test/out/find_barcodes.out.11
@@ -0,0 +1,78 @@
+SEQ_NAME: test_gs
+SEQ: ACGAGTGCGT
+SEQ_LEN: 10
+---
+SEQ_NAME: test_rl
+SEQ: ACACGACGACT
+SEQ_LEN: 11
+---
+SEQ_NAME: test_Il
+SEQ: ATCACG
+SEQ_LEN: 6
+---
+SEQ_NAME: test_gs_4p
+SEQ: atcgACGAGTGCGT
+SEQ_LEN: 14
+BARCODE: ACGAGTGCGT
+BARCODE_NAME: MID1
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_rl_4p
+SEQ: atcgACACGACGACT
+SEQ_LEN: 15
+BARCODE: ACATGACGAC
+BARCODE_NAME: MID76
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 1
+---
+SEQ_NAME: test_Il_4p
+SEQ: atcgATCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_1mm
+SEQ: atcgAgGAGTGCGT
+SEQ_LEN: 14
+BARCODE: ACGAGTGCGT
+BARCODE_NAME: MID1
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 1
+---
+SEQ_NAME: test_rl_4p_1mm
+SEQ: atcgAgACGACGACT
+SEQ_LEN: 15
+BARCODE: ACATGACGAC
+BARCODE_NAME: MID76
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 2
+---
+SEQ_NAME: test_Il_4p_1mm
+SEQ: atcgAaCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_2mm
+SEQ: atcgAgGAGTGCcT
+SEQ_LEN: 14
+BARCODE: ACGAGTGCGT
+BARCODE_NAME: MID1
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 2
+---
+SEQ_NAME: test_rl_4p_2mm
+SEQ: atcgAgACGACGAgT
+SEQ_LEN: 15
+BARCODE: ACACGACGACT
+BARCODE_NAME: RL1
+BARCODE_POS: 4
+BARCODE_LEN: 11
+BARCODE_MISMATCHES: 2
+---
+SEQ_NAME: test_Il_4p_2mm
+SEQ: atcgAaCAgG
+SEQ_LEN: 10
+---
diff --git a/bp_test/out/find_barcodes.out.12 b/bp_test/out/find_barcodes.out.12
new file mode 100644
index 0000000..7187155
--- /dev/null
+++ b/bp_test/out/find_barcodes.out.12
@@ -0,0 +1,93 @@
+SEQ_NAME: test_gs
+SEQ: ACGAGTGCGT
+SEQ_LEN: 10
+---
+SEQ_NAME: test_rl
+SEQ: ACACGACGACT
+SEQ_LEN: 11
+---
+SEQ_NAME: test_Il
+SEQ: ATCACG
+SEQ_LEN: 6
+---
+SEQ_NAME: test_gs_4p
+SEQ: atcgACGAGTGCGT
+SEQ_LEN: 14
+BARCODE: ACGAGTGCGT
+BARCODE_NAME: MID1
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_rl_4p
+SEQ: atcgACACGACGACT
+SEQ_LEN: 15
+BARCODE: ACATGACGAC
+BARCODE_NAME: MID76
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 1
+---
+SEQ_NAME: test_Il_4p
+SEQ: atcgATCACG
+SEQ_LEN: 10
+BARCODE: ATCACG
+BARCODE_NAME: Index_1
+BARCODE_POS: 4
+BARCODE_LEN: 6
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_gs_4p_1mm
+SEQ: atcgAgGAGTGCGT
+SEQ_LEN: 14
+BARCODE: ACGAGTGCGT
+BARCODE_NAME: MID1
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 1
+---
+SEQ_NAME: test_rl_4p_1mm
+SEQ: atcgAgACGACGACT
+SEQ_LEN: 15
+BARCODE: ACATGACGAC
+BARCODE_NAME: MID76
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 2
+---
+SEQ_NAME: test_Il_4p_1mm
+SEQ: atcgAaCACG
+SEQ_LEN: 10
+BARCODE: ATCACG
+BARCODE_NAME: Index_1
+BARCODE_POS: 4
+BARCODE_LEN: 6
+BARCODE_MISMATCHES: 1
+---
+SEQ_NAME: test_gs_4p_2mm
+SEQ: atcgAgGAGTGCcT
+SEQ_LEN: 14
+BARCODE: ACGAGTGCGT
+BARCODE_NAME: MID1
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 2
+---
+SEQ_NAME: test_rl_4p_2mm
+SEQ: atcgAgACGACGAgT
+SEQ_LEN: 15
+BARCODE: ACACGACGACT
+BARCODE_NAME: RL1
+BARCODE_POS: 4
+BARCODE_LEN: 11
+BARCODE_MISMATCHES: 2
+---
+SEQ_NAME: test_Il_4p_2mm
+SEQ: atcgAaCAgG
+SEQ_LEN: 10
+BARCODE: ATCACG
+BARCODE_NAME: Index_1
+BARCODE_POS: 4
+BARCODE_LEN: 6
+BARCODE_MISMATCHES: 2
+---
diff --git a/bp_test/out/find_barcodes.out.13 b/bp_test/out/find_barcodes.out.13
new file mode 100644
index 0000000..fed8c2d
--- /dev/null
+++ b/bp_test/out/find_barcodes.out.13
@@ -0,0 +1,78 @@
+SEQ_NAME: test_gs
+SEQ: ACGAGTGCGT
+SEQ_LEN: 10
+---
+SEQ_NAME: test_rl
+SEQ: ACACGACGACT
+SEQ_LEN: 11
+---
+SEQ_NAME: test_Il
+SEQ: ATCACG
+SEQ_LEN: 6
+---
+SEQ_NAME: test_gs_4p
+SEQ: 
+SEQ_LEN: 0
+BARCODE: ACGAGTGCGT
+BARCODE_NAME: MID1
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_rl_4p
+SEQ: T
+SEQ_LEN: 1
+BARCODE: ACATGACGAC
+BARCODE_NAME: MID76
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 1
+---
+SEQ_NAME: test_Il_4p
+SEQ: atcgATCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_1mm
+SEQ: 
+SEQ_LEN: 0
+BARCODE: ACGAGTGCGT
+BARCODE_NAME: MID1
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 1
+---
+SEQ_NAME: test_rl_4p_1mm
+SEQ: T
+SEQ_LEN: 1
+BARCODE: ACATGACGAC
+BARCODE_NAME: MID76
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 2
+---
+SEQ_NAME: test_Il_4p_1mm
+SEQ: atcgAaCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_2mm
+SEQ: 
+SEQ_LEN: 0
+BARCODE: ACGAGTGCGT
+BARCODE_NAME: MID1
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 2
+---
+SEQ_NAME: test_rl_4p_2mm
+SEQ: 
+SEQ_LEN: 0
+BARCODE: ACACGACGACT
+BARCODE_NAME: RL1
+BARCODE_POS: 4
+BARCODE_LEN: 11
+BARCODE_MISMATCHES: 2
+---
+SEQ_NAME: test_Il_4p_2mm
+SEQ: atcgAaCAgG
+SEQ_LEN: 10
+---
diff --git a/bp_test/out/find_barcodes.out.2 b/bp_test/out/find_barcodes.out.2
new file mode 100644
index 0000000..88e38ef
--- /dev/null
+++ b/bp_test/out/find_barcodes.out.2
@@ -0,0 +1,58 @@
+SEQ_NAME: test_gs
+SEQ: ACGAGTGCGT
+SEQ_LEN: 10
+BARCODE: ACGAGTGCGT
+BARCODE_NAME: MID1
+BARCODE_POS: 0
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_rl
+SEQ: ACACGACGACT
+SEQ_LEN: 11
+BARCODE: ACACGACGACT
+BARCODE_NAME: RL1
+BARCODE_POS: 0
+BARCODE_LEN: 11
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_Il
+SEQ: ATCACG
+SEQ_LEN: 6
+---
+SEQ_NAME: test_gs_4p
+SEQ: atcgACGAGTGCGT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p
+SEQ: atcgACACGACGACT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p
+SEQ: atcgATCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_1mm
+SEQ: atcgAgGAGTGCGT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p_1mm
+SEQ: atcgAgACGACGACT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p_1mm
+SEQ: atcgAaCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_2mm
+SEQ: atcgAgGAGTGCcT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p_2mm
+SEQ: atcgAgACGACGAgT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p_2mm
+SEQ: atcgAaCAgG
+SEQ_LEN: 10
+---
diff --git a/bp_test/out/find_barcodes.out.3 b/bp_test/out/find_barcodes.out.3
new file mode 100644
index 0000000..f6939ab
--- /dev/null
+++ b/bp_test/out/find_barcodes.out.3
@@ -0,0 +1,63 @@
+SEQ_NAME: test_gs
+SEQ: ACGAGTGCGT
+SEQ_LEN: 10
+BARCODE: ACGAGTGCGT
+BARCODE_NAME: MID1
+BARCODE_POS: 0
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_rl
+SEQ: ACACGACGACT
+SEQ_LEN: 11
+BARCODE: ACACGACGACT
+BARCODE_NAME: RL1
+BARCODE_POS: 0
+BARCODE_LEN: 11
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_Il
+SEQ: ATCACG
+SEQ_LEN: 6
+BARCODE: ATCACG
+BARCODE_NAME: Index_1
+BARCODE_POS: 0
+BARCODE_LEN: 6
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_gs_4p
+SEQ: atcgACGAGTGCGT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p
+SEQ: atcgACACGACGACT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p
+SEQ: atcgATCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_1mm
+SEQ: atcgAgGAGTGCGT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p_1mm
+SEQ: atcgAgACGACGACT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p_1mm
+SEQ: atcgAaCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_2mm
+SEQ: atcgAgGAGTGCcT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p_2mm
+SEQ: atcgAgACGACGAgT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p_2mm
+SEQ: atcgAaCAgG
+SEQ_LEN: 10
+---
diff --git a/bp_test/out/find_barcodes.out.4 b/bp_test/out/find_barcodes.out.4
new file mode 100644
index 0000000..63655c1
--- /dev/null
+++ b/bp_test/out/find_barcodes.out.4
@@ -0,0 +1,53 @@
+SEQ_NAME: test_gs
+SEQ: ACGAGTGCGT
+SEQ_LEN: 10
+---
+SEQ_NAME: test_rl
+SEQ: ACACGACGACT
+SEQ_LEN: 11
+---
+SEQ_NAME: test_Il
+SEQ: ATCACG
+SEQ_LEN: 6
+---
+SEQ_NAME: test_gs_4p
+SEQ: atcgACGAGTGCGT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p
+SEQ: atcgACACGACGACT
+SEQ_LEN: 15
+BARCODE: ACACGACGACT
+BARCODE_NAME: RL1
+BARCODE_POS: 4
+BARCODE_LEN: 11
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_Il_4p
+SEQ: atcgATCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_1mm
+SEQ: atcgAgGAGTGCGT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p_1mm
+SEQ: atcgAgACGACGACT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p_1mm
+SEQ: atcgAaCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_2mm
+SEQ: atcgAgGAGTGCcT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p_2mm
+SEQ: atcgAgACGACGAgT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p_2mm
+SEQ: atcgAaCAgG
+SEQ_LEN: 10
+---
diff --git a/bp_test/out/find_barcodes.out.5 b/bp_test/out/find_barcodes.out.5
new file mode 100644
index 0000000..b3bb5da
--- /dev/null
+++ b/bp_test/out/find_barcodes.out.5
@@ -0,0 +1,58 @@
+SEQ_NAME: test_gs
+SEQ: ACGAGTGCGT
+SEQ_LEN: 10
+---
+SEQ_NAME: test_rl
+SEQ: ACACGACGACT
+SEQ_LEN: 11
+---
+SEQ_NAME: test_Il
+SEQ: ATCACG
+SEQ_LEN: 6
+---
+SEQ_NAME: test_gs_4p
+SEQ: atcgACGAGTGCGT
+SEQ_LEN: 14
+BARCODE: ACGAGTGCGT
+BARCODE_NAME: MID1
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_rl_4p
+SEQ: atcgACACGACGACT
+SEQ_LEN: 15
+BARCODE: ACACGACGACT
+BARCODE_NAME: RL1
+BARCODE_POS: 4
+BARCODE_LEN: 11
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_Il_4p
+SEQ: atcgATCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_1mm
+SEQ: atcgAgGAGTGCGT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p_1mm
+SEQ: atcgAgACGACGACT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p_1mm
+SEQ: atcgAaCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_2mm
+SEQ: atcgAgGAGTGCcT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p_2mm
+SEQ: atcgAgACGACGAgT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p_2mm
+SEQ: atcgAaCAgG
+SEQ_LEN: 10
+---
diff --git a/bp_test/out/find_barcodes.out.6 b/bp_test/out/find_barcodes.out.6
new file mode 100644
index 0000000..d01dc99
--- /dev/null
+++ b/bp_test/out/find_barcodes.out.6
@@ -0,0 +1,63 @@
+SEQ_NAME: test_gs
+SEQ: ACGAGTGCGT
+SEQ_LEN: 10
+---
+SEQ_NAME: test_rl
+SEQ: ACACGACGACT
+SEQ_LEN: 11
+---
+SEQ_NAME: test_Il
+SEQ: ATCACG
+SEQ_LEN: 6
+---
+SEQ_NAME: test_gs_4p
+SEQ: atcgACGAGTGCGT
+SEQ_LEN: 14
+BARCODE: ACGAGTGCGT
+BARCODE_NAME: MID1
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_rl_4p
+SEQ: atcgACACGACGACT
+SEQ_LEN: 15
+BARCODE: ACACGACGACT
+BARCODE_NAME: RL1
+BARCODE_POS: 4
+BARCODE_LEN: 11
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_Il_4p
+SEQ: atcgATCACG
+SEQ_LEN: 10
+BARCODE: ATCACG
+BARCODE_NAME: Index_1
+BARCODE_POS: 4
+BARCODE_LEN: 6
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_gs_4p_1mm
+SEQ: atcgAgGAGTGCGT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p_1mm
+SEQ: atcgAgACGACGACT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p_1mm
+SEQ: atcgAaCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_2mm
+SEQ: atcgAgGAGTGCcT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p_2mm
+SEQ: atcgAgACGACGAgT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p_2mm
+SEQ: atcgAaCAgG
+SEQ_LEN: 10
+---
diff --git a/bp_test/out/find_barcodes.out.7 b/bp_test/out/find_barcodes.out.7
new file mode 100644
index 0000000..6895222
--- /dev/null
+++ b/bp_test/out/find_barcodes.out.7
@@ -0,0 +1,58 @@
+SEQ_NAME: test_gs
+SEQ: ACGAGTGCGT
+SEQ_LEN: 10
+---
+SEQ_NAME: test_rl
+SEQ: ACACGACGACT
+SEQ_LEN: 11
+---
+SEQ_NAME: test_Il
+SEQ: ATCACG
+SEQ_LEN: 6
+---
+SEQ_NAME: test_gs_4p
+SEQ: atcgACGAGTGCGT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p
+SEQ: atcgACACGACGACT
+SEQ_LEN: 15
+BARCODE: ACACGACGACT
+BARCODE_NAME: RL1
+BARCODE_POS: 4
+BARCODE_LEN: 11
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_Il_4p
+SEQ: atcgATCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_1mm
+SEQ: atcgAgGAGTGCGT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p_1mm
+SEQ: atcgAgACGACGACT
+SEQ_LEN: 15
+BARCODE: ACACGACGACT
+BARCODE_NAME: RL1
+BARCODE_POS: 4
+BARCODE_LEN: 11
+BARCODE_MISMATCHES: 1
+---
+SEQ_NAME: test_Il_4p_1mm
+SEQ: atcgAaCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_2mm
+SEQ: atcgAgGAGTGCcT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p_2mm
+SEQ: atcgAgACGACGAgT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p_2mm
+SEQ: atcgAaCAgG
+SEQ_LEN: 10
+---
diff --git a/bp_test/out/find_barcodes.out.8 b/bp_test/out/find_barcodes.out.8
new file mode 100644
index 0000000..4cae1ef
--- /dev/null
+++ b/bp_test/out/find_barcodes.out.8
@@ -0,0 +1,68 @@
+SEQ_NAME: test_gs
+SEQ: ACGAGTGCGT
+SEQ_LEN: 10
+---
+SEQ_NAME: test_rl
+SEQ: ACACGACGACT
+SEQ_LEN: 11
+---
+SEQ_NAME: test_Il
+SEQ: ATCACG
+SEQ_LEN: 6
+---
+SEQ_NAME: test_gs_4p
+SEQ: atcgACGAGTGCGT
+SEQ_LEN: 14
+BARCODE: ACGAGTGCGT
+BARCODE_NAME: MID1
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_rl_4p
+SEQ: atcgACACGACGACT
+SEQ_LEN: 15
+BARCODE: ACATGACGAC
+BARCODE_NAME: MID76
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 1
+---
+SEQ_NAME: test_Il_4p
+SEQ: atcgATCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_1mm
+SEQ: atcgAgGAGTGCGT
+SEQ_LEN: 14
+BARCODE: ACGAGTGCGT
+BARCODE_NAME: MID1
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 1
+---
+SEQ_NAME: test_rl_4p_1mm
+SEQ: atcgAgACGACGACT
+SEQ_LEN: 15
+BARCODE: ACACGACGACT
+BARCODE_NAME: RL1
+BARCODE_POS: 4
+BARCODE_LEN: 11
+BARCODE_MISMATCHES: 1
+---
+SEQ_NAME: test_Il_4p_1mm
+SEQ: atcgAaCACG
+SEQ_LEN: 10
+---
+SEQ_NAME: test_gs_4p_2mm
+SEQ: atcgAgGAGTGCcT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p_2mm
+SEQ: atcgAgACGACGAgT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p_2mm
+SEQ: atcgAaCAgG
+SEQ_LEN: 10
+---
diff --git a/bp_test/out/find_barcodes.out.9 b/bp_test/out/find_barcodes.out.9
new file mode 100644
index 0000000..178ebda
--- /dev/null
+++ b/bp_test/out/find_barcodes.out.9
@@ -0,0 +1,78 @@
+SEQ_NAME: test_gs
+SEQ: ACGAGTGCGT
+SEQ_LEN: 10
+---
+SEQ_NAME: test_rl
+SEQ: ACACGACGACT
+SEQ_LEN: 11
+---
+SEQ_NAME: test_Il
+SEQ: ATCACG
+SEQ_LEN: 6
+---
+SEQ_NAME: test_gs_4p
+SEQ: atcgACGAGTGCGT
+SEQ_LEN: 14
+BARCODE: ACGAGTGCGT
+BARCODE_NAME: MID1
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_rl_4p
+SEQ: atcgACACGACGACT
+SEQ_LEN: 15
+BARCODE: ACATGACGAC
+BARCODE_NAME: MID76
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 1
+---
+SEQ_NAME: test_Il_4p
+SEQ: atcgATCACG
+SEQ_LEN: 10
+BARCODE: ATCACG
+BARCODE_NAME: Index_1
+BARCODE_POS: 4
+BARCODE_LEN: 6
+BARCODE_MISMATCHES: 0
+---
+SEQ_NAME: test_gs_4p_1mm
+SEQ: atcgAgGAGTGCGT
+SEQ_LEN: 14
+BARCODE: ACGAGTGCGT
+BARCODE_NAME: MID1
+BARCODE_POS: 4
+BARCODE_LEN: 10
+BARCODE_MISMATCHES: 1
+---
+SEQ_NAME: test_rl_4p_1mm
+SEQ: atcgAgACGACGACT
+SEQ_LEN: 15
+BARCODE: ACACGACGACT
+BARCODE_NAME: RL1
+BARCODE_POS: 4
+BARCODE_LEN: 11
+BARCODE_MISMATCHES: 1
+---
+SEQ_NAME: test_Il_4p_1mm
+SEQ: atcgAaCACG
+SEQ_LEN: 10
+BARCODE: ATCACG
+BARCODE_NAME: Index_1
+BARCODE_POS: 4
+BARCODE_LEN: 6
+BARCODE_MISMATCHES: 1
+---
+SEQ_NAME: test_gs_4p_2mm
+SEQ: atcgAgGAGTGCcT
+SEQ_LEN: 14
+---
+SEQ_NAME: test_rl_4p_2mm
+SEQ: atcgAgACGACGAgT
+SEQ_LEN: 15
+---
+SEQ_NAME: test_Il_4p_2mm
+SEQ: atcgAaCAgG
+SEQ_LEN: 10
+---
diff --git a/bp_test/test/test_find_barcodes b/bp_test/test/test_find_barcodes
new file mode 100755
index 0000000..c8317bf
--- /dev/null
+++ b/bp_test/test/test_find_barcodes
@@ -0,0 +1,55 @@
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -I $in.1 -r -O $tmp"
+assert_no_diff $tmp $out.1
+clean
+
+run "$bp -I $in.1 -rg -O $tmp"
+assert_no_diff $tmp $out.2
+clean
+
+run "$bp -I $in.1 -rgb $in.2 -O $tmp"
+assert_no_diff $tmp $out.3
+clean
+
+run "$bp -I $in.1 -p 4 -r -O $tmp"
+assert_no_diff $tmp $out.4
+clean
+
+run "$bp -I $in.1 -p 4 -rg -O $tmp"
+assert_no_diff $tmp $out.5
+clean
+
+run "$bp -I $in.1 -p 4 -rgb $in.2 -O $tmp"
+assert_no_diff $tmp $out.6
+clean
+
+run "$bp -I $in.1 -p 4 -m 1 -r -O $tmp"
+assert_no_diff $tmp $out.7
+clean
+
+run "$bp -I $in.1 -p 4 -m 1 -rg -O $tmp"
+assert_no_diff $tmp $out.8
+clean
+
+run "$bp -I $in.1 -p 4 -m 1 -rgb $in.2 -O $tmp"
+assert_no_diff $tmp $out.9
+clean
+
+run "$bp -I $in.1 -p 4 -m 2 -r -O $tmp"
+assert_no_diff $tmp $out.10
+clean
+
+run "$bp -I $in.1 -p 4 -m 2 -rg -O $tmp"
+assert_no_diff $tmp $out.11
+clean
+
+run "$bp -I $in.1 -p 4 -m 2 -rgb $in.2 -O $tmp"
+assert_no_diff $tmp $out.12
+clean
+
+run "$bp -I $in.1 -p 4 -m 2 -Rrg -O $tmp"
+assert_no_diff $tmp $out.13
+clean
diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index 394d6fb..c3e4839 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -282,6 +282,7 @@ class Seq
   # Method to shuffle a sequence readomly inline.
   def shuffle!
     self.seq = self.seq.split('').shuffle!.join
+    self
   end
 
   # Method that returns a subsequence of from a given start position