nugen_barcode_splitter 0.0.17 → 0.0.18
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data/bin/nugen_barcode_splitter
CHANGED
@@ -147,13 +147,13 @@ Dir.glob(options[:project_dir]+"/*").each do |p|
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status = system('bash', '-c', cmd)
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raise "Calling the template for fwd did not succeed!" if !status
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end
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150
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-
cmd = nugen_temp.fill(lane,number,outdir, barcodes, rev, false)
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-
if options[:debug]
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-
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else
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-
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-
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end
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150
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+
#cmd = nugen_temp.fill(lane,number,outdir, barcodes, rev, false)
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#if options[:debug]
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# STDERR.puts cmd if options[:debug]
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#else
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# status = system('bash', '-c', cmd)
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# raise "Calling the template for rev did not succeed!" if !status
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+
#end
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# Merging
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merger = Merger.new(fwd,rev,outdir,number,barcodes)
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stats = merger.merge()
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@@ -3,8 +3,6 @@ require "zlib"
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class Merger
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def initialize(fwd,rev,outdir,number,barcodes)
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# get sampleID
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-
@values_fwd = []
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-
@values_rev = []
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@sample_ids = []
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i = 0
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File.open(barcodes).each do |line|
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@@ -19,7 +17,7 @@ class Merger
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@number = number
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end
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-
attr_accessor :sample_ids
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+
attr_accessor :sample_ids
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#def prepare_hash()
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# @sample_ids.each_with_index do |sample_id, i|
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@@ -61,7 +59,7 @@ class Merger
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@sample_ids.each_with_index do |sample_id, i|
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fwd_splitted_files[i] = File.open(@outdir+"/R1_#{@number}.#{sample_id}.fq")
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-
rev_splitted_files[i] = File.open(@outdir+"/R2_#{@number}.#{sample_id}.fq")
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+
#rev_splitted_files[i] = File.open(@outdir+"/R2_#{@number}.#{sample_id}.fq")
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#OUTFILES????
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fwd_out_files[i] = File.open(@outdir+"/R1_#{@number}.#{sample_id}.updated.fq",'w')
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rev_out_files[i] = File.open(@outdir+"/R2_#{@number}.#{sample_id}.updated.fq",'w')
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@@ -74,11 +72,12 @@ class Merger
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fwd_name = fwd_line.split(" ")
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marker = true
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+
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@sample_ids.each_with_index do |sample_id, i|
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-
if !fwd_splitted_files[i].eof?
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+
if !fwd_splitted_files[i].eof? && marker
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compare_line_fwd = fwd_splitted_files[i].readline()
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name_compare_fwd = compare_line_fwd.split(" ")
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-
if fwd_name[0] == name_compare_fwd[0]
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+
if fwd_name[0] == name_compare_fwd[0]
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marker = false
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statistics[i] += 1
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fwd_out_files[i].write(fwd_line)
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@@ -94,49 +93,52 @@ class Merger
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fwd_file.lineno = fwd_file.lineno - 1
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rev_file.lineno = rev_file.lineno - 1
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else
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-
#puts compare_line_fwd
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fwd_splitted_files[i].pos = fwd_splitted_files[i].pos - compare_line_fwd.length()
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end
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end
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-
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-
if !marker && !rev_splitted_files[i].eof?
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-
compare_line_rev = rev_splitted_files[i].readline()
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-
name_compare_rev = compare_line_rev.split(" ")
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-
if name_compare_rev[0] == name_compare_fwd[0]
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for k in 1..3
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compare_line_rev = rev_splitted_files[i].readline()
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end
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else
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#puts compare_line_rev
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-
rev_splitted_files[i].pos = rev_splitted_files[i].pos - compare_line_rev.length()
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end
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end
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-
break if !marker
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-
if !rev_splitted_files[i].eof?
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compare_line_rev = rev_splitted_files[i].readline()
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name_compare_rev = compare_line_rev.split(" ")
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if rev_name[0] == name_compare_rev[0] && marker
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marker = false
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statistics[i] += 1
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fwd_out_files[i].write(fwd_line)
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rev_out_files[i].write(rev_line)
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for k in 1..3
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rev_file.readline()
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compare_line_rev = rev_splitted_files[i].readline()
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-
rev_out_files[i].write(compare_line_rev.gsub(/[A-Z]{4}$/,"NNNN")) if k == 1
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rev_out_files[i].write(compare_line_rev) if k == 2
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rev_out_files[i].write(compare_line_rev.gsub(/[\S]{4}$/,"@@@@")) if k == 3
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fwd_out_files[i].write(fwd_file.readline())
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-
end
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-
fwd_file.lineno = fwd_file.lineno - 1
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rev_file.lineno = rev_file.lineno - 1
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else
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rev_splitted_files[i].pos = rev_splitted_files[i].pos - compare_line_rev.length()
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end
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end
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-
break if !marker
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end
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+
# if !marker && !rev_splitted_files[i].eof?
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# compare_line_rev = rev_splitted_files[i].readline()
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# name_compare_rev = compare_line_rev.split(" ")
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# if name_compare_rev[0] == name_compare_fwd[0]
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# for k in 1..3
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# compare_line_rev = rev_splitted_files[i].readline()
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# end
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# else
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# #puts compare_line_rev
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# rev_splitted_files[i].pos = rev_splitted_files[i].pos - compare_line_rev.length()
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# end
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# end
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# break if !marker
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# if !rev_splitted_files[i].eof? && marker
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# compare_line_rev = rev_splitted_files[i].readline()
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# name_compare_rev = compare_line_rev.split(" ")
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# puts "REV: " + compare_line_rev if i == 2
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# #puts name_compare_rev[0]
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# if rev_name[0] == name_compare_rev[0]
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# marker = false
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# statistics[i] += 1
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# fwd_out_files[i].write(fwd_line)
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# rev_out_files[i].write(rev_line)
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# for k in 1..3
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# rev_file.readline()
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# compare_line_rev = rev_splitted_files[i].readline()
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# rev_out_files[i].write(compare_line_rev.gsub(/[A-Z]{4}$/,"NNNN")) if k == 1
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# rev_out_files[i].write(compare_line_rev) if k == 2
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# rev_out_files[i].write(compare_line_rev.gsub(/[\S]{4}$/,"@@@@")) if k == 3
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# fwd_out_files[i].write(fwd_file.readline())
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# end
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# fwd_file.lineno = fwd_file.lineno - 1
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# rev_file.lineno = rev_file.lineno - 1
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# else
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# rev_splitted_files[i].pos = rev_splitted_files[i].pos - compare_line_rev.length()
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# end
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# end
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# break if !marker
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#end
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if marker
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statistics[-2] += 1
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fwd_out_unmatched.write(fwd_line)
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@@ -11,7 +11,7 @@ class NugenBarcodeSplitterTest < Test::Unit::TestCase
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assert template.to_s.include?("fastq-multx")
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assert template.to_s.include?("<%= @read %>")
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temp = template.fill("Lane_3", "33", "~/Lane3/", "bc", "fwd", true)
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assert_equal(temp.to_s, "fastq-multx
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assert_equal(temp.to_s, "gunzip -c fwd | fastq-multx \\\n --bcfile bc --bol \\\n --prefix ~/Lane3//R1_33. \\\n --suffix \".fq\"\n")
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end
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def test_fastq
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@@ -54,12 +54,17 @@ class NugenBarcodeSplitterTest < Test::Unit::TestCase
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end
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def test_merger
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merger = Merger.new("test/fixtures/Sample_Lane5/k.gz",
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assert_equal(merger.sample_ids, ["RX3", "RX4", "RX3X2", "RX4X2"])
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#merger = Merger.new("test/fixtures/Sample_Lane5/k.gz",
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# "test/fixtures/Sample_Lane5/l.gz",
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# "test/fixtures/Sample_Lane5", "001", "test/fixtures/barcode_5.txt")
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#assert_equal(merger.sample_ids, ["RX3", "RX4", "RX3X2", "RX4X2"])
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#stats = merger.merge()
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#assert_equal("RX3\t18\nRX4\t7\nRX3X2\t16\nRX4X2\t8\nunmatched\t1\ntotal\t50\n",stats)
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merger = Merger.new("test/fixtures/Sample_Lane8/Lane8_NoIndex_L008_R1_019.fastq.gz",
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"test/fixtures/Sample_Lane8/Lane8_NoIndex_L008_R2_019.fastq.gz",
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"test/fixtures/Sample_Lane8", "019", "test/fixtures/barcode_8.txt")
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stats = merger.merge()
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assert_equal([28, 18, 26, 21, 7],stats)
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#assert.equal(merger.values_fwd[1].value_at(),{"sfggf"=>"dffg"})
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assert_equal("RX9\t22464\nRX10\t28699\nRX9X2\t26434\nRX10X2\t22994\nunmatched\t15445\ntotal\t116036\n",stats)
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end
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end
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