nugen_barcode_splitter 0.0.4 → 0.0.5

data/bin/nugen_barcode_splitter

@@ -5,7 +5,7 @@ require "nugen_barcode_splitter"
 require "fileutils"
 
 usage =<<EOF
-      V E R S I O N - 0 . 0 . 4
+      V E R S I O N - 0 . 0 . 5
       #{$0} [options] -p project_dir -o out_dir -c sample_sheet_nugen
 _____________________________________________________________________________
 
@@ -138,7 +138,7 @@ Dir.glob(options[:project_dir]+"/*").each do |p|
     if options[:debug]
       STDERR.puts cmd if options[:debug]
     else
-      status = system(cmd)
+      status = system('bash', '-c', cmd)
       raise "Calling the template did not succeed!" if !status
     end
   end
@@ -147,7 +147,7 @@ Dir.glob(options[:project_dir]+"/*").each do |p|
   Dir.glob(outdir+"/*").each do |fwd|
     if fwd =~ /nugen_demultiplexing.log/
       sample_sheet.lanes
-      statistics = Statistics.new(fwd, )
+      statistics = Statistics.new(fwd)
     end
     next unless fwd =~ /R1_[0-9]{3}./
     cmd = "base_adder #{fwd} 4 #{fwd}_added"

data/lib/nugen_barcode_splitter/statistics.rb

@@ -1,6 +1,18 @@
 class Statistics
 
-  def initialize(lane_log, barcodes)
+  def initialize(lane_log)
+    # getting barcodes:
+    i = 0
+    @barcodes = []
+    File.open(lane_log).each do |line|
+      next if line.include?("Id")
+      next if line.empty?
+      break if line.include?("unmatched")
+      line = line.split("\t")
+      barcodes[i] = line[0]
+      i += 1
+    end
+
     @num_reads = Array.new(barcodes.length(),0)
     @num_unmatched = 0
     @total = 0

data/test/test_mutations_caller_pipeline.rb

@@ -47,7 +47,7 @@ class NugenBarcodeSplitterTest < Test::Unit::TestCase
 
   def test_statistics
     log_file = "test/fixtures/Lane4.log"
-    stats = Statistics.new(log_file, ["R1", "R2", "R12", "R22"])
+    stats = Statistics.new(log_file)
     assert_equal(stats.total, 31920000)
     assert_equal(stats.num_reads[0], 8533927)
     assert_equal(stats.num_unmatched, 2614681)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: nugen_barcode_splitter
 version: !ruby/object:Gem::Version
-  version: 0.0.4
+  version: 0.0.5
   prerelease: 
 platform: ruby
 authors: