nugen_barcode_splitter 0.0.10 → 0.0.11

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 . 10
+      V E R S I O N - 0 . 0 . 11
       #{$0} [options] -p project_dir -o out_dir -c sample_sheet_nugen
 _____________________________________________________________________________
 

data/lib/nugen_barcode_splitter/merger.rb

@@ -79,13 +79,14 @@ class Merger
             rev_out_files[i].write(rev_line)
             for k in 1..3
               fwd_file.readline()
-              rev_splitted_files[i].readline if marker2
               compare_line_fwd = fwd_splitted_files[i].readline()
               fwd_out_files[i].write("NNNN"+compare_line_fwd) if k == 1
               fwd_out_files[i].write(compare_line_fwd) if k == 2
               fwd_out_files[i].write("@@@@"+compare_line_fwd) if k == 3
               rev_out_files[i].write(rev_file.readline())
             end
+            fwd_file.lineno = fwd_file.lineno - 1
+            rev_file.lineno = rev_file.lineno - 1
           end
         end
         if !marker && !rev_splitted_files[i].eof?
@@ -111,6 +112,8 @@ class Merger
               rev_out_files[i].write("@@@@"+compare_line_rev) if k == 3
               fwd_out_files[i].write(fwd_file.readline())
             end
+            fwd_file.lineno = fwd_file.lineno - 1
+            rev_file.lineno = rev_file.lineno - 1
           end
         end
         break if !marker

data/lib/nugen_barcode_splitter/nugen_template.rb

@@ -4,18 +4,26 @@ class NugenTemplate
 
   def initialize(fastq_multx, options)
     @template =<<EOF
-#{fastq_multx} #{options}  <%= @barcodes %> \\
-  <(gunzip -c <%= @read %>) \\
-  -o <%= @lane_dir %>/<%= @direction %>.%.fq  \\
-  >> <%= @lane_dir %>/nugen_demultiplexing.log
+gunzip -c <%= @read %> | #{fastq_multx} \\
+  --bcfile <%= @barcodes %> #{options} <%= @options %> \\
+  --prefix <%= @lane_dir %>/<%= @direction %> \\
+  --suffix ".fq"
 EOF
+#    @template =<<EOF
+##{fastq_multx} #{options}  <%= @barcodes %> \\
+#  <(gunzip -c <%= @read %>) \\
+#  -o <%= @lane_dir %>/<%= @direction %>.%.fq  \\
+#  >> <%= @lane_dir %>/nugen_demultiplexing.log
+#EOF
   end
 
   def fill(lane, number, lane_dir, barcodes, read, is_fwd)
     if is_fwd
-      direction = "R1_#{number}"
+      direction = "R1_#{number}_"
+      options = "--bol"
     else
-      direction = "R2_#{number}"
+      direction = "R2_#{number}_"
+      options = "--eol"
     end
     context = {
       :lane => lane,
@@ -23,7 +31,8 @@ EOF
       :lane_dir => lane_dir,
       :barcodes => barcodes,
       :read => read,
-      :direction => direction
+      :direction => direction,
+      :options => options
     }
 
     eruby = Erubis::Eruby.new(@template)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: nugen_barcode_splitter
 version: !ruby/object:Gem::Version
-  version: 0.0.10
+  version: 0.0.11
   prerelease: 
 platform: ruby
 authors: