demultiplexer 0.1.0 → 0.1.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 9fd3a1561408ab33687de0b73f424873850cb55e
-  data.tar.gz: f57280b5897b453d43b0de72ecd72414ed4ac428
+  metadata.gz: 8ff1437c217ab2d8153534938b2712511a3c5b4e
+  data.tar.gz: 0271db4840b41e5172a9bee4d55c85813a7a1140
 SHA512:
-  metadata.gz: 4db2e0c15013c7a03ae483d0595b87feb147ff7284f2ae3541f0fe21c7b3e57e86d25cb4c1edd71e12042f5cce58f6c8773968d756f4d9812a20886205d71475
-  data.tar.gz: 1cfea327fdda5aa1d7f263d9b6f2e43890f4fcdcdac5c1380964c62cc39918e84b9121bfa0724625601a71f65202933066229b2abd267203b01398a231b36118
+  metadata.gz: 3fd4d46a4ed3775ed6168893fa023ff89bacb3c3e76b3de5ca676945218bfef1bcaec8b64ca6e91c94070318ac1521d630b75fbea8760e594738f2aeda44ceca
+  data.tar.gz: 241e58b5cbbe9822980a001997042b11b8b72a0b57b5a41f54e9d4b971126328bd223f2e3795b6aaf5280e1ba7b9cf1bdec3e360b7c5aa587b5398e166782a9e

data/bin/demultiplexer

@@ -73,7 +73,7 @@ USAGE = <<USAGE.gsub(/^\s+\|/, '')
   |
   |Usage: #{File.basename(__FILE__)} [options] <FASTQ files>
   |
-  |Example: #{File.basename(__FILE__)} -m samples.tsv Data*.fastq.gz
+  |Example: #{File.basename(__FILE__)} -s samples.tsv Data*.fastq.gz
   |
   |Options:
 USAGE
@@ -89,54 +89,55 @@ options = {}
 OptionParser.new do |opts|
   opts.banner = USAGE
 
-  opts.on('-h', '--help', 'Display this screen') do
+  opts.on('-h', '--help', 'Display this screen.') do
     $stderr.puts opts
     exit
   end
 
-  opts.on('-s', '--samples_file <file>', String, 'Path to samples file') do |o|
+  opts.on('-s', '--samples_file <file>', String, 'Path to samples file.') do |o|
     options[:samples_file] = o
   end
 
   opts.on('-m', '--mismatches_max <uint>', Integer, 'Maximum mismatches_max ',
-          "allowed (default=#{DEFAULT_MISMATCHES})") do |o|
+          "allowed (default=#{DEFAULT_MISMATCHES}).") do |o|
     options[:mismatches_max] = o
   end
 
-  opts.on('--revcomp_index1', 'Reverse complement index1') do |o|
+  opts.on('--revcomp_index1', 'Reverse complement index1.') do |o|
     options[:revcomp_index1] = o
   end
 
-  opts.on('--revcomp_index2', 'Reverse complement index2') do |o|
+  opts.on('--revcomp_index2', 'Reverse complement index2.') do |o|
     options[:revcomp_index2] = o
   end
 
   opts.on('--scores_min <uint>', Integer, 'Drop reads if a single position in ',
           'the index have a quality score ',
-          'below scores_min (default= ' \
-          "#{DEFAULT_SCORE_MIN})") do |o|
+          'below scores_min (default=' \
+          "#{DEFAULT_SCORE_MIN}).") do |o|
     options[:scores_min] = o
   end
 
   opts.on('--scores_mean <uint>', Integer, 'Drop reads if the mean index',
           'quality score is below ',
-          'scores_mean (default= ' \
-          "#{DEFAULT_SCORE_MEAN})") do |o|
+          'scores_mean (default=' \
+          "#{DEFAULT_SCORE_MEAN}).") do |o|
     options[:scores_mean] = o
   end
 
-  opts.on('-o', '--output_dir <dir>', String, 'Output directory') do |o|
+  opts.on('-o', '--output_dir <dir>', String, 'Output directory' \
+          '(default=<pwd>).') do |o|
     options[:output_dir] = o
   end
 
   opts.on('-c', '--compress <gzip|bzip2>', String, 'Compress output using ' \
           'gzip or bzip2 ',
           '(default=' \
-          '<no compression>)') do |o|
+          '<no compression>).') do |o|
     options[:compress] = o.to_sym
   end
 
-  opts.on('-v', '--verbose', 'Verbose output') do |o|
+  opts.on('-v', '--verbose', 'Verbose output.') do |o|
     options[:verbose] = o
   end
 end.parse!

data/demultiplexer.gemspec

@@ -15,6 +15,7 @@ Gem::Specification.new do |s|
   s.homepage          = 'http://github.com/maasha/demultiplexer'
   s.license           = 'GPL2'
   s.rubygems_version  = '2.0.0'
+  s.executables       << 'demultiplexer'
   s.files             = `git ls-files`.split("\n")
   s.test_files        = `git ls-files -- {test,spec,features}/*`.split("\n")
   s.require_paths     = ['lib']

data/lib/demultiplexer/version.rb

@@ -23,5 +23,5 @@
 
 # Adding VERSION constant to class.
 class Demultiplexer
-  VERSION = '0.1.0'
+  VERSION = '0.1.2'
 end

data/lib/sample_reader.rb

@@ -117,9 +117,13 @@ class SampleReader
   def samples_read(file)
     samples = []
 
-    CSV.read(file, col_sep: "\t").each do |id, index1, index2|
+    CSV.read(file, col_sep: ' ').each do |id, index1, index2|
       next if id[0] == '#'
 
+      fail SampleReaderError, "Id not found in file: #{file}" if id.nil?
+      fail SampleReaderError, "Index1 not found in file: #{file}" if index1.nil?
+      fail SampleReaderError, "Index2 not found in file: #{file}" if index2.nil?
+
       samples << Sample.new(id, index1.upcase, index2.upcase)
     end
 

data/test/helper.rb

@@ -21,6 +21,14 @@
 #                                                                              #
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< #
 
+require 'simplecov'
+
+SimpleCov.start do
+  add_filter "/test/"
+end
+
+SimpleCov.command_name 'test:units'
+
 require 'pp'
 require 'fileutils'
 require 'tempfile'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: demultiplexer
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.1.2
 platform: ruby
 authors:
 - Martin A. Hansen
@@ -68,7 +68,8 @@ dependencies:
         version: 0.9.2
 description: Demultiplex sequences from the Illumina platform.
 email: mail@maasha.dk
-executables: []
+executables:
+- demultiplexer
 extensions: []
 extra_rdoc_files: []
 files: