bio-fastqc 0.8.0 → 0.8.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 6cbdb6a0b5125d4d90dc3e5b17f451b6a35db13f
-  data.tar.gz: 2bf19899ae60a2ce06f129adcffb2b14ba345191
+  metadata.gz: 97952edf408e39ea12f758937a842327541bcdca
+  data.tar.gz: 065a3530efa2d3c4bb0d74b3079686314b1f3469
 SHA512:
-  metadata.gz: 3a29404861f22e429d96f6253a7f8d3a4b3bb2c6960343bf21e627603f1f3276709004ed2e5c001d02ac1456c20d13e5e89a354b6a82d099fe085e73b86abc52
-  data.tar.gz: c2de3c14c3d844792e1ac00e1ed5c7107754886ebdfb98be6a07071b497da108a7e6ee0ad153cf27e41380984eecbe289d8692f74032c82d9382f3202b0b5e22
+  metadata.gz: 7fba5f8517a7f02e5bce12cfa0928e13b4c478d5c4a74aa6398ab458bff682bec1b96b5fb8fde26632925da771f070277822024bd9395efe5c706253ffe7e2f5
+  data.tar.gz: 3575372ede801a2dbae8623854e13d8857472a95134d98810c3aac33e90c7fd592743a050ec380bf15ef70ae0ad4c23545de3e8fed81eec74b823773d50f9321

data/VERSION

@@ -1 +1 @@
-0.8.0
+0.8.2

data/lib/bio/fastqc.rb

@@ -1,4 +1,4 @@
 module Bio
   module FastQC
   end
-end
+end

data/lib/bio/fastqc/data.rb

@@ -5,32 +5,37 @@ require 'zip'
 module Bio
   module FastQC
     class Data
-  		class << self
-  			def read(file)
-  				read_zipfile(file)
-  			rescue Zip::Error
-  				read_flatfile(file)
+      class << self
+        def read(file)
+          read_zipfile(file)
+        rescue Zip::Error
+          read_flatfile(file)
         rescue Errno::EISDIR
           read_dir(file)
-  			end
+        end
 
-  			def read_zipfile(file)
-  				Zip::File.open(file) do |zipfile|
-  					zipfile.glob('*/fastqc_data.txt').first.get_input_stream.read
-  				end
-  			end
+        def read_zipfile(file)
+          Zip::File.open(file) do |zipfile|
+            d = zipfile.glob('*/fastqc_data.txt').first
+            filenotfound(file) if !d
+            d.get_input_stream.read
+          end
+        end
 
-  			def read_flatfile(file)
-  				open(file).read
-  			end
+        def read_flatfile(file)
+          open(file).read
+        end
 
-  			def read_dir(file)
-  				open(File.join(file, "fastqc_data.txt")).read
-  			rescue Errno::ENOENT
-  				puts "FastQC data file fastqc_data.txt not found"
-  				exit
-  			end
-  		end
-  	end
+        def read_dir(file)
+          open(File.join(file, "fastqc_data.txt")).read
+        rescue Errno::ENOENT
+          filenotfound(file)
+        end
+
+        def filenotfound(file)
+          raise "FastQC data file fastqc_data.txt not found, input file: #{file}"
+        end
+      end
+    end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-fastqc
 version: !ruby/object:Gem::Version
-  version: 0.8.0
+  version: 0.8.2
 platform: ruby
 authors:
 - Tazro Inutano Ohta
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-07-08 00:00:00.000000000 Z
+date: 2016-09-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rubyzip
@@ -228,6 +228,7 @@ files:
 - lib/bio/fastqc/parser.rb
 - lib/bio/fastqc/semantics.rb
 - spec/bio-fastqc_spec.rb
+- spec/corrupt_example_fastqc.zip
 - spec/example_fastqc.zip
 - spec/example_fastqc_454.zip
 - spec/spec_helper.rb