bio-ucsc-api 0.6.1 → 0.6.2

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data/ChangeLog.md

@@ -1,4 +1,6 @@
 #Change Log
+ * **BUG-FIX** (v.0.6.2) NoMemoryError in Bio::Ucsc::File::Twobit.open. Now internally File.open is used instead of Kernel.open.
+ * **UPDATE** (v.0.6.1) Support new human hg38 reference. Newer tables after this release will be supported in later varsions.
  * **NEW** (v0.6.0): Support ActiveRecord v4.0 (a part of Ruby on Ralils v4.0). Other related library dependencies are also updated. To Supress deprecation warnings for using dynamic finders such as 'find_by_name_and_chrom', use `ActiveSupport::Deprecation.silenced = true`. Because ActiveRecord v4.0 does not support Ruby v1.8.7 and earlier, Ruby UCSC API no longer supports these older Rubies.
  * **UPDATE** (v0.6.0): Ruby UCSC API is now licensed under the MIT License. See also the LICENSE.txt file.
  * **BUG-FIX** (v 0.5.3): Support ActiveRecord/ActiveSupport version 3 only.

data/README.md

@@ -1,4 +1,4 @@
-# bio-ucsc-api version 0.6.1
+# bio-ucsc-api version 0.6.2
 
 **The Ruby UCSC API**: accessing the UCSC Genome Database using Ruby.
 
@@ -72,9 +72,10 @@ See also:
 * UCSCBin library - https://github.com/misshie/UCSCBin
  
 # Change Log
- * **UPDATE** (v.0.6.1) Support new human hg38 reference. Newer tables after this release will be supported in later varsions. 
- * **NEW** (v0.6.0): Support ActiveRecord v4.0 (a part of Ruby on Ralils v4.0). Other related library dependencies are also updated. To Supress deprecation warnings for using dynamic finders such as 'find_by_name_and_chrom', use `ActiveSupport::Deprecation.silenced = true`. Because ActiveRecord v4.0 does not support Ruby v1.8.7 and earlier, Ruby UCSC API no longer supports these older Rubies. 
- * **UPDATE** (v0.6.0): Ruby UCSC API is now licensed under the MIT License. See also the LICENSE.txt file.
+* **BUG-FIX** (v.0.6.2) NoMemoryError in Bio::Ucsc::File::Twobit.open. Now internally File.open is used instead of Kernel.open.  
+* **UPDATE** (v.0.6.1) Support new human hg38 reference. Newer tables after this release will be supported in later varsions. 
+* **NEW** (v0.6.0): Support ActiveRecord v4.0 (a part of Ruby on Ralils v4.0). Other related library dependencies are also updated. To Supress deprecation warnings for using dynamic finders such as 'find_by_name_and_chrom', use `ActiveSupport::Deprecation.silenced = true`. Because ActiveRecord v4.0 does not support Ruby v1.8.7 and earlier, Ruby UCSC API no longer supports these older Rubies. 
+* **UPDATE** (v0.6.0): Ruby UCSC API is now licensed under the MIT License. See also the LICENSE.txt file.
  
 See 'ChangeLog.md' for older changes.
 
@@ -255,6 +256,6 @@ puts Bio::Ucsc::Hg19::Snp138.find_by_name("rs242").snp138Seq.first.file_offset
 ```
 
 # Copyright
-**Copyright**: (c) 2011-2013 MISHIMA, Hiroyuki (hmishima at nagasaki-u.ac.jp / Twitter: @mishima_eng (in English) and @mishimahryk (in Japanese)  
+**Copyright**: (c) 2011-2014 MISHIMA, Hiroyuki (hmishima at nagasaki-u.ac.jp / Twitter: @mishima_eng (in English) and @mishimahryk (in Japanese)  
 **Copyright**: (c) 2010 Jan Aerts  
 **License**: The MIT license. See LICENSE.txt for further details..

data/VERSION

@@ -1 +1 @@
-0.6.1
+0.6.2

data/bio-ucsc-api.gemspec

@@ -2,15 +2,15 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-ucsc-api 0.6.1 ruby lib
+# stub: bio-ucsc-api 0.6.2 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-ucsc-api"
-  s.version = "0.6.1"
+  s.version = "0.6.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Hiroyuki Mishima", "Jan Aerts"]
-  s.date = "2014-03-13"
+  s.date = "2014-03-26"
   s.description = "Ruby UCSC API: accessing the UCSC Genome Database using Ruby"
   s.email = "missy@be.to"
   s.extra_rdoc_files = [

data/lib/bio-ucsc/file/twobit.rb

@@ -2,9 +2,9 @@
 # = twobit.rb
 # handle UCSC's 2bit file (locally stored) to retrieve the reference sequence
 #
-# Copyright::   Copyright (C) 2011, 2012
+# Copyright::   Copyright (C) 2011, 2012, 2014
 #               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# License::     Ruby license (Ryby's / GPLv2 dual)
+# License::     The MIT license
 
 module Bio
   module Ucsc
@@ -34,7 +34,7 @@ module Bio
 
         def self.load(filename)
           two_bit = nil
-          Kernel.open(filename, 'rb') {|f| two_bit = f.read}
+          ::File.open(filename, 'rb') {|f|two_bit = f.read}
           tbq = Bio::Ucsc::File::ByteQueue.new(two_bit)
           
           twobit_header = TwoBitHeader.new

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-ucsc-api
 version: !ruby/object:Gem::Version
-  version: 0.6.1
+  version: 0.6.2
 platform: ruby
 authors:
 - Hiroyuki Mishima
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-13 00:00:00.000000000 Z
+date: 2014-03-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord