bio-samtools 2.3.1 → 2.3.2

checksums.yaml

@@ -1,7 +1,7 @@
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data/VERSION

@@ -1 +1 @@
-2.3.1
+2.3.2

data/bio-samtools.gemspec

@@ -2,17 +2,17 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-samtools 2.3.1 ruby lib
+# stub: bio-samtools 2.3.2 ruby lib
 # stub: ext/mkrf_conf.rb
 
 Gem::Specification.new do |s|
   s.name = "bio-samtools"
-  s.version = "2.3.1"
+  s.version = "2.3.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["Ricardo Ramirez-Gonzalez", "Dan MacLean", "Raoul J.P. Bonnal"]
-  s.date = "2015-02-25"
+  s.date = "2015-02-26"
   s.description = "Binder of samtools for ruby, on the top of FFI. \n\n  This project was born from the need to add support of BAM files to \n  the gee_fu genome browser (http://github.com/danmaclean/gee_fu)."
   s.email = "ilpuccio.febo@gmail.com"
   s.executables = ["bam_consensus.rb"]

data/lib/bio/db/sam.rb

@@ -79,7 +79,7 @@ module Bio
         end
         command = String.new
         command = form_opt_string(@samtools, 'view', opts, [:b, :h, :H, :S, :u, '1', :x, :X, :c, :B]) 
-        commad = command + " '#{region}'" if region.size > 0
+        command = command + " '#{region}'" if region.size > 0
         @last_command = command
         type = (opts[:u] or opts[:b]) ? :binary : :text
         klass = (type == :binary) ? String : Bio::DB::Alignment

data/test/test_sam.rb

@@ -110,8 +110,18 @@ class TestBioDbSam < Test::Unit::TestCase
   
   def test_fetch_with_function
     #pass the assert to method
-    block = Proc.new {|a| assert_equal(a.class, Bio::DB::Alignment)}
+    count = 0
+    block = Proc.new do |a| 
+      assert_equal(a.class, Bio::DB::Alignment)
+      count += 1
+    end
+
     @sam.fetch_with_function("chr_1", 10, 1000, &block)
+    assert_equal(count, 9)
+    
+    count = 0
+    @sam.fetch_with_function("chr_1", 82, 140, &block)
+    assert_equal(count, 4)
   end
   
   def test_chromosome_coverage

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-samtools
 version: !ruby/object:Gem::Version
-  version: 2.3.1
+  version: 2.3.2
 platform: ruby
 authors:
 - Ricardo Ramirez-Gonzalez
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-02-25 00:00:00.000000000 Z
+date: 2015-02-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio-svgenes