Fixes #46

rjpbonnal · Feb 26, 2015 · 1b077fa · 1b077fa
1 parent 7a95df6
commit 1b077fa
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Showing 2 changed files with 12 additions and 2 deletions.
diff --git a/lib/bio/db/sam.rb b/lib/bio/db/sam.rb
@@ -79,7 +79,7 @@ def view(opts={},&block)
         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

diff --git a/test/test_sam.rb b/test/test_sam.rb
@@ -110,8 +110,18 @@ def test_fetch
 
   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