From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 23 Aug 2011 14:06:02 +0000 (+0000)
Subject: worked on unit tests for sam.rb
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=e476daac131c17dc82b1e97484b73bbdbb7c16d8;p=biopieces.git

worked on unit tests for sam.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1492 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/lib/maasha/sam.rb b/code_ruby/lib/maasha/sam.rb
index df518e6..3ffc56d 100644
--- a/code_ruby/lib/maasha/sam.rb
+++ b/code_ruby/lib/maasha/sam.rb
@@ -288,6 +288,17 @@ class Sam < Filesys
       end
     end
   end
+
+  # Method to check if rnext, when not '*' or '='
+  # and @SQ header lines are present, is located
+  # in the header hash.
+  def check_rnext(rnext)
+    unless @header.empty? or rnext == '*' or rnext == '='
+      unless @header[:SQ][:SN].has_key? rnext.to_sym
+        raise SamError, "rnext not found in header hash: #{rnext}"
+      end
+    end
+  end
 end
 
 
diff --git a/code_ruby/test/maasha/test_sam.rb b/code_ruby/test/maasha/test_sam.rb
index e056b21..8642f64 100755
--- a/code_ruby/test/maasha/test_sam.rb
+++ b/code_ruby/test/maasha/test_sam.rb
@@ -340,7 +340,7 @@ class SamTest < Test::Unit::TestCase
     assert_raise(SamError) { sam.each }
   end
 
-  def test_Sam_each_wtih_rname_present_in_header_dont_raise
+  def test_Sam_each_with_rname_present_in_header_dont_raise
     sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\n*\t*\tref\t*\t*\t*\t*\t*\t\*\t*\t*\n"))
     assert_nothing_raised { sam.each }