From cd42ff6de25b58c553b37f7b4bff9cb4afc3db07 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 24 Aug 2011 20:54:33 +0000
Subject: [PATCH] worked on unit tests for sam.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1497 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_ruby/lib/maasha/sam.rb       |  5 +++++
 code_ruby/test/maasha/test_sam.rb | 23 +++++++++++++++++++++++
 2 files changed, 28 insertions(+)

diff --git a/code_ruby/lib/maasha/sam.rb b/code_ruby/lib/maasha/sam.rb
index 2a3e586..92b8d95 100644
--- a/code_ruby/lib/maasha/sam.rb
+++ b/code_ruby/lib/maasha/sam.rb
@@ -313,6 +313,11 @@ class Sam < Filesys
   def check_cigar(cigar, seq)
     raise SamError, "Bad cigar: #{cigar}" unless cigar =~ /^(\*|([0-9]+[MIDNSHPX=])+)$/
 
+    # Check cigar hard clipping only at ends.
+    if cigar.gsub(/^[0-9]+H|[0-9]+H$/, "").match('H')
+      raise SamError, "Bad cigar with internal H: #{cigar}"
+    end
+
     # Check cigar length matches sequence length.
     unless cigar == '*' or seq == '*'
       cigar_len = 0
diff --git a/code_ruby/test/maasha/test_sam.rb b/code_ruby/test/maasha/test_sam.rb
index cb24b46..c189585 100755
--- a/code_ruby/test/maasha/test_sam.rb
+++ b/code_ruby/test/maasha/test_sam.rb
@@ -359,6 +359,29 @@ class SamTest < Test::Unit::TestCase
     assert_nothing_raised { sam.each }
   end
 
+  def test_Sam_each_with_bad_cigar_hard_clip_raises
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t1M1H1M\t*\t*\t\*\tAAA\t*\n"))
+    assert_raise(SamError) { sam.each }
+
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t1H1M1H1M\t*\t*\t\*\tAAA\t*\n"))
+    assert_raise(SamError) { sam.each }
+
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t1M1H1M1H\t*\t*\t\*\tAAA\t*\n"))
+    assert_raise(SamError) { sam.each }
+  end
+
+  def test_Sam_each_with_ok_cigar_hard_clip_dont_raise
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t1H1M\t*\t*\t\*\tA\t*\n"))
+    assert_nothing_raised { sam.each }
+
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t1M1H\t*\t*\t\*\tA\t*\n"))
+    assert_nothing_raised { sam.each }
+
+    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t1H1M1H\t*\t*\t\*\tA\t*\n"))
+    assert_nothing_raised { sam.each }
+    #assert_raise(SamError) { sam.each }
+  end
+
   def test_Sam_each_with_bad_cigar_length_raise
     sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t6M\t*\t*\t\*\tAAAAA\t*\n"))
     assert_raise(SamError) { sam.each }
-- 
2.39.2