worked on unit tests for sam.rb

[biopieces.git] / code_ruby / test / maasha / test_sam.rb

diff --git a/code_ruby/test/maasha/test_sam.rb b/code_ruby/test/maasha/test_sam.rb
index 8642f64c31a92a142df57e61797d5d23848d20dc..6421ffbe14e49d9e9517b15ea853c245d13d5ae5 100755 (executable)
--- a/code_ruby/test/maasha/test_sam.rb
+++ b/code_ruby/test/maasha/test_sam.rb
@@ -46,124 +46,119 @@ class SamTest < Test::Unit::TestCase
     @sam = Sam.new(StringIO.new(SAM_DATA))
   end
 
-#  def test_Sam_header_without_entry_returns_nil
-#    @sam.io = StringIO.new
-#    assert_nil(@sam.header)
-#  end
-
-  def test_Sam_header_parse_with_missing_version_number_raises
+  def test_Sam_new_with_missing_version_number_raises
     assert_raise(SamError) { Sam.new(StringIO.new("@HD")) }
   end
 
-  def test_Sam_header_parse_with_bad_version_number_raises
+  def test_Sam_new_with_bad_version_number_raises
     assert_raise(SamError) { Sam.new(StringIO.new("@HD\tXN:1.3")) }
   end
 
-  def test_Sam_header_parse_with_ok_version_number_returns_correctly
+  def test_Sam_new_with_ok_version_number_returns_correctly
     sam = Sam.new(StringIO.new("@HD\tVN:1.3"))
     assert_equal(1.3, sam.header[:HD][:VN])
   end
 
-  def test_Sam_header_parse_with_bad_sort_order_raises
+  def test_Sam_new_with_bad_sort_order_raises
     assert_raise(SamError) { Sam.new(StringIO.new("@HD\tVN:1.3\tSO:fish")) }
   end
 
-  def test_Sam_header_parse_with_ok_sort_order_returns_correctly
+  def test_Sam_new_with_ok_sort_order_returns_correctly
     %w{unknown unsorted queryname coordinate}.each do |order|
       sam = Sam.new(StringIO.new("@HD\tVN:1.3\tSO:#{order}"))
       assert_equal(order, sam.header[:HD][:SO])
     end
   end
 
-  def test_Sam_header_parse_with_missing_sequence_name_raises
+  def test_Sam_new_with_missing_sequence_name_raises
     assert_raise(SamError) { Sam.new(StringIO.new("@SQ")) }
   end
 
-  def test_Sam_header_parse_with_bad_sequence_name_raises
+  def test_Sam_new_with_bad_sequence_name_raises
     assert_raise(SamError) { Sam.new(StringIO.new("@SQ\tSN:")) }
   end
 
-  def test_Sam_header_parse_with_ok_sequence_name_returns_correctly
+  def test_Sam_new_with_ok_sequence_name_returns_correctly
     sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45"))
     assert_equal({:LN=>45}, sam.header[:SQ][:SN][:ref])
   end
 
-  def test_Sam_header_parse_with_duplicate_sequence_name_raises
+  def test_Sam_new_with_duplicate_sequence_name_raises
     assert_raise(SamError) { Sam.new(StringIO.new("@SQ\tSN:ref\n@SQ\tSN:ref")) }
   end
 
-  def test_Sam_header_parse_with_missing_sequence_length_raises
+  def test_Sam_new_with_missing_sequence_length_raises
     assert_raise(SamError) { Sam.new(StringIO.new("@SQ\tSN:ref")) }
   end
 
-  def test_Sam_header_parse_with_bad_sequence_length_raises
+  def test_Sam_new_with_bad_sequence_length_raises
     assert_raise(SamError) { Sam.new(StringIO.new("@SQ\tSN:scaffold17_1_MH0083\tLN:x")) }
   end
 
-  def test_Sam_header_parse_with_ok_sequence_length_returns_correctly
+  def test_Sam_new_with_ok_sequence_length_returns_correctly
     sam = Sam.new(StringIO.new("@SQ\tSN:scaffold17_1_MH0083\tLN:995"))
     assert_equal(995, sam.header[:SQ][:SN][:scaffold17_1_MH0083][:LN])
   end
 
-  def test_Sam_header_parse_with_full_SQ_dont_raise
+  def test_Sam_new_with_full_SQ_dont_raise
     sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\tAS:ident\tM5:87e6b2aedf51b1f9c89becfab9267f41\tSP:E.coli\tUR:http://www.biopieces.org"))
     assert_nothing_raised { sam.header }
   end
 
-  def test_Sam_header_parse_with_bad_read_group_identifier_raises
+  def test_Sam_new_with_bad_read_group_identifier_raises
     assert_raise(SamError) { Sam.new(StringIO.new("@RG\tID:")) }
   end
 
-  def test_Sam_header_parse_with_missing_read_group_identifier_raises
+  def test_Sam_new_with_missing_read_group_identifier_raises
     assert_raise(SamError) { Sam.new(StringIO.new("@RG")) }
   end
 
-  def test_Sam_header_parse_with_duplicate_read_group_identifier_raises
+  def test_Sam_new_with_duplicate_read_group_identifier_raises
     assert_raise(SamError) { Sam.new(StringIO.new("@RG\tID:123\n@RG\tID:123")) }
   end
 
-  def test_Sam_header_parse_with_ok_read_group_identifier_dont_raise
+  def test_Sam_new_with_ok_read_group_identifier_dont_raise
     sam = Sam.new(StringIO.new("@RG\tID:123\n@RG\tID:124"))
     assert_nothing_raised { sam.header }
   end
 
-  def test_Sam_header_parse_with_bad_flow_order_raises
+  def test_Sam_new_with_bad_flow_order_raises
     assert_raise(SamError) { Sam.new(StringIO.new("@RG\tID:123\tFO:3")) }
   end
 
-  def test_Sam_header_parse_with_ok_flow_order_dont_raise
+  def test_Sam_new_with_ok_flow_order_dont_raise
     sam = Sam.new(StringIO.new("@RG\tID:123\tFO:*"))
     assert_nothing_raised { sam.header }
     sam = Sam.new(StringIO.new("@RG\tID:123\tFO:ACMGRSVTWYHKDBN"))
     assert_nothing_raised { sam.header }
   end
 
-  def test_Sam_header_parse_with_bad_platform_raises
+  def test_Sam_new_with_bad_platform_raises
     assert_raise(SamError) { Sam.new(StringIO.new("@RG\tID:123\tPL:maersk")) }
   end
 
-  def test_Sam_header_parse_with_ok_platform_dont_raise
+  def test_Sam_new_with_ok_platform_dont_raise
     sam = Sam.new(StringIO.new("@RG\tID:123\tPL:ILLUMINA"))
     assert_nothing_raised { sam.header }
   end
 
-  def test_Sam_header_parse_with_bad_program_identifier_raises
+  def test_Sam_new_with_bad_program_identifier_raises
     assert_raise(SamError) { Sam.new(StringIO.new("@PG\tID:")) }
   end
 
-  def test_Sam_header_parse_with_missing_program_identifier_raises
+  def test_Sam_new_with_missing_program_identifier_raises
     assert_raise(SamError) { Sam.new(StringIO.new("@PG")) }
   end
 
-  def test_Sam_header_parse_with_duplicate_program_identifier_raises
+  def test_Sam_new_with_duplicate_program_identifier_raises
     assert_raise(SamError) { Sam.new(StringIO.new("@PG\tID:123\n@PG\tID:123")) }
   end
 
-  def test_Sam_header_parse_with_bad_comment_raises
+  def test_Sam_new_with_bad_comment_raises
     assert_raise(SamError) { Sam.new(StringIO.new("@CO\t")) }
   end 
 
-  def test_Sam_header_parse_with_ok_comment_dont_raise
+  def test_Sam_new_with_ok_comment_dont_raise
     sam = Sam.new(StringIO.new("@CO\tfubar"))
     assert_nothing_raised { sam.header }
   end
@@ -347,5 +342,21 @@ class SamTest < Test::Unit::TestCase
     sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\n*\t*\t*\t*\t*\t*\t*\t*\t\*\t*\t*\n"))
     assert_nothing_raised { sam.each }
   end
+
+  def test_Sam_each_with_rnext_missing_from_header_raises
+    sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\n*\t*\t*\t*\t*\t*\tMIS\t*\t\*\t*\t*\n"))
+    assert_raise(SamError) { sam.each }
+  end
+
+  def test_Sam_each_with_rnext_present_in_header_dont_raise
+    sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\n*\t*\t*\t*\t*\t*\t*\t*\t\*\t*\t*\n"))
+    assert_nothing_raised { sam.each }
+
+    sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\n*\t*\t*\t*\t*\t*\t=\t*\t\*\t*\t*\n"))
+    assert_nothing_raised { sam.each }
+
+    sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\n*\t*\t*\t*\t*\t*\tref\t*\t\*\t*\t*\n"))
+    assert_nothing_raised { sam.each }
+  end
 end