polishing on 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 3671a8dca2b72423016e6c8bb55d38b47eb4d5ce..d02d710942680300290bddd3ac42ef35c249e766 100755 (executable)
--- a/code_ruby/test/maasha/test_sam.rb
+++ b/code_ruby/test/maasha/test_sam.rb
@@ -246,19 +246,6 @@ class SamTest < Test::Unit::TestCase
     assert_nothing_raised { sam.each }
   end
 
-  def test_Sam_each_with_bad_cigar_raises
-    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t24\t*\t*\t*\t*\t*\n"))
-    assert_raise(SamError) { sam.each }
-  end
-
-  def test_Sam_each_with_ok_cigar_dont_raise
-    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t24M2I3D\t*\t*\t*\t*\t*\n"))
-    assert_nothing_raised { sam.each }
-
-    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t*\t*\t*\t*\t*\n"))
-    assert_nothing_raised { sam.each }
-  end
-
   def test_Sam_each_with_bad_rnext_raises
     sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t \t*\t*\t*\t*\n"))
     assert_raise(SamError) { sam.each }
@@ -359,36 +346,22 @@ 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 }
+  def test_Sam_to_bp_returns_correctly
+    string = "ID00036734\t0\tgi48994873\t366089\t37\t37M1I62M\t*\t0\t0\tGTTCCGCTATCGGCTGAATTTGATTGCGAGTGAGATATTTTATGCCAGCCAGCCAGACGCAGACGCGCCGAGACAGAACTTAATGGGCCCGCTAACAGCG\t*\tXT:A:U\tNM:i:1\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:1\tXG:i:1\tMD:Z:99\n"
 
-    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(string))
 
-    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t1H1M1H\t*\t*\t\*\tA\t*\n"))
-    assert_nothing_raised { 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 }
-  end
-
-  def test_Sam_each_with_ok_cigar_length_dont_raise
-    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t6M\t*\t*\t\*\tAAAAAA\t*\n"))
-    assert_nothing_raised { sam.each }
+    sam.each do |s|
+      assert_equal("SAM", Sam.to_bp(s)[:REC_TYPE])
+      assert_equal("ID00036734", Sam.to_bp(s)[:Q_ID])
+      assert_equal("-", Sam.to_bp(s)[:STRAND])
+        assert_equal("gi48994873", Sam.to_bp(s)[:S_ID])
+      assert_equal(366089, Sam.to_bp(s)[:S_BEG])
+      assert_equal(37, Sam.to_bp(s)[:MAPQ])
+      assert_equal("37M1I62M", Sam.to_bp(s)[:CIGAR])
+      assert_equal("GTTCCGCTATCGGCTGAATTTGATTGCGAGTGAGATATTTTATGCCAGCCAGCCAGACGCAGACGCGCCGAGACAGAACTTAATGGGCCCGCTAACAGCG", Sam.to_bp(s)[:SEQ])
+      assert_equal("37:->T", Sam.to_bp(s)[:ALIGN])
+    end
   end
 end