Fix the tests

src/Source/Framework/Bio.Core/IO/PacBio/PacBioCCSBamReader.cs

@@ -11,7 +11,7 @@ namespace Bio.IO.PacBio
     /// <summary>
     /// Reads the data from a PacBio BAM file produced by the pbccs program. 
     /// </summary>
-    public class PacBioCCSBamReader
+    public class PacBioCCSBamReader : ISequenceParser
     {
         /// <summary>
         /// Parse the CCS reads in a PacBio CCS BAM File.
@@ -51,6 +51,43 @@ namespace Bio.IO.PacBio
             }
         }
 
+        #region IParser implementation
+        IEnumerable<ISequence> IParser<ISequence>.Parse (Stream stream)
+        {
+            return PacBioCCSBamReader.Parse (stream);
+        }
+        public ISequence ParseOne (Stream stream)
+        {
+            return PacBioCCSBamReader.Parse (stream).First();
+        }
+        #endregion
+        #region IParserWithAlphabet implementation
+        public IAlphabet Alphabet {
+            get {
+                return DnaAlphabet.Instance;
+            }
+            set {
+                throw new NotImplementedException ();
+            }
+        }
+        #endregion
+        #region IParser implementation
+        public string Name {
+            get {
+                return "CCS-BAM-Parser";
+            }
+        }
+        public string Description {
+            get {
+                return "Parses BAM Files output by the PacBio CCS Program";
+            }
+        }
+        public string SupportedFileTypes {
+            get {
+                return Properties.Resource.BAM_FILEEXTENSION;
+            }
+        }
+        #endregion
     }
 }
 

src/Source/Tests/Bio.Tests/PacBio/ParserTests.cs

@@ -19,15 +19,15 @@ namespace Bio.Tests.PacBio
             var seqs = csp.Parse (fname).Select(z => z as PacBioCCSRead).ToList();
 
             var seq4 = seqs [4];
-            Assert.AreEqual (146331, seq4.HoleNumber);
-            Assert.AreEqual (124, seq4.NumPasses);
-            Assert.AreEqual (2, seq4.ReadCountBadZscore);
-            Assert.AreEqual (136, seq4.Sequence.Count);
-            Assert.AreEqual (128, seq4.ZScores.Length);
-            Assert.AreEqual("m141008_060349_42194_c100704972550000001823137703241586_s1_p0/146331/ccs",
+            Assert.AreEqual (273, seq4.HoleNumber);
+            Assert.AreEqual (12, seq4.NumPasses);
+            Assert.AreEqual (1, seq4.ReadCountBadZscore);
+            Assert.AreEqual (1946, seq4.Sequence.Count);
+            Assert.AreEqual (14, seq4.ZScores.Length);
+            Assert.AreEqual("m150930_045019_42194_c100916310150000001823201204291662_s1_p0/273/ccs",
                              seq4.Sequence.ID);
             var seq = new Sequence (DnaAlphabet.Instance, seq4.Sequence.ToArray (), true);
-            Assert.AreEqual("CCCGGGGATCCTCTAGAATGCTCATACACTGGGGGATACATATACGGGGGGGGGCACATCATCTAGACAGACGACTTTTTTTTTTCGAGCGCAGCTTTTTGAGCGACGCACAAGCTTGCTGAGGACTAGTAGCTTC",
+            Assert.AreEqual("TGTCACTCATCTGAGTGATCCCGCGAAATTAATACGACTCACTATAGGGGAATTGTGAGCGGATAACAATTCCCCTCTAGAAATAATTTTGTTTAACTTTAAGAAGGAGATATACATATGAAACACATGCCACGTAAAATGTATTCCTGCGACTTTGAGACTACACCAAGGTTGAAGATTGCCGCGTATGGGCATACGGTTACATGAACATCGAAGACCACTCCGAGTATAAGATTGGTAACTCCCTGGATGAATTTATGGCTTGGGTTCTGAAAGTTCAGGCTGACCTGTACTTCCACAATCTGAAATTTGATGGCGCATTCATCATCAACTGGCTGGAACGTAACGGTTTTAAATGGTCCGCAGATGGTCTGCCAAATACCTACAACACCATCATTTCTCGCATGGGCCAGTGGTATATGATTGATATTTGCCTGGGTTACAAGGGTAAACGCAAGATCCACACCGTGATCTACGACTCTCTGAAGAAACTGCCGTTTCCGGTTAAGAAAATTGCGAAAGACTTTAAGCTGACGGTACTGAAAGGCGACATCGACTATCATAAGGAGCGCCCGGTCGTTACAAAATCACCCGGAAGAATATGCCTACATTAAAAACGATATTCAGATTATCGCAGAAGCTCTGCTGATCCAGTTCAAGCAGGGTCTGGATCGTATGACGGCAGGTTCTGACTCTCTGAAAGGCTTCAAAGACATTATCACCACCAAGAAGTTTAAAAAGGTTTCCCGACCCTGAGCCTGGGTCTGGACAAGGAAGTTCGTTATGCCTACCGTGGTGGTTTCACCTGGCTGAATGACCGTTTTAAAGAAAAAGAGATCGGCGAAGGTATGGTTTTTGATGTTAATTCCCTGTACCCAGCGCAAATGTACTCTCGCCTGCTGCCGTACGGCGAGCCGATCGTATTCGAGGGTAAATACGTCTGGGACGAGGACTACCCTCTGCACATTCAGCACATTCGTTGTGAATTTGAACTGAAGGAAGGCTACATCCCGACCATCCAGATCAATCGTTCCCGTTTCTACAAGGGTAACGAATACCTGAAATCTTCCGGCGGTGAAATTGCTGACCTGTGGCTGTCTAATGTTGATCTGGAACTGATGAAAGAGCACTACGACCTGTACAATGTTGAATATATCTCTGGTCTGAAGTTCAAAGCAACCACTGGCCTGTTCAAGGACTTTATCGACAAATGGACGTATATCAAAACTACCTCTGAAGGCGCCATCAAACAGCTGGCGAAGCTGATCCTGAACAGCCTGTACGGTAAATTCGCGTCCAACCCGGACGTTACCGGTAAAGTGCCATACCTGAAAGAGAACGGTGCTCTGGGTTTTCGTCTGGGTGAGGAGGAAACGAAAGACCCTGTATATACCCGATGGGTGTCTTTATCACGGCCTGGGCACGCTATACGACCATCACGGCAGCGCAGGCTTGTTATGATCGTATTATCTACTGCGATACCGATTCTATTCACCTGACTGGTACTGAAATTCCGGACGTTATCAAAGACATCGTAGACCCGAAGAAACTGGGCTACTGGGCGCACGAATCTACTTTTAAGCGTGCAAAATATCTGCGTCAGAAAACCTACATCCAGGATATTTACATGAAAGAAGTAGACGGCAAATTGGTAGAGGGCTCTCCTGACGACTACACTGACATCAAGTTCTCTGTGAAATGCGCAGGCATGACGGACAAAATCAAAAAGGAAGTGACTTTCGAAAACTTCAAAGTGGGTTTTTCTCGTAAAATGAAACCGAAGCCTGTTCAGGTACCGGGTGGCGTAGTGCTGGTTGATGACACTTTTACTATCAAATAACTCGAGCTGCAGGAATTCAAGCTTGGATCCGGCTGCTAACAAAGCCCGAAAGGAAGCTGAGTTGGCTGCTGCCACCGCTGAGCAATAACTTGTCACTCATCTGAGT",
                 seq.ConvertToString());
 
             Assert.AreEqual (seqs.Count, 7);