Merge pull request #81 from chmille4/master

[bamtools.git] / src / api / SamReadGroup.h

diff --git a/src/api/SamReadGroup.h b/src/api/SamReadGroup.h
index 538617d972d0e66928867b0506b2ae8dcd91a624..093ce2d76eea1d0624e6fa075508bd56e03be8ed 100644 (file)
--- a/src/api/SamReadGroup.h
+++ b/src/api/SamReadGroup.h
@@ -1,9 +1,8 @@
 // ***************************************************************************
 // SamReadGroup.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 4 March 2011 (DB)
+// Last modified: 10 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Provides direct read/write access to the SAM read group data fields.
 // ***************************************************************************
@@ -25,29 +24,36 @@ struct API_EXPORT SamReadGroup {
     ~SamReadGroup(void);
 
     // query/modify entire read group
-    void Clear(void);                           // clears all data fields
+    void Clear(void);                          // clears all data fields
 
     // convenience query methods
-    bool HasID(void) const;                     // returns true if read group has a group ID
-    bool HasSample(void) const;                 // returns true if read group has a sample name
-    bool HasLibrary(void) const;                // returns true if read group has a library name
-    bool HasDescription(void) const;            // returns true if read group has a description
-    bool HasPlatformUnit(void) const;           // returns true if read group has a platform unit ID
-    bool HasPredictedInsertSize(void) const;    // returns true if read group has a predicted insert size
-    bool HasSequencingCenter(void) const;       // returns true if read group has a sequencing center ID
-    bool HasProductionDate(void) const;         // returns true if read group has a production date
-    bool HasSequencingTechnology(void) const;   // returns true if read group has a sequencing technology ID
-
-    // data members
-    std::string ID;                   // ID:<ID>
-    std::string Sample;               // SM:<Sample>
-    std::string Library;              // LB:<Library>
-    std::string Description;          // DS:<Description>
-    std::string PlatformUnit;         // PU:<PlatformUnit>
-    std::string PredictedInsertSize;  // PI:<PredictedInsertSize>
-    std::string SequencingCenter;     // CN:<SequencingCenter>
-    std::string ProductionDate;       // DT:<ProductionDate>
-    std::string SequencingTechnology; // PL:<SequencingTechnology>
+    bool HasDescription(void) const;           // returns true if read group has a description
+    bool HasFlowOrder(void) const;             // returns true if read group has a flow order entry
+    bool HasID(void) const;                    // returns true if read group has a group ID
+    bool HasKeySequence(void) const;           // returns true if read group has a key sequence
+    bool HasLibrary(void) const;               // returns true if read group has a library name
+    bool HasPlatformUnit(void) const;          // returns true if read group has a platform unit ID
+    bool HasPredictedInsertSize(void) const;   // returns true if read group has a predicted insert size
+    bool HasProductionDate(void) const;        // returns true if read group has a production date
+    bool HasProgram(void) const;               // returns true if read group has a program entry
+    bool HasSample(void) const;                // returns true if read group has a sample name
+    bool HasSequencingCenter(void) const;      // returns true if read group has a sequencing center ID
+    bool HasSequencingTechnology(void) const;  // returns true if read group has a sequencing technology ID
+
+
+    // data fields
+    std::string Description;                   // DS:<Description>
+    std::string FlowOrder;                     // FO:<FlowOrder>
+    std::string ID;                            // ID:<ID>              *Required for valid SAM header*
+    std::string KeySequence;                   // KS:<KeySequence>
+    std::string Library;                       // LB:<Library>
+    std::string PlatformUnit;                  // PU:<PlatformUnit>
+    std::string PredictedInsertSize;           // PI:<PredictedInsertSize>
+    std::string ProductionDate;                // DT:<ProductionDate>
+    std::string Program;                       // PG:<Program>
+    std::string Sample;                        // SM:<Sample>
+    std::string SequencingCenter;              // CN:<SequencingCenter>
+    std::string SequencingTechnology;          // PL:<SequencingTechnology>
 };
 
 /*! \fn bool operator==(const SamReadGroup& lhs, const SamReadGroup& rhs)