Added SAM header-handling classes for read/write/validate.

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

diff --git a/src/api/SamReadGroup.h b/src/api/SamReadGroup.h
new file mode 100644 (file)
index 0000000..fac4612
--- /dev/null
+++ b/src/api/SamReadGroup.h
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+// ***************************************************************************
+// SamReadGroup.h (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 23 December 2010 (DB)
+// ---------------------------------------------------------------------------
+// Provides functionality for querying/manipulating read group data
+// **************************************************************************
+
+#ifndef SAM_READGROUP_H
+#define SAM_READGROUP_H
+
+#include "api/api_global.h"
+#include <string>
+
+namespace BamTools {
+
+class API_EXPORT SamReadGroup {
+
+    // ctor & dtor
+    public:
+        SamReadGroup(void);
+        SamReadGroup(const std::string& id);
+        ~SamReadGroup(void);
+
+    // public methods
+    public:
+
+        // clear all contents
+        void Clear(void);
+
+        // convenience methods to check if SamReadGroup contains these values:
+        bool HasID(void) const;
+        bool HasSample(void) const;
+        bool HasLibrary(void) const;
+        bool HasDescription(void) const;
+        bool HasPlatformUnit(void) const;
+        bool HasPredictedInsertSize(void) const;
+        bool HasSequencingCenter(void) const;
+        bool HasProductionDate(void) const;
+        bool HasSequencingTechnology(void) const;
+
+    // data members
+    public:
+        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>
+};
+
+// ---------------------------------------------------
+// comparison operators
+
+// for equality: compare IDs
+inline bool operator==(const SamReadGroup& lhs, const SamReadGroup& rhs) {
+    return lhs.ID == rhs.ID;
+}
+
+} // namespace BamTools
+
+#endif // SAM_READGROUP_H