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

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

diff --git a/src/api/SamHeader.h b/src/api/SamHeader.h
new file mode 100644 (file)
index 0000000..b51f175
--- /dev/null
+++ b/src/api/SamHeader.h
@@ -0,0 +1,81 @@
+// ***************************************************************************
+// SamHeader.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 SAM header data
+// **************************************************************************
+
+#ifndef SAM_HEADER_H
+#define SAM_HEADER_H
+
+#include <api/api_global.h>
+#include <api/SamReadGroupDictionary.h>
+#include <api/SamSequenceDictionary.h>
+#include <string>
+#include <vector>
+
+namespace BamTools {
+
+struct API_EXPORT SamHeader {
+
+    // ctor & dtor
+    public:
+        explicit SamHeader(const std::string& headerText = "");
+        ~SamHeader(void);
+
+    // query/modify entire SamHeader at once
+    public:
+
+        // clear all header contents
+        void Clear(void);
+
+        // checks if SAM header is well-formed
+        // @verbose - if true, validation errors & warnings will be printed to stderr
+        // otherwise, output is suppressed and only validation check occurs
+        bool IsValid(bool verbose = false) const;
+
+        // retrieves the printable, SAM-formatted header
+        // (with any local modifications since construction)
+        std::string ToString(void) const;
+
+    // query if header contains data elements
+    public:
+        bool HasVersion(void) const;
+        bool HasSortOrder(void) const;
+        bool HasGroupOrder(void) const;
+        bool HasSequences(void) const;
+        bool HasReadGroups(void) const;
+        bool HasProgramName(void) const;
+        bool HasProgramVersion(void) const;
+        bool HasProgramCommandLine(void) const;
+        bool HasComments(void) const;
+
+    // data members
+    public:
+
+        // header metadata (@HD line)
+        std::string Version;                // VN:<Version>
+        std::string SortOrder;              // SO:<SortOrder>
+        std::string GroupOrder;             // GO:<GroupOrder>
+
+        // header sequences (@SQ entries)
+        SamSequenceDictionary Sequences;
+
+        // header read groups (@RG entries)
+        SamReadGroupDictionary ReadGroups;
+
+        // header program data (@PG entries)
+        std::string ProgramName;            // ID:<ProgramName>
+        std::string ProgramVersion;         // VN:<ProgramVersion>
+        std::string ProgramCommandLine;     // CL:<ProgramCommandLine>
+
+        // header comments (@CO entries)
+        std::vector<std::string> Comments;
+};
+
+} // namespace BamTools
+
+#endif // SAM_HEADER_H