Cleaned up intra-API includes & moved version numbers to 2.0.0

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

diff --git a/src/api/SamHeader.h b/src/api/SamHeader.h
index 3ff4946dc18fe6d57f08c3629c6609ff783ae6c2..50049947e627a29f5b077cb719b0c1a7874bb75a 100644 (file)
--- a/src/api/SamHeader.h
+++ b/src/api/SamHeader.h
@@ -1,9 +1,8 @@
 // ***************************************************************************
 // SamHeader.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 header data fields.
 // ***************************************************************************
@@ -11,9 +10,10 @@
 #ifndef SAM_HEADER_H
 #define SAM_HEADER_H
 
-#include <api/api_global.h>
-#include <api/SamReadGroupDictionary.h>
-#include <api/SamSequenceDictionary.h>
+#include "api/api_global.h"
+#include "api/SamProgramChain.h"
+#include "api/SamReadGroupDictionary.h"
+#include "api/SamSequenceDictionary.h"
 #include <string>
 #include <vector>
 
@@ -28,27 +28,29 @@ struct API_EXPORT SamHeader {
 
     // query/modify entire SamHeader
     void Clear(void);                                   // clears all header contents
+    std::string GetErrorString(void) const;
+    bool HasError(void) const;
     bool IsValid(bool verbose = false) const;           // returns true if SAM header is well-formed
     void SetHeaderText(const std::string& headerText);  // replaces data fields with contents of SAM-formatted text
     std::string ToString(void) const;                   // returns the printable, SAM-formatted header text
 
     // convenience query methods
-    bool HasVersion(void) const;            // returns true if header contains format version entry
-    bool HasSortOrder(void) const;          // returns true if header contains sort order entry
-    bool HasGroupOrder(void) const;         // returns true if header contains group order entry
-    bool HasSequences(void) const;          // returns true if header contains any sequence entries
-    bool HasReadGroups(void) const;         // returns true if header contains any read group entries
-    bool HasProgramName(void) const;        // returns true if header contains program name
-    bool HasProgramVersion(void) const;     // returns true if header contains program version
-    bool HasProgramCommandLine(void) const; // returns true if header contains program command line
-    bool HasComments(void) const;           // returns true if header contains comments
+    bool HasVersion(void) const;     // returns true if header contains format version entry
+    bool HasSortOrder(void) const;   // returns true if header contains sort order entry
+    bool HasGroupOrder(void) const;  // returns true if header contains group order entry
+    bool HasSequences(void) const;   // returns true if header contains any sequence entries
+    bool HasReadGroups(void) const;  // returns true if header contains any read group entries
+    bool HasPrograms(void) const;    // returns true if header contains any program record entries
+    bool HasComments(void) const;    // returns true if header contains comments
 
+    // --------------
     // data members
+    // --------------
 
     // header metadata (@HD line)
-    std::string Version;                // VN:<Version>
-    std::string SortOrder;              // SO:<SortOrder>
-    std::string GroupOrder;             // GO:<GroupOrder>
+    std::string Version;             // VN:<Version>  *Required, if @HD record is present*
+    std::string SortOrder;           // SO:<SortOrder>
+    std::string GroupOrder;          // GO:<GroupOrder>
 
     // header sequences (@SQ entries)
     SamSequenceDictionary Sequences;
@@ -57,12 +59,14 @@ struct API_EXPORT SamHeader {
     SamReadGroupDictionary ReadGroups;
 
     // header program data (@PG entries)
-    std::string ProgramName;            // ID:<ProgramName>
-    std::string ProgramVersion;         // VN:<ProgramVersion>
-    std::string ProgramCommandLine;     // CL:<ProgramCommandLine>
+    SamProgramChain Programs;
 
     // header comments (@CO entries)
     std::vector<std::string> Comments;
+
+    // internal data
+    private:
+        mutable std::string m_errorString;
 };
 
 } // namespace BamTools