X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2FSamHeader.h;h=50049947e627a29f5b077cb719b0c1a7874bb75a;hb=9f1ce8c47aeadb6dc1320b52ee671c3341b97935;hp=3b67621ac4dca6bd94aba4293b7d944bf7eba5e8;hpb=72f5b82ad353b4cc9d6f8153f1ad19cc387b9597;p=bamtools.git

diff --git a/src/api/SamHeader.h b/src/api/SamHeader.h
index 3b67621..5004994 100644
--- a/src/api/SamHeader.h
+++ b/src/api/SamHeader.h
@@ -2,7 +2,7 @@
 // SamHeader.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
 // ---------------------------------------------------------------------------
-// Last modified: 18 April 2011 (DB)
+// Last modified: 10 October 2011 (DB)
 // ---------------------------------------------------------------------------
 // Provides direct read/write access to the SAM header data fields.
 // ***************************************************************************
@@ -10,10 +10,10 @@
 #ifndef SAM_HEADER_H
 #define SAM_HEADER_H
 
-#include <api/api_global.h>
-#include <api/SamProgramChain.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 HasPrograms(void) const;           // returns true if header contains any program record entries
-    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>  *Required for valid SAM header, if @HD record is present*
-    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;
@@ -61,6 +63,10 @@ struct API_EXPORT SamHeader {
 
     // header comments (@CO entries)
     std::vector<std::string> Comments;
+
+    // internal data
+    private:
+        mutable std::string m_errorString;
 };
 
 } // namespace BamTools