// ***************************************************************************
// 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.
// ***************************************************************************
#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>
// 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;
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