18 #ifndef __SAM_REFERENCE_INFO_H__
19 #define __SAM_REFERENCE_INFO_H__
21 #include "StringArray.h"
22 #include "StringHash.h"
35 void add(
const char* referenceSequenceName,
36 int32_t referenceSequenceLength);
72 return(!
operator==(rhs));
Class for tracking the reference information mapping between the reference ids and the reference name...
void clear()
Reset this reference info.
int getReferenceID(const String &referenceName, bool addID=false)
Get the reference ID for the specified name, if addID is set to true, a reference id will be created ...
int32_t getNumEntries() const
Get the number of entries contained here.
SamReferenceInfo & operator=(const SamReferenceInfo &rhs)
Copy the reference information.
static const int NO_REF_ID
Constant for the value returned if a reference id does not exist for a queried reference name.
SamReferenceInfo()
Constructor.
const char * getReferenceName(int index) const
Return the reference name at the specified index, returning "" if the index is out of bounds.
const String & getReferenceLabel(int id) const
Get the reference name for the specified id, if the id is not found, return "*".
void add(const char *referenceSequenceName, int32_t referenceSequenceLength)
Add reference sequence name and reference sequence length.
~SamReferenceInfo()
Destructor.
int32_t getReferenceLength(int index) const
Return the reference length at the specified index, returning 0 if the index is out of bounds.