18 #ifndef __PILEUP_ELEMENT_H__
19 #define __PILEUP_ELEMENT_H__
21 #include "SamRecord.h"
29 static const int32_t UNSET_POSITION = -1;
48 virtual void reset(int32_t refPosition);
68 int32_t myRefPosition;
69 std::string myChromosome;
Create/Access/Modify/Load Genome Sequences stored as binary mapped files.
This is a base class pileup component, representing the information for one reference position.
static void setReference(GenomeSequence *reference)
Set the reference to use for all pilepElements.
int32_t getRefPosition() const
Get the reference position stored in this element.
const char * getChromosome() const
Get the chromosome name stored in this element.
static GenomeSequence * getReference()
Get a pointer to the reference.
PileupElement()
Pileup element constructor.
virtual void addEntry(SamRecord &record)
Add an entry to this pileup element.
virtual void analyze()
Perform the analysis associated with this class.
virtual ~PileupElement()
Pileup element destructor.
virtual void reset(int32_t refPosition)
Resets the entry, setting the new position associated with this element.
char getRefBase()
Returns the reference base for this pileup element.
Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record.