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;
const char * getChromosome() const
Get the chromosome name stored in this element.
char getRefBase()
Returns the reference base for this pileup element.
virtual ~PileupElement()
Pileup element destructor.
virtual void analyze()
Perform the analysis associated with this class.
Create/Access/Modify/Load Genome Sequences stored as binary mapped files.
virtual void reset(int32_t refPosition)
Resets the entry, setting the new position associated with this element.
PileupElement()
Pileup element constructor.
static GenomeSequence * getReference()
Get a pointer to the reference.
int32_t getRefPosition() const
Get the reference position stored in this element.
static void setReference(GenomeSequence *reference)
Set the reference to use for all pilepElements.
virtual void addEntry(SamRecord &record)
Add an entry to this pileup element.
Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record.
This is a base class pileup component, representing the information for one reference position.