18 #include "PileupElement.h"
25 : myRefPosition(UNSET_POSITION),
33 : myRefPosition(UNSET_POSITION),
46 if(myChromosome.empty())
59 if(myRefPosition != UNSET_POSITION)
61 std::cout << myChromosome <<
"\t" << myRefPosition <<
"\n";
70 myRefPosition = refPosition;
79 return(myRefPtr->
getBase(myChromosome.c_str(), myRefPosition+1));
const char * getReferenceName()
Get the reference sequence name (RNAME) of the record.
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.
char getBase(const char *chromosomeName, unsigned int chromosomeIndex) const
given a chromosome name and 1-based position, return the reference base.
virtual void reset(int32_t refPosition)
Resets the entry, setting the new position associated with this element.
PileupElement()
Pileup element constructor.
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.