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));
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.
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.
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.
const char * getReferenceName()
Get the reference sequence name (RNAME) of the record.