libStatGen Software 1
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This class inherits from the base class and stores base and qualities. More...
#include <PileupElementBaseQual.h>
Public Member Functions | |
PileupElementBaseQual (const PileupElementBaseQual &q) | |
virtual void | addEntry (SamRecord &record) |
Add an entry to this pileup element. More... | |
virtual void | analyze () |
Perform the analysis associated with this class. More... | |
virtual void | reset (int32_t refPosition) |
Resets the entry, setting the new position associated with this element. More... | |
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PileupElement () | |
Pileup element constructor. More... | |
PileupElement (const PileupElement &q) | |
Constructor that resets the pileup element, does not copy, just resets. More... | |
virtual | ~PileupElement () |
Pileup element destructor. More... | |
virtual void | addEntry (SamRecord &record) |
Add an entry to this pileup element. More... | |
virtual void | analyze () |
Perform the analysis associated with this class. More... | |
virtual void | reset (int32_t refPosition) |
Resets the entry, setting the new position associated with this element. More... | |
const char * | getChromosome () const |
Get the chromosome name stored in this element. More... | |
int32_t | getRefPosition () const |
Get the reference position stored in this element. More... | |
char | getRefBase () |
Returns the reference base for this pileup element. More... | |
Additional Inherited Members | |
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static void | setReference (GenomeSequence *reference) |
Set the reference to use for all pilepElements. More... | |
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static const int32_t | UNSET_POSITION = -1 |
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static GenomeSequence * | getReference () |
Get a pointer to the reference. More... | |
This class inherits from the base class and stores base and qualities.
Definition at line 25 of file PileupElementBaseQual.h.
PileupElementBaseQual::PileupElementBaseQual | ( | ) |
Definition at line 22 of file PileupElementBaseQual.cpp.
PileupElementBaseQual::PileupElementBaseQual | ( | const PileupElementBaseQual & | q | ) |
Definition at line 41 of file PileupElementBaseQual.cpp.
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virtual |
Definition at line 60 of file PileupElementBaseQual.cpp.
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Add an entry to this pileup element.
Reimplemented from PileupElement.
Definition at line 76 of file PileupElementBaseQual.cpp.
References PileupElement::addEntry(), SamRecord::get0BasedPosition(), SamRecord::getCigarInfo(), SamRecord::getQuality(), Cigar::getQueryIndex(), PileupElement::getRefPosition(), SamRecord::getSequence(), and Cigar::INDEX_NA.
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Perform the analysis associated with this class.
Reimplemented from PileupElement.
Reimplemented in TestPileupElement.
Definition at line 144 of file PileupElementBaseQual.cpp.
References PileupElement::getChromosome(), and PileupElement::getRefPosition().
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virtual |
Resets the entry, setting the new position associated with this element.
Reimplemented from PileupElement.
Definition at line 157 of file PileupElementBaseQual.cpp.
References PileupElement::reset().