CigarRoller Member List

This is the complete list of members for CigarRoller, including all inherited members.
Add(Operation operation, int count) (defined in CigarRoller)CigarRoller
Add(char operation, int count) (defined in CigarRoller)CigarRoller
Add(const char *cigarString) (defined in CigarRoller)CigarRoller
Add(CigarRoller &rhs) (defined in CigarRoller)CigarRoller [inline]
Cigar() (defined in Cigar)Cigar [inline]
cigarOperations (defined in Cigar)Cigar [protected]
CigarRoller() (defined in CigarRoller)CigarRoller [inline]
CigarRoller(const char *cigarString) (defined in CigarRoller)CigarRoller [inline]
clear() (defined in CigarRoller)CigarRoller
clearQueryAndReferenceIndexes() (defined in Cigar)Cigar [protected]
del enum value (defined in Cigar)Cigar
Dump() const (defined in Cigar)Cigar [inline]
foundInQuery(Operation op) (defined in Cigar)Cigar [inline, static]
getCigarString(String &cigarString) const (defined in Cigar)Cigar
getCigarString(std::string &cigarString) const (defined in Cigar)Cigar
getExpandedString(std::string &s) const Cigar
getExpectedQueryBaseCount() const Cigar
getExpectedReferenceBaseCount() const Cigar
getMatchPositionOffset() (defined in CigarRoller)CigarRoller
getNumBeginClips() const Cigar
getNumEndClips() const Cigar
getNumOverlaps(int32_t start, int32_t end, int32_t queryStartPos) (defined in Cigar)Cigar
getOperator(int i) const (defined in Cigar)Cigar [inline]
getQueryIndex(int32_t refOffset) (defined in Cigar)Cigar
getQueryIndex(int32_t refPosition, int32_t queryStartPos) (defined in Cigar)Cigar
getRefOffset(int32_t queryIndex) (defined in Cigar)Cigar
getRefPosition(int32_t queryIndex, int32_t queryStartPos) (defined in Cigar)Cigar
getString() (defined in CigarRoller)CigarRoller
hardClip enum value (defined in Cigar)Cigar
INDEX_NA (defined in Cigar)Cigar [static]
insert enum value (defined in Cigar)Cigar
isClip(Operation op) (defined in Cigar)Cigar [inline, static]
match enum value (defined in Cigar)Cigar
mismatch enum value (defined in Cigar)Cigar
none enum value (defined in Cigar)Cigar
Operation enum name (defined in Cigar)Cigar
operator+=(CigarRoller &rhs) (defined in CigarRoller)CigarRoller
operator+=(const CigarOperator &rhs) (defined in CigarRoller)CigarRoller
operator<< (defined in CigarRoller)CigarRoller [friend]
operator<< (defined in Cigar)Cigar [friend]
operator=(CigarRoller &rhs) (defined in CigarRoller)CigarRoller
operator==(Cigar &rhs) const (defined in Cigar)Cigar
operator[](int i) const (defined in Cigar)Cigar [inline]
pad enum value (defined in Cigar)Cigar
Set(const char *cigarString) (defined in CigarRoller)CigarRoller
Set(const uint32_t *cigarBuffer, uint16_t bufferLen) (defined in CigarRoller)CigarRoller
setQueryAndReferenceIndexes() (defined in Cigar)Cigar [protected]
size() const (defined in Cigar)Cigar [inline]
skip enum value (defined in Cigar)Cigar
softClip enum value (defined in Cigar)Cigar
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