This is the complete list of members for Cigar, including all inherited members.

Cigar()	Cigar	`[inline]`
cigarOperations (defined in Cigar)	Cigar	`[protected]`
clearQueryAndReferenceIndexes() (defined in Cigar)	Cigar	`[protected]`
del enum value	Cigar
Dump() const	Cigar	`[inline]`
foundInQuery(Operation op)	Cigar	`[inline, static]`
foundInQuery(char op)	Cigar	`[inline, static]`
foundInQuery(const CigarOperator &op)	Cigar	`[inline, static]`
foundInReference(Operation op)	Cigar	`[inline, static]`
foundInReference(char op)	Cigar	`[inline, static]`
foundInReference(const CigarOperator &op)	Cigar	`[inline, static]`
getCigarCharOp(int32_t expandedCigarIndex)	Cigar
getCigarCharOpFromQueryIndex(int32_t queryIndex)	Cigar
getCigarCharOpFromRefOffset(int32_t refOffset)	Cigar
getCigarCharOpFromRefPos(int32_t refPosition, int32_t queryStartPos)	Cigar
getCigarString(String &cigarString) const	Cigar
getCigarString(std::string &cigarString) const	Cigar
getExpandedCigarIndexFromQueryIndex(int32_t queryIndex)	Cigar
getExpandedCigarIndexFromRefOffset(int32_t refOffset)	Cigar
getExpandedCigarIndexFromRefPos(int32_t refPosition, int32_t queryStartPos)	Cigar
getExpandedString(std::string &s) const	Cigar
getExpectedQueryBaseCount() const	Cigar
getExpectedReferenceBaseCount() const	Cigar
getNumBeginClips() const	Cigar
getNumEndClips() const	Cigar
getNumOverlaps(int32_t start, int32_t end, int32_t queryStartPos)	Cigar
getOperator(int i) const	Cigar	`[inline]`
getQueryIndex(int32_t refOffset)	Cigar
getQueryIndex(int32_t refPosition, int32_t queryStartPos)	Cigar
getRefOffset(int32_t queryIndex)	Cigar
getRefPosition(int32_t queryIndex, int32_t queryStartPos)	Cigar
hardClip enum value	Cigar
hasIndel()	Cigar
INDEX_NA	Cigar	`[static]`
insert enum value	Cigar
isClip(Operation op)	Cigar	`[inline, static]`
isClip(char op)	Cigar	`[inline, static]`
isClip(const CigarOperator &op)	Cigar	`[inline, static]`
isMatchOrMismatch(Operation op)	Cigar	`[inline, static]`
isMatchOrMismatch(const CigarOperator &op)	Cigar	`[inline, static]`
match enum value	Cigar
MAX_OP_VALUE (defined in Cigar)	Cigar	`[static]`
mismatch enum value	Cigar
none enum value	Cigar
Operation enum name	Cigar
operator<<(std::ostream &stream, const Cigar &cigar)	Cigar	`[friend]`
operator==(Cigar &rhs) const	Cigar
operator[](int i) const	Cigar	`[inline]`
pad enum value	Cigar
setQueryAndReferenceIndexes() (defined in Cigar)	Cigar	`[protected]`
size() const	Cigar	`[inline]`
skip enum value	Cigar
softClip enum value	Cigar