Cigar Member List

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

Cigar() (defined in Cigar)	Cigar	[inline]
cigarOperations (defined in Cigar)	Cigar	[protected]
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
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
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<< (defined in Cigar)	Cigar	[friend]
operator==(Cigar &rhs) const (defined in Cigar)	Cigar
operator[](int i) const (defined in Cigar)	Cigar	[inline]
pad enum value (defined in Cigar)	Cigar
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