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
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