Cigar Member List

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<< | 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 |