, including all inherited members.
| Add(Operation operation, int count) | CigarRoller | |
| Add(char operation, int count) | CigarRoller | |
| Add(const char *cigarString) | CigarRoller | |
| Add(CigarRoller &rhs) | CigarRoller | [inline] |
| Cigar() | Cigar | [inline] |
| cigarOperations (defined in Cigar) | Cigar | [protected] |
| CigarRoller() | CigarRoller | [inline] |
| CigarRoller(const char *cigarString) | CigarRoller | [inline] |
| clear() | CigarRoller | |
| 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 | |
| getMatchPositionOffset() | CigarRoller | |
| 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 | |
| getString() | CigarRoller | |
| hardClip enum value | Cigar | |
| hasIndel() | Cigar | |
| IncrementCount(int index, int increment) | CigarRoller | |
| 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+=(CigarRoller &rhs) | CigarRoller | |
| operator+=(const CigarOperator &rhs) | CigarRoller | |
| operator<<(std::ostream &stream, const CigarRoller &roller) | CigarRoller | [friend] |
| Cigar::operator<<(std::ostream &stream, const Cigar &cigar) | Cigar | [friend] |
| operator=(CigarRoller &rhs) | CigarRoller | |
| operator==(Cigar &rhs) const | Cigar | |
| operator[](int i) const | Cigar | [inline] |
| pad enum value | Cigar | |
| Remove(int index) | CigarRoller | |
| Set(const char *cigarString) | CigarRoller | |
| Set(const uint32_t *cigarBuffer, uint16_t bufferLen) | CigarRoller | |
| setQueryAndReferenceIndexes() (defined in Cigar) | Cigar | [protected] |
| size() const | Cigar | [inline] |
| skip enum value | Cigar | |
| softClip enum value | Cigar | |
| Update(int index, Operation op, int count) | CigarRoller | |
1.7.6.1 
