CigarRoller Member List

This is the complete list of members for CigarRoller, 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
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 |