Add(Operation operation, int count) (defined in CigarRoller) | CigarRoller | |
Add(char operation, int count) (defined in CigarRoller) | CigarRoller | |
Add(const char *cigarString) (defined in CigarRoller) | CigarRoller | |
Add(CigarRoller &rhs) (defined in CigarRoller) | CigarRoller | [inline] |
Cigar() (defined in Cigar) | Cigar | [inline] |
cigarOperations (defined in Cigar) | Cigar | [protected] |
CigarRoller() (defined in CigarRoller) | CigarRoller | [inline] |
CigarRoller(const char *cigarString) (defined in CigarRoller) | CigarRoller | [inline] |
clear() (defined in CigarRoller) | CigarRoller | |
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 | |
getMatchPositionOffset() (defined in CigarRoller) | CigarRoller | |
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 | |
getString() (defined in CigarRoller) | CigarRoller | |
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+=(CigarRoller &rhs) (defined in CigarRoller) | CigarRoller | |
operator+=(const CigarOperator &rhs) (defined in CigarRoller) | CigarRoller | |
operator<< (defined in CigarRoller) | CigarRoller | [friend] |
operator<< (defined in Cigar) | Cigar | [friend] |
operator=(CigarRoller &rhs) (defined in CigarRoller) | CigarRoller | |
operator==(Cigar &rhs) const (defined in Cigar) | Cigar | |
operator[](int i) const (defined in Cigar) | Cigar | [inline] |
pad enum value (defined in Cigar) | Cigar | |
Set(const char *cigarString) (defined in CigarRoller) | CigarRoller | |
Set(const uint32_t *cigarBuffer, uint16_t bufferLen) (defined in CigarRoller) | CigarRoller | |
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 |