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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 valueCigar
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 valueCigar
hasIndel()Cigar
IncrementCount(int index, int increment)CigarRoller
INDEX_NACigar [static]
insert enum valueCigar
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 valueCigar
MAX_OP_VALUE (defined in Cigar)Cigar [static]
mismatch enum valueCigar
none enum valueCigar
Operation enum nameCigar
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 valueCigar
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 valueCigar
softClip enum valueCigar
Update(int index, Operation op, int count)CigarRoller
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