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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)CigarRollerinline
Cigar()Cigarinline
cigarOperations (defined in Cigar)Cigarprotected
CigarRoller()CigarRollerinline
CigarRoller(const char *cigarString)CigarRollerinline
clear()CigarRoller
clearQueryAndReferenceIndexes() (defined in Cigar)Cigarprotected
del enum valueCigar
Dump() constCigarinline
foundInQuery(Operation op)Cigarinlinestatic
foundInQuery(char op)Cigarinlinestatic
foundInQuery(const CigarOperator &op)Cigarinlinestatic
foundInReference(Operation op)Cigarinlinestatic
foundInReference(char op)Cigarinlinestatic
foundInReference(const CigarOperator &op)Cigarinlinestatic
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) constCigar
getCigarString(std::string &cigarString) constCigar
getExpandedCigarIndexFromQueryIndex(int32_t queryIndex)Cigar
getExpandedCigarIndexFromRefOffset(int32_t refOffset)Cigar
getExpandedCigarIndexFromRefPos(int32_t refPosition, int32_t queryStartPos)Cigar
getExpandedString(std::string &s) constCigar
getExpectedQueryBaseCount() constCigar
getExpectedReferenceBaseCount() constCigar
getMatchPositionOffset()CigarRoller
getNumBeginClips() constCigar
getNumEndClips() constCigar
getNumOverlaps(int32_t start, int32_t end, int32_t queryStartPos)Cigar
getOperator(int i) constCigarinline
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_NACigarstatic
insert enum valueCigar
isClip(Operation op)Cigarinlinestatic
isClip(char op)Cigarinlinestatic
isClip(const CigarOperator &op)Cigarinlinestatic
isMatchOrMismatch(Operation op)Cigarinlinestatic
isMatchOrMismatch(const CigarOperator &op)Cigarinlinestatic
match enum valueCigar
MAX_OP_VALUE (defined in Cigar)Cigarstatic
mismatch enum valueCigar
none enum valueCigar
Operation enum nameCigar
operator+=(CigarRoller &rhs)CigarRoller
operator+=(const CigarOperator &rhs)CigarRoller
operator<<CigarRollerfriend
operator=(CigarRoller &rhs)CigarRoller
operator==(Cigar &rhs) constCigar
operator[](int i) constCigarinline
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)Cigarprotected
size() constCigarinline
skip enum valueCigar
softClip enum valueCigar
Update(int index, Operation op, int count)CigarRoller