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Cigar Member List

This is the complete list of members for Cigar, including all inherited members.

Cigar()Cigarinline
cigarOperations (defined in Cigar)Cigarprotected
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
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
hardClip enum valueCigar
hasIndel()Cigar
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<<Cigarfriend
operator==(Cigar &rhs) constCigar
operator[](int i) constCigarinline
pad enum valueCigar
setQueryAndReferenceIndexes() (defined in Cigar)Cigarprotected
size() constCigarinline
skip enum valueCigar
softClip enum valueCigar