, including all inherited members.
addTag(const char *tag, char vtype, const char *value) (defined in SamRecord) | SamRecord | |
checkDouble(const char *tag) (defined in SamRecord) | SamRecord | [inline] |
checkInteger(const char *tag) (defined in SamRecord) | SamRecord | [inline] |
checkString(const char *tag) (defined in SamRecord) | SamRecord | [inline] |
checkTag(const char *tag, char type) (defined in SamRecord) | SamRecord | |
clearTags() (defined in SamRecord) | SamRecord | |
get0BasedAlignmentEnd() (defined in SamRecord) | SamRecord | |
get0BasedMatePosition() (defined in SamRecord) | SamRecord | |
get0BasedPosition() (defined in SamRecord) | SamRecord | |
get0BasedUnclippedEnd() (defined in SamRecord) | SamRecord | |
get0BasedUnclippedStart() (defined in SamRecord) | SamRecord | |
get1BasedAlignmentEnd() (defined in SamRecord) | SamRecord | |
get1BasedMatePosition() (defined in SamRecord) | SamRecord | |
get1BasedPosition() (defined in SamRecord) | SamRecord | |
get1BasedUnclippedEnd() (defined in SamRecord) | SamRecord | |
get1BasedUnclippedStart() (defined in SamRecord) | SamRecord | |
getAlignmentLength() (defined in SamRecord) | SamRecord | |
getBin() (defined in SamRecord) | SamRecord | |
getBlockSize() (defined in SamRecord) | SamRecord | |
getCigar() (defined in SamRecord) | SamRecord | |
getCigarInfo() (defined in SamRecord) | SamRecord | |
getCigarLength() (defined in SamRecord) | SamRecord | |
getDouble(const char *tag) (defined in SamRecord) | SamRecord | |
getFields(bamRecordStruct &recStruct, String &readName, String &cigar, String &sequence, String &quality) (defined in SamRecord) | SamRecord | |
getFlag() (defined in SamRecord) | SamRecord | |
getInsertSize() (defined in SamRecord) | SamRecord | |
getInteger(const char *tag) (defined in SamRecord) | SamRecord | |
getMapQuality() (defined in SamRecord) | SamRecord | |
getMateReferenceID() (defined in SamRecord) | SamRecord | |
getMateReferenceName() (defined in SamRecord) | SamRecord | |
getMateReferenceNameOrEqual() (defined in SamRecord) | SamRecord | |
getNextSamTag(char *tag, char &vtype, void **value) (defined in SamRecord) | SamRecord | |
getNumOverlaps(int32_t start, int32_t end) (defined in SamRecord) | SamRecord | |
getQuality() (defined in SamRecord) | SamRecord | |
getQuality(int index) (defined in SamRecord) | SamRecord | |
getReadLength() (defined in SamRecord) | SamRecord | |
getReadName() (defined in SamRecord) | SamRecord | |
getReadNameLength() (defined in SamRecord) | SamRecord | |
getRecordBuffer() (defined in SamRecord) | SamRecord | |
getReferenceID() (defined in SamRecord) | SamRecord | |
getReferenceName() (defined in SamRecord) | SamRecord | |
getSequence() (defined in SamRecord) | SamRecord | |
getSequence(int index) (defined in SamRecord) | SamRecord | |
getStatus() (defined in SamRecord) | SamRecord | |
getString(const char *tag) (defined in SamRecord) | SamRecord | |
getTagLength() (defined in SamRecord) | SamRecord | |
isCharType(char vtype) const (defined in SamRecord) | SamRecord | |
isDoubleType(char vtype) const (defined in SamRecord) | SamRecord | |
isIntegerType(char vtype) const (defined in SamRecord) | SamRecord | |
isStringType(char vtype) const (defined in SamRecord) | SamRecord | |
isValid(SamFileHeader &header) (defined in SamRecord) | SamRecord | |
resetRecord() (defined in SamRecord) | SamRecord | |
resetTagIter() (defined in SamRecord) | SamRecord | |
SamRecord() | SamRecord | |
SamRecord(ErrorHandler::HandlingType errorHandlingType) | SamRecord | |
set0BasedMatePosition(int32_t matePosition) (defined in SamRecord) | SamRecord | |
set0BasedPosition(int32_t position) (defined in SamRecord) | SamRecord | |
set1BasedMatePosition(int32_t matePosition) (defined in SamRecord) | SamRecord | |
set1BasedPosition(int32_t position) (defined in SamRecord) | SamRecord | |
setBuffer(const char *fromBuffer, uint32_t fromBufferSize, SamFileHeader &header) (defined in SamRecord) | SamRecord | |
setBufferFromFile(IFILE filePtr, SamFileHeader &header) (defined in SamRecord) | SamRecord | |
setCigar(const char *cigar) (defined in SamRecord) | SamRecord | |
setCigar(const Cigar &cigar) (defined in SamRecord) | SamRecord | |
setFlag(uint16_t flag) (defined in SamRecord) | SamRecord | |
setInsertSize(int32_t insertSize) (defined in SamRecord) | SamRecord | |
setMapQuality(uint8_t mapQuality) (defined in SamRecord) | SamRecord | |
setMateReferenceName(SamFileHeader &header, const char *mateReferenceName) (defined in SamRecord) | SamRecord | |
setQuality(const char *quality) (defined in SamRecord) | SamRecord | |
setReadName(const char *readName) (defined in SamRecord) | SamRecord | |
setReferenceName(SamFileHeader &header, const char *referenceName) (defined in SamRecord) | SamRecord | |
setSequence(const char *seq) (defined in SamRecord) | SamRecord | |
writeRecordBuffer(IFILE filePtr) (defined in SamRecord) | SamRecord | |
~SamRecord() (defined in SamRecord) | SamRecord | |