, 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 | |
