, including all inherited members.
| addIntTag(const char *tag, int32_t value) | SamRecord | |
| addTag(const char *tag, char vtype, const char *value) | SamRecord | |
| BASES enum value | SamRecord | |
| checkDouble(const char *tag) | SamRecord | [inline] |
| checkInteger(const char *tag) | SamRecord | [inline] |
| checkString(const char *tag) | SamRecord | [inline] |
| checkTag(const char *tag, char type) | SamRecord | |
| clearTags() | SamRecord | |
| EQUAL enum value | SamRecord | |
| get0BasedAlignmentEnd() | SamRecord | |
| get0BasedMatePosition() | SamRecord | |
| get0BasedPosition() | SamRecord | |
| get0BasedUnclippedEnd() | SamRecord | |
| get0BasedUnclippedStart() | SamRecord | |
| get1BasedAlignmentEnd() | SamRecord | |
| get1BasedMatePosition() | SamRecord | |
| get1BasedPosition() | SamRecord | |
| get1BasedUnclippedEnd() | SamRecord | |
| get1BasedUnclippedStart() | SamRecord | |
| getAlignmentLength() | SamRecord | |
| getBin() | SamRecord | |
| getBlockSize() | SamRecord | |
| getChar(const char *tag) | SamRecord | |
| getCharTag(const char *tag) | SamRecord | |
| getCigar() | SamRecord | |
| getCigarInfo() | SamRecord | |
| getCigarLength() | SamRecord | |
| getDouble(const char *tag) | SamRecord | |
| getDoubleTag(const char *tag) | SamRecord | |
| getFields(bamRecordStruct &recStruct, String &readName, String &cigar, String &sequence, String &quality) | SamRecord | |
| getFields(bamRecordStruct &recStruct, String &readName, String &cigar, String &sequence, String &quality, SequenceTranslation translation) | SamRecord | |
| getFlag() | SamRecord | |
| getInsertSize() | SamRecord | |
| getInteger(const char *tag) | SamRecord | |
| getIntegerTag(const char *tag) | SamRecord | |
| getMapQuality() | SamRecord | |
| getMateReferenceID() | SamRecord | |
| getMateReferenceName() | SamRecord | |
| getMateReferenceNameOrEqual() | SamRecord | |
| getNextSamTag(char *tag, char &vtype, void **value) | SamRecord | |
| getNumOverlaps(int32_t start, int32_t end) | SamRecord | |
| getQuality() | SamRecord | |
| getQuality(int index) | SamRecord | |
| getReadLength() | SamRecord | |
| getReadName() | SamRecord | |
| getReadNameLength() | SamRecord | |
| getRecordBuffer() | SamRecord | |
| getRecordBuffer(SequenceTranslation translation) | SamRecord | |
| getReference() | SamRecord | |
| getReferenceID() | SamRecord | |
| getReferenceName() | SamRecord | |
| getSequence() | SamRecord | |
| getSequence(SequenceTranslation translation) | SamRecord | |
| getSequence(int index) | SamRecord | |
| getSequence(int index, SequenceTranslation translation) | SamRecord | |
| getStatus() | SamRecord | |
| getString(const char *tag) | SamRecord | |
| getStringTag(const char *tag) | SamRecord | |
| getTagLength() | SamRecord | |
| getTagsString(const char *tags, String &returnString, char delim= '\t') | SamRecord | |
| isCharType(char vtype) const | SamRecord | |
| isDoubleType(char vtype) const | SamRecord | |
| isIntegerType(char vtype) const | SamRecord | |
| isStringType(char vtype) const | SamRecord | |
| isValid(SamFileHeader &header) | SamRecord | |
| NONE enum value | SamRecord | |
| resetRecord() | SamRecord | |
| resetTagIter() | SamRecord | |
| rmTag(const char *tag, char type) | SamRecord | |
| rmTags(const char *tags) | SamRecord | |
| SamRecord() | SamRecord | |
| SamRecord(ErrorHandler::HandlingType errorHandlingType) | SamRecord | |
| SequenceTranslation enum name | SamRecord | |
| set0BasedMatePosition(int32_t matePosition) | SamRecord | |
| set0BasedPosition(int32_t position) | SamRecord | |
| set1BasedMatePosition(int32_t matePosition) | SamRecord | |
| set1BasedPosition(int32_t position) | SamRecord | |
| setBuffer(const char *fromBuffer, uint32_t fromBufferSize, SamFileHeader &header) | SamRecord | |
| setBufferFromFile(IFILE filePtr, SamFileHeader &header) | SamRecord | |
| setCigar(const char *cigar) | SamRecord | |
| setCigar(const Cigar &cigar) | SamRecord | |
| setFlag(uint16_t flag) | SamRecord | |
| setInsertSize(int32_t insertSize) | SamRecord | |
| setMapQuality(uint8_t mapQuality) | SamRecord | |
| setMateReferenceName(SamFileHeader &header, const char *mateReferenceName) | SamRecord | |
| setQuality(const char *quality) | SamRecord | |
| setReadName(const char *readName) | SamRecord | |
| setReference(GenomeSequence *reference) | SamRecord | |
| setReferenceName(SamFileHeader &header, const char *referenceName) | SamRecord | |
| setSequence(const char *seq) | SamRecord | |
| setSequenceTranslation(SequenceTranslation translation) | SamRecord | |
| shiftIndelsLeft() | SamRecord | |
| writeRecordBuffer(IFILE filePtr) | SamRecord | |
| writeRecordBuffer(IFILE filePtr, SequenceTranslation translation) | SamRecord | |
| ~SamRecord() | SamRecord | |
