SamRecord Member List

This is the complete list of members for SamRecord, 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 |
checkFloat(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 |
getCigar() | SamRecord |
getCigarInfo() | SamRecord |
getCigarLength() | 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 |
getFloatTag(const char *tag, float &tagVal) | SamRecord |
getInsertSize() | SamRecord |
getInteger(const char *tag) | SamRecord |
getIntegerTag(const char *tag) | SamRecord |
getIntegerTag(const char *tag, int &tagVal) | 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) | SamRecord | static
isFloatType(char vtype) | SamRecord | static
isIntegerType(char vtype) | SamRecord | static
isStringType(char vtype) | SamRecord | static
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 |