SamRecord Member List

This is the complete list of members for SamRecord, 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
Generated on Wed Nov 17 13:24:05 2010 for StatGen Software by  doxygen 1.6.3