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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 valueSamRecord
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 valueSamRecord
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 valueSamRecord
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 nameSamRecord
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
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