SamFileWriter Member List

This is the complete list of members for SamFileWriter, including all inherited members.

attemptRecoverySync(bool(*checkSignature)(void *data), int length) (defined in SamFile) | SamFile |
checkRecordInSection(SamRecord &record) (defined in SamFile) | SamFile | protected
Close() | SamFile |
COORDINATE enum value | SamFile |
DisableBuffering() | SamFile | inline
ensureIndexedReadPosition() (defined in SamFile) | SamFile | protected
FLAG enum value | SamFile |
GenerateStatistics(bool genStats) | SamFile |
GetBamIndex() | SamFile |
GetCurrentPosition() | SamFile | inline
GetCurrentRecordCount() | SamFile |
GetFailure() | SamFile | inline
getNumMappedReadsFromIndex(int32_t refID) | SamFile |
getNumMappedReadsFromIndex(const char *refName, SamFileHeader &header) | SamFile |
GetNumOverlaps(SamRecord &samRecord) | SamFile |
getNumUnMappedReadsFromIndex(int32_t refID) | SamFile |
getNumUnMappedReadsFromIndex(const char *refName, SamFileHeader &header) | SamFile |
getSortOrderFromHeader(SamFileHeader &header) (defined in SamFile) | SamFile | protected
GetStatus() | SamFile | inline
GetStatusMessage() | SamFile | inline
init() (defined in SamFile) | SamFile | protected
init(const char *filename, OpenType mode, SamFileHeader *header) (defined in SamFile) | SamFile | protected
IsEOF() | SamFile |
IsOpen() | SamFile |
IsStream() | SamFile |
myBamIndex (defined in SamFile) | SamFile | protected
myChunksToRead (defined in SamFile) | SamFile | protected
myCurrentChunkEnd (defined in SamFile) | SamFile | protected
myEndPos (defined in SamFile) | SamFile | protected
myFilePtr (defined in SamFile) | SamFile | protected
myHasHeader | SamFile | protected
myInterfacePtr (defined in SamFile) | SamFile | protected
myIsBamOpenForRead | SamFile | protected
myIsOpenForRead | SamFile | protected
myIsOpenForWrite | SamFile | protected
myNewSection (defined in SamFile) | SamFile | protected
myOverlapSection (defined in SamFile) | SamFile | protected
myPrevCoord | SamFile | protected
myPrevReadName (defined in SamFile) | SamFile | protected
myPrevRefID (defined in SamFile) | SamFile | protected
myReadTranslation (defined in SamFile) | SamFile | protected
myRecordCount | SamFile | protected
myRefID (defined in SamFile) | SamFile | protected
myRefName (defined in SamFile) | SamFile | protected
myRefPtr (defined in SamFile) | SamFile | protected
mySortedType (defined in SamFile) | SamFile | protected
myStartPos (defined in SamFile) | SamFile | protected
myStatistics | SamFile | protected
myStatus | SamFile | protected
myWriteTranslation (defined in SamFile) | SamFile | protected
OpenForRead(const char *filename, SamFileHeader *header=NULL) | SamFile |
OpenForWrite(const char *filename, SamFileHeader *header=NULL) | SamFile |
OpenType enum name | SamFile |
PrintStatistics() | SamFile | inline
processNewSection(SamFileHeader &header) (defined in SamFile) | SamFile | protected
QUERY_NAME enum value | SamFile |
READ enum value | SamFile |
ReadBamIndex(const char *filename) | SamFile |
ReadBamIndex() | SamFile |
ReadHeader(SamFileHeader &header) | SamFile |
ReadRecord(SamFileHeader &header, SamRecord &record) | SamFile |
resetFile() | SamFile | protected
SamFile() | SamFile |
SamFile(ErrorHandler::HandlingType errorHandlingType) | SamFile |
SamFile(const char *filename, OpenType mode) | SamFile |
SamFile(const char *filename, OpenType mode, ErrorHandler::HandlingType errorHandlingType) | SamFile |
SamFile(const char *filename, OpenType mode, SamFileHeader *header) | SamFile |
SamFile(const char *filename, OpenType mode, ErrorHandler::HandlingType errorHandlingType, SamFileHeader *header) | SamFile |
SamFileWriter() | SamFileWriter |
SamFileWriter(const char *filename) | SamFileWriter |
SamFileWriter(const char *filename, ErrorHandler::HandlingType errorHandlingType) | SamFileWriter |
SamFileWriter(const char *filename, SamFileHeader *header) | SamFileWriter |
SamFileWriter(const char *filename, ErrorHandler::HandlingType errorHandlingType, SamFileHeader *header) | SamFileWriter |
setAttemptRecovery(bool flag=false) (defined in SamFile) | SamFile | inline
SetReadFlags(uint16_t requiredFlags, uint16_t excludedFlags) | SamFile |
SetReadSection(int32_t refID) | SamFile |
SetReadSection(const char *refName) | SamFile |
SetReadSection(int32_t refID, int32_t start, int32_t end, bool overlap=true) | SamFile |
SetReadSection(const char *refName, int32_t start, int32_t end, bool overlap=true) | SamFile |
SetReadSequenceTranslation(SamRecord::SequenceTranslation translation) | SamFile |
SetReference(GenomeSequence *reference) | SamFile |
setSortedValidation(SortedType sortType) | SamFile |
SetWriteSequenceTranslation(SamRecord::SequenceTranslation translation) | SamFile |
SortedType enum name | SamFile |
UNSORTED enum value | SamFile |
validateSortOrder(SamRecord &record, SamFileHeader &header) | SamFile | protected
WRITE enum value | SamFile |
WriteHeader(SamFileHeader &header) | SamFile |
WriteRecord(SamFileHeader &header, SamRecord &record) | SamFile |
~SamFile() | SamFile | virtual
~SamFileWriter() (defined in SamFileWriter) | SamFileWriter | virtual