SamFileReader Member List

This is the complete list of members for SamFileReader, including all inherited members.
Close()SamFile
COORDINATE enum valueSamFile
FLAG enum valueSamFile
GenerateStatistics(bool genStats)SamFile
GetCurrentRecordCount()SamFile
GetFailure()SamFile [inline]
GetNumOverlaps(SamRecord &samRecord)SamFile
getSortOrderFromHeader(SamFileHeader &header) (defined in SamFile)SamFile [protected]
GetStatus()SamFile [inline]
GetStatusMessage()SamFile [inline]
IsEOF()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]
myHasHeaderSamFile [protected]
myInterfacePtr (defined in SamFile)SamFile [protected]
myIsBamOpenForReadSamFile [protected]
myIsOpenForReadSamFile [protected]
myIsOpenForWriteSamFile [protected]
myNewSection (defined in SamFile)SamFile [protected]
myPrevCoordSamFile [protected]
myPrevReadName (defined in SamFile)SamFile [protected]
myPrevRefID (defined in SamFile)SamFile [protected]
myRecordCountSamFile [protected]
myRefID (defined in SamFile)SamFile [protected]
myRefName (defined in SamFile)SamFile [protected]
mySortedType (defined in SamFile)SamFile [protected]
myStartPos (defined in SamFile)SamFile [protected]
myStatisticsSamFile [protected]
myStatusSamFile [protected]
OpenForRead(const char *filename)SamFile
OpenForWrite(const char *filename)SamFile
OpenType enum name (defined in SamFile)SamFile
PrintStatistics() (defined in SamFile)SamFile [inline]
processNewSection(SamFileHeader &header) (defined in SamFile)SamFile [protected]
QUERY_NAME enum valueSamFile
READ enum value (defined in SamFile)SamFile
ReadBamIndex(const char *filename)SamFile
ReadHeader(SamFileHeader &header)SamFile
readIndexedRecord(SamFileHeader &header, SamRecord &record)SamFile [protected]
ReadRecord(SamFileHeader &header, SamRecord &record)SamFile
resetFile() (defined in SamFile)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
SamFileReader()SamFileReader
SamFileReader(const char *filename)SamFileReader
SetReadSection(int32_t refID)SamFile
SetReadSection(const char *refName)SamFile
SetReadSection(int32_t refID, int32_t start, int32_t end)SamFile
SetReadSection(const char *refName, int32_t start, int32_t end)SamFile
setSortedValidation(SortedType sortType)SamFile
SortedType enum nameSamFile
UNSORTED enum valueSamFile
validateSortOrder(SamRecord &record, SamFileHeader &header)SamFile [protected]
WRITE enum value (defined in SamFile)SamFile
WriteHeader(SamFileHeader &header)SamFile
WriteRecord(SamFileHeader &header, SamRecord &record)SamFile
~SamFile() (defined in SamFile)SamFile [virtual]
~SamFileReader() (defined in SamFileReader)SamFileReader [virtual]
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