, including all inherited members.
Close() | SamFile | |
COORDINATE enum value | SamFile | |
FLAG enum value | SamFile | |
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] |
myHasHeader | SamFile | [protected] |
myInterfacePtr (defined in SamFile) | SamFile | [protected] |
myIsBamOpenForRead | SamFile | [protected] |
myIsOpenForRead | SamFile | [protected] |
myIsOpenForWrite | SamFile | [protected] |
myNewSection (defined in SamFile) | SamFile | [protected] |
myPrevCoord | SamFile | [protected] |
myPrevReadName (defined in SamFile) | SamFile | [protected] |
myPrevRefID (defined in SamFile) | SamFile | [protected] |
myRecordCount | SamFile | [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] |
myStatistics | SamFile | [protected] |
myStatus | SamFile | [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 value | SamFile | |
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 | |
SamFileWriter() | SamFileWriter | |
SamFileWriter(const char *filename) | SamFileWriter | |
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 name | SamFile | |
UNSORTED enum value | SamFile | |
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] |
~SamFileWriter() (defined in SamFileWriter) | SamFileWriter | [virtual] |