, 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 | |
| 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 | |
| SamFileReader() | SamFileReader | |
| SamFileReader(const char *filename) | SamFileReader | |
| SamFileReader(const char *filename, ErrorHandler::HandlingType errorHandlingType) | SamFileReader | |
| SamFileReader(const char *filename, SamFileHeader *header) | SamFileReader | |
| SamFileReader(const char *filename, ErrorHandler::HandlingType errorHandlingType, SamFileHeader *header) | SamFileReader | |
| 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] |
| ~SamFileReader() (defined in SamFileReader) | SamFileReader | [virtual] |
1.7.6.1 
