libStatGen Software  1
SamFile Member List
This is the complete list of members for SamFile, 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 valueSamFile
DisableBuffering()SamFile [inline]
ensureIndexedReadPosition() (defined in SamFile)SamFile [protected]
FLAG enum valueSamFile
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]
myHasHeaderSamFile [protected]
myInterfacePtr (defined in SamFile)SamFile [protected]
myIsBamOpenForReadSamFile [protected]
myIsOpenForReadSamFile [protected]
myIsOpenForWriteSamFile [protected]
myNewSection (defined in SamFile)SamFile [protected]
myOverlapSection (defined in SamFile)SamFile [protected]
myPrevCoordSamFile [protected]
myPrevReadName (defined in SamFile)SamFile [protected]
myPrevRefID (defined in SamFile)SamFile [protected]
myReadTranslation (defined in SamFile)SamFile [protected]
myRecordCountSamFile [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]
myStatisticsSamFile [protected]
myStatusSamFile [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 nameSamFile
PrintStatistics()SamFile [inline]
processNewSection(SamFileHeader &header) (defined in SamFile)SamFile [protected]
QUERY_NAME enum valueSamFile
READ enum valueSamFile
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
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 nameSamFile
UNSORTED enum valueSamFile
validateSortOrder(SamRecord &record, SamFileHeader &header)SamFile [protected]
WRITE enum valueSamFile
WriteHeader(SamFileHeader &header)SamFile
WriteRecord(SamFileHeader &header, SamRecord &record)SamFile
~SamFile()SamFile [virtual]
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