libStatGen Software 1
BamIndexFileTest Member List

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

attemptRecoverySync(bool(*checkSignature)(void *data), int length) (defined in SamFile)SamFile
checkRecordInSection(SamRecord &record) (defined in SamFile)SamFileprotected
Close()SamFile
COORDINATE enum valueSamFile
DisableBuffering()SamFileinline
ensureIndexedReadPosition() (defined in SamFile)SamFileprotected
FLAG enum valueSamFile
GenerateStatistics(bool genStats)SamFile
GetBamIndex()SamFile
getBamIndex() (defined in BamIndexFileTest)BamIndexFileTestinline
GetCurrentPosition()SamFileinline
GetCurrentRecordCount()SamFile
GetFailure()SamFileinline
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)SamFileprotected
GetStatus()SamFileinline
GetStatusMessage()SamFileinline
init() (defined in SamFile)SamFileprotected
init(const char *filename, OpenType mode, SamFileHeader *header) (defined in SamFile)SamFileprotected
IsEOF()SamFile
IsOpen()SamFile
IsStream()SamFile
myBamIndex (defined in SamFile)SamFileprotected
myChunksToRead (defined in SamFile)SamFileprotected
myCurrentChunkEnd (defined in SamFile)SamFileprotected
myEndPos (defined in SamFile)SamFileprotected
myFilePtr (defined in SamFile)SamFileprotected
myHasHeaderSamFileprotected
myInterfacePtr (defined in SamFile)SamFileprotected
myIsBamOpenForReadSamFileprotected
myIsOpenForReadSamFileprotected
myIsOpenForWriteSamFileprotected
myNewSection (defined in SamFile)SamFileprotected
myOverlapSection (defined in SamFile)SamFileprotected
myPrevCoordSamFileprotected
myPrevReadName (defined in SamFile)SamFileprotected
myPrevRefID (defined in SamFile)SamFileprotected
myReadTranslation (defined in SamFile)SamFileprotected
myRecordCountSamFileprotected
myRefID (defined in SamFile)SamFileprotected
myRefName (defined in SamFile)SamFileprotected
myRefPtr (defined in SamFile)SamFileprotected
mySortedType (defined in SamFile)SamFileprotected
myStartPos (defined in SamFile)SamFileprotected
myStatisticsSamFileprotected
myStatusSamFileprotected
myWriteTranslation (defined in SamFile)SamFileprotected
OpenForRead(const char *filename, SamFileHeader *header=NULL)SamFile
OpenForWrite(const char *filename, SamFileHeader *header=NULL)SamFile
OpenType enum nameSamFile
PrintStatistics()SamFileinline
processNewSection(SamFileHeader &header) (defined in SamFile)SamFileprotected
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()SamFileprotected
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)SamFileinline
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)SamFileprotected
WRITE enum valueSamFile
WriteHeader(SamFileHeader &header)SamFile
WriteRecord(SamFileHeader &header, SamRecord &record)SamFile
~SamFile()SamFilevirtual