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GenomeSequence Member List

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

allocate() (defined in MemoryMap) | MemoryMap | virtual
BasePair(char c) const (defined in GenomeSequence) | GenomeSequence | inline
checkRead(std::string &read, std::string &qualities, std::string &cigar, int &sumQ, int &gapOpenCount, int &gapExtendCount, int &gapDeleteCount, std::string &result) const | GenomeSequence |
chromosomeName(int chr) const (defined in GenomeSequence) | GenomeSequence | inline
close() (defined in MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >) | MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass > | inline
constructor_clear() (defined in MemoryMap) | MemoryMap |
constructorClear() (defined in GenomeSequence) | GenomeSequence |
create(bool isColor=false) (defined in GenomeSequence) | GenomeSequence |
MemoryMapArray::create(const char *file, indexT elementCount, int optionalHeaderCount=0) | MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass > | inline
MemoryMapArray::create(indexT elementCount, int optionalHeaderCount=0) | MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass > | inline
MemoryMap::create(const char *file, size_t size) | MemoryMap | virtual
MemoryMap::create(size_t size) | MemoryMap | virtual
data (defined in MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >) | MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass > | protected
debug_print() (defined in MemoryMap) | MemoryMap |
debugPrint(FILE *f) (defined in MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >) | MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass > | inline
debugPrintReadValidation(std::string &read, std::string &quality, char direction, genomeIndex_t readLocation, int sumQuality, int mismatchCount, bool recurse=true) (defined in GenomeSequence) | GenomeSequence |
destructor_clear() (defined in MemoryMap) | MemoryMap |
dumpHeaderTSV(std::ostream &) const (defined in GenomeSequence) | GenomeSequence |
dumpSequenceSAMDictionary(std::ostream &) const (defined in GenomeSequence) | GenomeSequence |
errorStr (defined in MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >) | MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass > | protected
GenomeSequence() | GenomeSequence |
GenomeSequence(std::string &referenceFilename) | GenomeSequence | inline
GenomeSequence(const char *referenceFilename) | GenomeSequence | inline
getBase(const char *chromosomeName, unsigned int chromosomeIndex) const | GenomeSequence | inline
getBaseFilename() const (defined in GenomeSequence) | GenomeSequence | inline
getChromosome(genomeIndex_t position) const | GenomeSequence |
getChromosome(const char *chromosomeName) const | GenomeSequence |
getChromosomeAndIndex(std::string &, genomeIndex_t) const (defined in GenomeSequence) | GenomeSequence |
getChromosomeAndIndex(String &, genomeIndex_t) const (defined in GenomeSequence) | GenomeSequence |
getChromosomeCount() const | GenomeSequence |
getChromosomeName(int chromosomeIndex) const (defined in GenomeSequence) | GenomeSequence | inline
getChromosomeSize(int chromosomeIndex) const | GenomeSequence | inline
getChromosomeStart(int chromosomeIndex) const | GenomeSequence | inline
getDataPtr(genomeIndex_t index) | GenomeSequence | inline
getElementCount() const (defined in MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >) | MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass > | inline
getErrorString() (defined in MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >) | MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass > | inline
getFastaName() const (defined in GenomeSequence) | GenomeSequence | inline
getGenomePosition(const char *chromosomeName, unsigned int chromosomeIndex) const | GenomeSequence |
getGenomePosition(int chromosome, unsigned int chromosomeIndex) const | GenomeSequence |
getGenomePosition(const char *chromosomeName) const | GenomeSequence |
getGenomePosition(int chromosomeIndex) const (defined in GenomeSequence) | GenomeSequence |
getHeader() (defined in MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >) | MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass > | inline
getHighLightedString(std::string &str, genomeIndex_t index, int baseCount, genomeIndex_t highLightStart, genomeIndex_t highLightEnd) const (defined in GenomeSequence) | GenomeSequence |
getInteger(genomeIndex_t index) const (defined in GenomeSequence) | GenomeSequence | inline
getMismatchCount(std::string &read, genomeIndex_t location, char exclude='\0') const | GenomeSequence | inline
getMismatchHatString(std::string &result, const std::string &read, genomeIndex_t location) const (defined in GenomeSequence) | GenomeSequence |
getMismatchString(std::string &result, const std::string &read, genomeIndex_t location) const (defined in GenomeSequence) | GenomeSequence |
getNumberBases() const | GenomeSequence | inline
getReferenceName() const (defined in GenomeSequence) | GenomeSequence | inline
getReverseRead(std::string &read) (defined in GenomeSequence) | GenomeSequence |
getReverseRead(String &read) (defined in GenomeSequence) | GenomeSequence |
getString(std::string &str, int chromosome, uint32_t index, int baseCount) const (defined in GenomeSequence) | GenomeSequence |
getString(String &str, int chromosome, uint32_t index, int baseCount) const (defined in GenomeSequence) | GenomeSequence |
getString(std::string &str, genomeIndex_t index, int baseCount) const (defined in GenomeSequence) | GenomeSequence |
getString(String &str, genomeIndex_t index, int baseCount) const (defined in GenomeSequence) | GenomeSequence |
getSumQ(std::string &read, std::string &qualities, genomeIndex_t location) const | GenomeSequence | inline
header (defined in MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >) | MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass > | protected
IntegerToSeq(unsigned int n, unsigned int wordsize) const (defined in GenomeSequence) | GenomeSequence |
isColorSpace() const | GenomeSequence | inline
length() (defined in MemoryMap) | MemoryMap | inline
loadDBSNP(mmapArrayBool_t &dbSNP, const char *inputFileName) const | GenomeSequence |
loadFastaData(const char *filename) (defined in GenomeSequence) | GenomeSequence |
MemoryMap() (defined in MemoryMap) | MemoryMap |
MemoryMapArray() (defined in MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >) | MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass > | inline
open(bool isColorSpace=false, int flags=O_RDONLY) | GenomeSequence |
open(const char *filename, int flags=O_RDONLY) | GenomeSequence | inline virtual
operator[](genomeIndex_t index) const | GenomeSequence | inline
operator[](indexT i) (defined in MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >) | MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass > | inline
operator[](unsigned int index) (defined in MemoryMap) | MemoryMap | inline
populateDBSNP(mmapArrayBool_t &dbSNP, IFILE inputFile) const (defined in GenomeSequence) | GenomeSequence |
prefetch() (defined in MemoryMap) | MemoryMap |
print30(genomeIndex_t) const (defined in GenomeSequence) | GenomeSequence |
printNearbyWords(unsigned int index, unsigned int variance, std::string &word) const (defined in GenomeSequence) | GenomeSequence |
sanityCheck(MemoryMap &fasta) const (defined in GenomeSequence) | GenomeSequence |
sequenceLength() const (defined in GenomeSequence) | GenomeSequence | inline
set(genomeIndex_t index, char value) (defined in GenomeSequence) | GenomeSequence | inline
set(indexT i, elementT v) (defined in MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >) | MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass > | inline
setApplication(std::string application) | GenomeSequence | inline
setColorSpace(bool colorSpace) (defined in GenomeSequence) | GenomeSequence | inline
setContentCookie(uint32_t c) (defined in MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >) | MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass > | inline
setContentVersion(uint32_t v) (defined in MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >) | MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass > | inline
setCreateOverwrite(bool createOverwrite) (defined in GenomeSequence) | GenomeSequence | inline
setDebugFlag(bool d) (defined in GenomeSequence) | GenomeSequence | inline
setProgressStream(std::ostream &progressStream) | GenomeSequence | inline
setReferenceName(std::string referenceFilename) | GenomeSequence |
setSearchCommonFileSuffix(bool searchCommonFileSuffix) (defined in GenomeSequence) | GenomeSequence | inline
simpleLocalAligner(std::string &read, std::string &quality, genomeIndex_t index, int windowSize) const (defined in GenomeSequence) | GenomeSequence |
test() (defined in MemoryMap) | MemoryMap |
useMemoryMap(bool flag=true) (defined in MemoryMap) | MemoryMap | inline
wordMatch(unsigned int index, std::string &word) const (defined in GenomeSequence) | GenomeSequence |
~GenomeSequence() | GenomeSequence |
~MemoryMap() (defined in MemoryMap) | MemoryMap | virtual
~MemoryMapArray() (defined in MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >) | MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass > | inline