, including all inherited members.
| base2complement (defined in GenomeSequence) | GenomeSequence | [static] |
| base2int (defined in GenomeSequence) | GenomeSequence | [static] |
| baseAIndex (defined in GenomeSequence) | GenomeSequence | [static] |
| baseCIndex (defined in GenomeSequence) | GenomeSequence | [static] |
| baseGIndex (defined in GenomeSequence) | GenomeSequence | [static] |
| baseNIndex (defined in GenomeSequence) | GenomeSequence | [static] |
| BasePair(char c) const (defined in GenomeSequence) | GenomeSequence | [inline] |
| baseTIndex (defined in GenomeSequence) | GenomeSequence | [static] |
| baseXIndex (defined in GenomeSequence) | GenomeSequence | [static] |
| 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() (defined in GenomeSequence) | GenomeSequence | |
| create(bool isColor) (defined in GenomeSequence) | GenomeSequence | [inline] |
| 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] |
| 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, genomeIndex_t index, int baseCount) const (defined in GenomeSequence) | GenomeSequence | |
| getString(String &str, int chromosome, genomeIndex_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] |
| int2base (defined in GenomeSequence) | GenomeSequence | [static] |
| int2colorSpace (defined in GenomeSequence) | GenomeSequence | [static] |
| 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, std::ifstream &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] |
| setDebugFlag(bool d) (defined in GenomeSequence) | GenomeSequence | [inline] |
| setProgressStream(std::ostream &progressStream) (defined in GenomeSequence) | 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] |
