- Generated by
1.15.0
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libStatGen Software 1
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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 |
| constructor_clear() (defined in MemoryMap) | MemoryMap | |
| constructorClear() (defined in GenomeSequence) | GenomeSequence | |
| create(bool isColor=false) (defined in GenomeSequence) | GenomeSequence | |
| MemoryMapArray< uint32_t, genomeIndex_t, UMFA_COOKIE, UMFA_VERSION, PackedAccess_4Bit, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader >::create(const char *file, genomeIndex_t elementCount, int optionalHeaderCount=0) | MemoryMapArray< uint32_t, genomeIndex_t, UMFA_COOKIE, UMFA_VERSION, PackedAccess_4Bit, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader > | inline |
| MemoryMapArray< uint32_t, genomeIndex_t, UMFA_COOKIE, UMFA_VERSION, PackedAccess_4Bit, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader >::create(genomeIndex_t elementCount, int optionalHeaderCount=0) | MemoryMapArray< uint32_t, genomeIndex_t, UMFA_COOKIE, UMFA_VERSION, PackedAccess_4Bit, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader > | inline |
| MemoryMap::create(const char *file, size_t size) | MemoryMap | virtual |
| MemoryMap::create(size_t size) | MemoryMap | virtual |
| debug_print() (defined in MemoryMap) | MemoryMap | |
| 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 | |
| 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 |
| 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 | |
| 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 |
| 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 | |
| open(bool isColorSpace=false, int flags=O_RDONLY) | GenomeSequence | |
| open(const char *filename, int flags=O_RDONLY) | GenomeSequence | inlinevirtual |
| operator[](genomeIndex_t index) const | GenomeSequence | 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 |
| setApplication(std::string application) | GenomeSequence | inline |
| setColorSpace(bool colorSpace) (defined in GenomeSequence) | GenomeSequence | 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 |
1.15.0