libStatGen Software 1
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GenomeSequence Member List

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

allocate() (defined in MemoryMap)MemoryMapvirtual
BasePair(char c) const (defined in GenomeSequence)GenomeSequenceinline
checkRead(std::string &read, std::string &qualities, std::string &cigar, int &sumQ, int &gapOpenCount, int &gapExtendCount, int &gapDeleteCount, std::string &result) constGenomeSequence
chromosomeName(int chr) const (defined in GenomeSequence)GenomeSequenceinline
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)MemoryMapvirtual
MemoryMap::create(size_t size)MemoryMapvirtual
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)GenomeSequenceinline
GenomeSequence(const char *referenceFilename)GenomeSequenceinline
getBase(const char *chromosomeName, unsigned int chromosomeIndex) constGenomeSequenceinline
getBaseFilename() const (defined in GenomeSequence)GenomeSequenceinline
getChromosome(genomeIndex_t position) constGenomeSequence
getChromosome(const char *chromosomeName) constGenomeSequence
getChromosomeAndIndex(std::string &, genomeIndex_t) const (defined in GenomeSequence)GenomeSequence
getChromosomeAndIndex(String &, genomeIndex_t) const (defined in GenomeSequence)GenomeSequence
getChromosomeCount() constGenomeSequence
getChromosomeName(int chromosomeIndex) const (defined in GenomeSequence)GenomeSequenceinline
getChromosomeSize(int chromosomeIndex) constGenomeSequenceinline
getChromosomeStart(int chromosomeIndex) constGenomeSequenceinline
getDataPtr(genomeIndex_t index)GenomeSequenceinline
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)GenomeSequenceinline
getGenomePosition(const char *chromosomeName, unsigned int chromosomeIndex) constGenomeSequence
getGenomePosition(int chromosome, unsigned int chromosomeIndex) constGenomeSequence
getGenomePosition(const char *chromosomeName) constGenomeSequence
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)GenomeSequenceinline
getMismatchCount(std::string &read, genomeIndex_t location, char exclude='\0') constGenomeSequenceinline
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() constGenomeSequenceinline
getReferenceName() const (defined in GenomeSequence)GenomeSequenceinline
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) constGenomeSequenceinline
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() constGenomeSequenceinline
length() (defined in MemoryMap)MemoryMapinline
loadDBSNP(mmapArrayBool_t &dbSNP, const char *inputFileName) constGenomeSequence
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)GenomeSequenceinlinevirtual
operator[](genomeIndex_t index) constGenomeSequenceinline
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)MemoryMapinline
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)GenomeSequenceinline
set(genomeIndex_t index, char value) (defined in GenomeSequence)GenomeSequenceinline
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)GenomeSequenceinline
setColorSpace(bool colorSpace) (defined in GenomeSequence)GenomeSequenceinline
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)GenomeSequenceinline
setDebugFlag(bool d) (defined in GenomeSequence)GenomeSequenceinline
setProgressStream(std::ostream &progressStream)GenomeSequenceinline
setReferenceName(std::string referenceFilename)GenomeSequence
setSearchCommonFileSuffix(bool searchCommonFileSuffix) (defined in GenomeSequence)GenomeSequenceinline
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)MemoryMapinline
wordMatch(unsigned int index, std::string &word) const (defined in GenomeSequence)GenomeSequence
~GenomeSequence()GenomeSequence
~MemoryMap() (defined in MemoryMap)MemoryMapvirtual
~MemoryMapArray() (defined in MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >)MemoryMapArray< elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass >inline