- s - Variable in class uni.bielefeld.cmg.sparkhit.struct.BinaryBlock
-
- ScoreMatrix - Class in uni.bielefeld.cmg.sparkhit.matrix
-
Returns an instance of data structure class that stores scoring matrix
for sequence alignment.
- ScoreMatrix() - Constructor for class uni.bielefeld.cmg.sparkhit.matrix.ScoreMatrix
-
A constructor that construct an object of
ScoreMatrix class.
- scoreMatrix - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
-
- screenDump() - Method in class uni.bielefeld.cmg.sparkhit.util.InfoDumper
-
This method prints the structured message to the screen.
- screenDump() - Method in class uni.bielefeld.cmg.sparkhit.util.InfoLogger
-
This method prints the structured message to the screen.
- seq(String) - Method in class uni.bielefeld.cmg.sparkhit.struct.ReadInfo
-
This method sets the sequence of a read.
- setAlignmentParameter() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.BatchAlignPipe
-
- setBufferReader() - Method in class uni.bielefeld.cmg.sparkhit.io.TextFileBufferInput
-
This method sets the BufferedReader based on the preset InputStreamReader.
- setBufferWriter() - Method in class uni.bielefeld.cmg.sparkhit.io.TextFileBufferOutput
-
set class BufferedWriter object outputBufferWriter.
- setFastqUnitBuffer(FastqUnitBuffer) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method sets a buffer for loading fastq units.
- setFileOutputStream(boolean) - Method in class uni.bielefeld.cmg.sparkhit.io.TextFileBufferOutput
-
set class FileOutputStream object outputFileStream.
- setInput(String) - Method in class uni.bielefeld.cmg.sparkhit.io.ObjectFileInput
-
This method sets up an input file stream based on an input file path.
- setInput(String) - Method in class uni.bielefeld.cmg.sparkhit.io.TextFileBufferInput
-
This method sets up an input file stream for an input file.
- setInput(BufferedReader) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.FastPipe
-
This method sets the buffer for reading the input data.
- setInput(BufferedReader) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.OnePipe
-
This method sets the buffer for loading input data.
- setInput(BufferedReader) - Method in interface uni.bielefeld.cmg.sparkhit.pipeline.Pipeline
-
Sets input buffer reader.
- setInput(BufferedReader) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method sets input buffer reader.
- setInputBufferedReader(BufferedReader) - Method in class uni.bielefeld.cmg.sparkhit.io.ReadFastq
-
This method sets the BufferedReader.
- setInputFastqUnitBuffer(FastqUnitBuffer) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.OnePipe
-
This method sets the buffer for loading fastq units.
- setKmerOverlap(int) - Method in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-
This method initiates the overlap between k-mers.
- setKmerSize(int) - Method in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-
This method initiates the K-mer size parameter.
- setMatrix(ScoreMatrix) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.BatchAlignPipe
-
This method sets the scoring matrix.
- setMatrix(ScoreMatrix) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.OnePipe
-
This method sets the scoring matrix for sequence alignment.
- setMatrix(ScoreMatrix) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkPipe
-
This method sets the scoring matrix for sequence alignment.
- setOutput(String, boolean) - Method in class uni.bielefeld.cmg.sparkhit.io.ObjectFileOutput
-
This method sets up an output file stream based on an output file path.
- setOutput(String, boolean) - Method in class uni.bielefeld.cmg.sparkhit.io.TextFileBufferOutput
-
This method sets up an output file stream for an output file.
- setOutput(BufferedWriter) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.FastPipe
-
This method sets the buffer for writing the output data.
- setOutput(BufferedWriter) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.OnePipe
-
This method sets the buffer for writing output data.
- setOutput(BufferedWriter) - Method in interface uni.bielefeld.cmg.sparkhit.pipeline.Pipeline
-
Sets output buffer writer.
- setOutput(BufferedWriter) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method sets output buffer writer.
- setOutput(String, boolean) - Method in class uni.bielefeld.cmg.sparkhit.util.InfoLogger
-
This method parses the output path and sets a BufferedWriter for the output
- setOutputStreamWriter() - Method in class uni.bielefeld.cmg.sparkhit.io.TextFileBufferOutput
-
set class OutputStreamWriter object outputStreamWriter.
- setParam(DefaultParam) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.BatchAlignPipe
-
This method sets the input parameters.
- setParam(DefaultParam) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkBamPipe
-
This method sets the input parameters.
- setParam(DefaultParam) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkChiSquarePipe
-
This method sets the input parameters.
- setParam(DefaultParam) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkClusterPipe
-
This method sets the input parameters.
- setParam(DefaultParam) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkConvertPipe
-
This method sets the input parameters.
- setParam(DefaultParam) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkCorrelationPipe
-
This method sets the input parameters.
- setParam(DefaultParam) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkDecompressPipe
-
This method sets the input parameters.
- setParam(DefaultParam) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkHWEPipe
-
This method sets the input parameters.
- setParam(DefaultParam) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkParallelPipe
-
This method sets the input parameters.
- setParam(DefaultParam) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkPipe
-
This method sets the input parameters.
- setParam(DefaultParam) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkReductionPipe
-
This method sets the input parameters.
- setParam(DefaultParam) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkRegressionPipe
-
This method sets the input parameters.
- setParam(DefaultParam) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkReportPipe
-
This method sets the input parameters.
- setParam(DefaultParam) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkScriptPipe
-
This method sets the input parameters.
- setParameter(DefaultParam) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.FastPipe
-
This method sets the parameters.
- setParameter(DefaultParam) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.OnePipe
-
This method sets the input parameters.
- setParameter(DefaultParam) - Method in interface uni.bielefeld.cmg.sparkhit.pipeline.Pipeline
-
Sets correspond parameter.
- setParameter(DefaultParam) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method sets correspond parameters.
- setParameter(DefaultParam) - Method in interface uni.bielefeld.cmg.sparkhit.reference.RefManager
-
This is an abstract method for passing input parameters to each class.
- setParameter(DefaultParam) - Method in interface uni.bielefeld.cmg.sparkhit.reference.RefSerializer
-
This is an abstract method for passing input parameters to each class.
- setParameter(DefaultParam) - Method in class uni.bielefeld.cmg.sparkhit.reference.RefStructBuilder
-
This method sets all correspond parameters for reference
data structure construction.
- setParameter(DefaultParam) - Method in interface uni.bielefeld.cmg.sparkhit.reference.RefStructManager
-
This is an abstract method for passing input parameters to each class.
- setParameter(DefaultParam) - Method in class uni.bielefeld.cmg.sparkhit.reference.RefStructSerializer
-
This method sets the input parameters.
- setRegisterClass(Class, int) - Method in class uni.bielefeld.cmg.sparkhit.serializer.kryoSerializer
-
This method registers a class to kryo serializer.
- setStruct(RefStructBuilder) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.BatchAlignPipe
-
This method passes the reference index to the recruitment pipeline.
- setStruct(RefStructBuilder) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.OnePipe
-
This method sets the reference index.
- setStruct(RefStructBuilder) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkPipe
-
This method sets the reference builder object.
- setStruct(RefStructBuilder) - Method in class uni.bielefeld.cmg.sparkhit.reference.RefStructSerializer
-
- ShAlgorithm - Interface in uni.bielefeld.cmg.sparkhit.algorithm
-
An interface class for varies algorithms.
- ShJavaSerializer - Interface in uni.bielefeld.cmg.sparkhit.serializer
-
This is an interface for default Java serializers.
- ShKryoSerializer - Interface in uni.bielefeld.cmg.sparkhit.serializer
-
This is an interface for kryo serializers.
- ShMatrix - Interface in uni.bielefeld.cmg.sparkhit.matrix
-
This is an interface for different matrix used in sequence alignment.
- ShSerializer - Interface in uni.bielefeld.cmg.sparkhit.serializer
-
This is an interface for different serializers.
- singleNtBit - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
-
- singleNtBitComplement - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
-
- size(String) - Method in class uni.bielefeld.cmg.sparkhit.struct.ReadInfo
-
This method sets the length of a sequencing read.
- size(long) - Method in class uni.bielefeld.cmg.sparkhit.struct.RefInfo
-
This method sets the size of a reference genome.
- size - Variable in class uni.bielefeld.cmg.sparkhit.struct.RefTitle
-
- skipThreshold - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-
- spark() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method starts the recruiter pipeline
- spark() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkBamPipe
-
runs the Sparkhit pipeline using Spark RDD operations.
- spark() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkChiSquarePipe
-
runs the Sparkhit pipeline using Spark RDD operations.
- spark() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkClusterPipe
-
runs the Sparkhit pipeline using Spark RDD operations.
- spark() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkConvertPipe
-
runs the Sparkhit pipeline using Spark RDD operations.
- spark() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkCorrelationPipe
-
runs the Sparkhit pipeline using Spark RDD operations.
- spark() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkDecompressPipe
-
runs the Sparkhit pipeline using Spark RDD operations.
- spark() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkHWEPipe
-
runs the Sparkhit pipeline using Spark RDD operations.
- spark() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkParallelPipe
-
runs the Sparkhit pipeline using Spark RDD operations.
- spark() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkPipe
-
This method runs the Sparkhit pipeline using Spark RDD operations.
- spark() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkReductionPipe
-
runs the Sparkhit pipeline using Spark RDD operations.
- spark() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkRegressionPipe
-
runs the Sparkhit pipeline using Spark RDD operations.
- spark() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkReportPipe
-
runs the Sparkhit pipeline using Spark RDD operations.
- spark() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkScriptPipe
-
runs the Sparkhit pipeline using Spark RDD operations.
- SparkBamPipe - Class in uni.bielefeld.cmg.sparkhit.pipeline
-
Returns an object for reading BAM files from HDFS.
- SparkBamPipe() - Constructor for class uni.bielefeld.cmg.sparkhit.pipeline.SparkBamPipe
-
- SparkChiSquarePipe - Class in uni.bielefeld.cmg.sparkhit.pipeline
-
Returns an object for running the Sparkhit Chi-square test pipeline.
- SparkChiSquarePipe() - Constructor for class uni.bielefeld.cmg.sparkhit.pipeline.SparkChiSquarePipe
-
- sparkChisquareTester() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method starts the chi-square test pipeline
- sparkCluster() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method starts the cluster pipeline
- SparkClusterPipe - Class in uni.bielefeld.cmg.sparkhit.pipeline
-
Returns an object for running the Sparkhit cluster pipeline.
- SparkClusterPipe() - Constructor for class uni.bielefeld.cmg.sparkhit.pipeline.SparkClusterPipe
-
- sparkConverter() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method starts the converter pipeline
- SparkConvertPipe - Class in uni.bielefeld.cmg.sparkhit.pipeline
-
Returns an object for running the Sparkhit converter pipeline.
- SparkConvertPipe() - Constructor for class uni.bielefeld.cmg.sparkhit.pipeline.SparkConvertPipe
-
- sparkCorrelationer() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method starts the correlation pipeline
- SparkCorrelationPipe - Class in uni.bielefeld.cmg.sparkhit.pipeline
-
Returns an object for running the Sparkhit correlation test pipeline.
- SparkCorrelationPipe() - Constructor for class uni.bielefeld.cmg.sparkhit.pipeline.SparkCorrelationPipe
-
- sparkDecompresser() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method starts the decompression pipeline
- SparkDecompressPipe - Class in uni.bielefeld.cmg.sparkhit.pipeline
-
Returns an object for running the Sparkhit decompression pipeline.
- SparkDecompressPipe() - Constructor for class uni.bielefeld.cmg.sparkhit.pipeline.SparkDecompressPipe
-
- sparkFastqToLine() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkPipe
-
This method transforms fastq format to line-based format.
- SparkHWEPipe - Class in uni.bielefeld.cmg.sparkhit.pipeline
-
Returns an object for running the Sparkhit HWE test pipeline.
- SparkHWEPipe() - Constructor for class uni.bielefeld.cmg.sparkhit.pipeline.SparkHWEPipe
-
- SparkKryoRegistrator - Class in uni.bielefeld.cmg.sparkhit.serializer
-
An class used to register all classes for Spark kryo serializer.
- SparkKryoRegistrator() - Constructor for class uni.bielefeld.cmg.sparkhit.serializer.SparkKryoRegistrator
-
- sparkLineFile() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkPipe
-
reading line based fastq data
- sparkMapper() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method starts the mapper pipeline
- sparkParallelizer() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method starts the parallelizer pipeline
- SparkParallelPipe - Class in uni.bielefeld.cmg.sparkhit.pipeline
-
Returns an object for running the Sparkhit piper pipeline.
- SparkParallelPipe() - Constructor for class uni.bielefeld.cmg.sparkhit.pipeline.SparkParallelPipe
-
- SparkPipe - Class in uni.bielefeld.cmg.sparkhit.pipeline
-
Returns an object for running the Sparkhit-recruiter pipeline.
- SparkPipe() - Constructor for class uni.bielefeld.cmg.sparkhit.pipeline.SparkPipe
-
- sparkPiper() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method starts the piper pipeline
- sparkRecruit(String) - Method in class uni.bielefeld.cmg.sparkhit.pipeline.BatchAlignPipe
-
This method recruits one sequencing read to the reference genomes.
- sparkReductioner() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method starts the reduction pipeline
- SparkReductionPipe - Class in uni.bielefeld.cmg.sparkhit.pipeline
-
Returns an object for running the Sparkhit reduction pipeline.
- SparkReductionPipe() - Constructor for class uni.bielefeld.cmg.sparkhit.pipeline.SparkReductionPipe
-
- sparkRegressioner() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method starts the regression pipeline
- SparkRegressionPipe - Class in uni.bielefeld.cmg.sparkhit.pipeline
-
Returns an object for running the Sparkhit regression pipeline.
- SparkRegressionPipe() - Constructor for class uni.bielefeld.cmg.sparkhit.pipeline.SparkRegressionPipe
-
- sparkReporter() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method starts the reporter pipeline
- SparkReportPipe - Class in uni.bielefeld.cmg.sparkhit.pipeline
-
Returns an object for running the Sparkhit reporter pipeline.
- SparkReportPipe() - Constructor for class uni.bielefeld.cmg.sparkhit.pipeline.SparkReportPipe
-
- SparkScriptPipe - Class in uni.bielefeld.cmg.sparkhit.pipeline
-
Returns an object for running the Sparkhit piper pipeline.
- SparkScriptPipe() - Constructor for class uni.bielefeld.cmg.sparkhit.pipeline.SparkScriptPipe
-
- sparkSpecific() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.SparkReportPipe
-
runs the Sparkhit pipeline using Spark RDD operations.
- sparkStatisticer() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method starts the HWE test pipeline
- sparkVariantCaller() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.Pipelines
-
This method starts the variant detection pipeline
- start() - Method in class uni.bielefeld.cmg.sparkhit.pipeline.OnePipe
-
the pipeline starts by calling the thread start() function
- Statistic - Class in uni.bielefeld.cmg.sparkhit.algorithm
-
Returns an object that can then be used for varies statistic tests.
- Statistic() - Constructor for class uni.bielefeld.cmg.sparkhit.algorithm.Statistic
-