- id - Variable in class uni.bielefeld.cmg.sparkhit.struct.Block
-
- id - Variable in class uni.bielefeld.cmg.sparkhit.struct.KmerLoc
-
- identity - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
-
- identityMatrix - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter
-
- importCommandLine() - Method in class uni.bielefeld.cmg.sparkhit.util.Parameter
-
This method parses input commandline arguments and sets correspond
parameters.
- importCommandLine() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForChisquareTester
-
This method parses input commandline arguments and sets correspond
parameters.
- importCommandLine() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForCluster
-
This method parses input commandline arguments and sets correspond
parameters.
- importCommandLine() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForConverter
-
This method parses input commandline arguments and sets correspond
parameters.
- importCommandLine() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForCorrelationer
-
This method parses input commandline arguments and sets correspond
parameters.
- importCommandLine() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForDecompresser
-
This method parses input commandline arguments and sets correspond
parameters.
- importCommandLine() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForMapper
-
This method parses input commandline arguments and sets correspond
parameters.
- importCommandLine() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForParallelizer
-
This method parses input commandline arguments and sets correspond
parameters.
- importCommandLine() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForReductioner
-
This method parses input commandline arguments and sets correspond
parameters.
- importCommandLine() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForRegressioner
-
This method parses input commandline arguments and sets correspond
parameters.
- importCommandLine() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForReporter
-
This method parses input commandline arguments and sets correspond
parameters.
- importCommandLine() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForScriptPiper
-
This method parses input commandline arguments and sets correspond
parameters.
- importCommandLine() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForStatisticer
-
This method parses input commandline arguments and sets correspond
parameters.
- importCommandLine() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForVariantCaller
-
This method parses input commandline arguments and sets correspond
parameters.
- index - Variable in class uni.bielefeld.cmg.sparkhit.pipeline.BatchAlignPipe
-
- index - Variable in class uni.bielefeld.cmg.sparkhit.reference.RefStructBuilder
-
- InfoDumper - Class in uni.bielefeld.cmg.sparkhit.util
-
Returns an object for printing messages in a structured format to the screen.
- InfoDumper() - Constructor for class uni.bielefeld.cmg.sparkhit.util.InfoDumper
-
- InfoLogger - Class in uni.bielefeld.cmg.sparkhit.util
-
Returns an object for logging messages in a structured format.
- InfoLogger() - Constructor for class uni.bielefeld.cmg.sparkhit.util.InfoLogger
-
- InfoManager - Interface in uni.bielefeld.cmg.sparkhit.util
-
This is an interface for managing program information.
- initialAlphaCode() - Method in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-
This method initiates the ASCII code for each nucleotide.
- initialAlphaCodeComplement() - Method in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-
This method initiates the ASCII code for the reverse-complement of each nucleotide.
- initialNNNNNFilter() - Method in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-
This method initiates the codes for unidentified nucleotides.
- initiateMatrix(int, int) - Method in class uni.bielefeld.cmg.sparkhit.matrix.ScoreMatrix
-
This method initiates the scoring matrix based on the gap penalty
and gap extension penalty.
- initiateMatrix(int, int) - Method in interface uni.bielefeld.cmg.sparkhit.matrix.ShMatrix
-
- inputBufferedFastqUnit - Variable in class uni.bielefeld.cmg.sparkhit.pipeline.OnePipe
-
- inputBufferedReader - Variable in class uni.bielefeld.cmg.sparkhit.io.FastqUnitBuffer
-
- inputBufferedReader - Variable in class uni.bielefeld.cmg.sparkhit.pipeline.OnePipe
-
- inputBufferReader - Variable in class uni.bielefeld.cmg.sparkhit.io.TextFileBufferInput
-
- inputBuildPath - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-
- inputFaPath - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-
- InputFileManager - Interface in uni.bielefeld.cmg.sparkhit.io
-
This is an interface for managing input files via different input
buffers.
- inputFileStream - Variable in class uni.bielefeld.cmg.sparkhit.io.TextFileBufferInput
-
- inputFqLinePath - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-
- inputFqPath - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-
- inputList - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-
- inputNodes - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-
- inputObjectStream - Variable in class uni.bielefeld.cmg.sparkhit.io.ObjectFileInput
-
- inputResultPath - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-
- inputStream - Variable in class uni.bielefeld.cmg.sparkhit.io.ObjectFileInput
-
- inputStreamReader - Variable in class uni.bielefeld.cmg.sparkhit.io.TextFileBufferInput
-
- inputTabPath - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-
- inputTrainPath - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-
- invalidNt - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-
- iterationNum - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
-