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A

addParameterInfo() - Method in class uni.bielefeld.cmg.sparkhit.util.Parameter

This method adds descriptions to each parameter.

addParameterInfo() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForChisquareTester

This method adds descriptions to each parameter.

addParameterInfo() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForCluster

This method adds descriptions to each parameter.

addParameterInfo() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForConverter

This method adds descriptions to each parameter.

addParameterInfo() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForCorrelationer

This method adds descriptions to each parameter.

addParameterInfo() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForDecompresser

This method adds descriptions to each parameter.

addParameterInfo() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForMapper

This method adds descriptions to each parameter.

addParameterInfo() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForParallelizer

This method adds descriptions to each parameter.

addParameterInfo() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForReductioner

This method adds descriptions to each parameter.

addParameterInfo() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForRegressioner

This method adds descriptions to each parameter.

addParameterInfo() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForReporter

This method adds descriptions to each parameter.

addParameterInfo() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForScriptPiper

This method adds descriptions to each parameter.

addParameterInfo() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForStatisticer

This method adds descriptions to each parameter.

addParameterInfo() - Method in class uni.bielefeld.cmg.sparkhit.util.ParameterForVariantCaller

This method adds descriptions to each parameter.

addReadUnit(readInfo, int) - Method in class uni.bielefeld.cmg.sparkhit.io.FastqUnitBuffer

This method adds a read into the Fastq unit buffer.

addReadUnit(readInfo, int) - Method in interface uni.bielefeld.cmg.sparkhit.io.NGSfileUnitBuffer

This is an abstract method for buffering input fastq units.

align - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter

alignLength - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter

alignLength - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam

alignMatrix - Variable in class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter

AlignmentParameter - Class in uni.bielefeld.cmg.sparkhit.struct

A data structure class that stores all parameters for sequence alignment.

AlignmentParameter(DefaultParam) - Constructor for class uni.bielefeld.cmg.sparkhit.struct.AlignmentParameter

A constructor that construct an object of AlignmentParameter class.

alphaCode - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam

alphaCodeComplement - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam

alphaCodeNNNNN - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam

Arithmetic - Class in uni.bielefeld.cmg.sparkhit.algorithm

Returns an object that can then be used for varies calculations.

Arithmetic() - Constructor for class uni.bielefeld.cmg.sparkhit.algorithm.Arithmetic

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