All Classes
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All Classes Interface Summary Class Summary Enum Summary Exception Summary Class Description AccuracyCalculator Calculates accuracy statisticsAccuracyCalculator.AccuracyMethod Represents the accuracy method to be used for optimizationAccuracyStats Represents accuracy statisticsAlgorithmException Exception for when there is a problem with one of the algorithmsAvailable Class that gets the appropiate object for filters and callers given the configuration describing the filter or callerBiallelicFilter Filters positions for biallelic positionsBiasedBinomialCaller A biased binomial caller, that is one where each read is not equally likely in the case of a hetrozygoteBinomialCaller Simple binomial callerByteMapper Maps from a text string to a byteByteToGeno A simple convenience class used to convert a byte genotype to a text string representing itCaller Represents a genotype callerCase Represent the LinkImputeR inputs for a single case (filters, caller, imputer and combiner)ClassList<X,Y> Represents a map of constructors so that a new object of the appropriate child class (given by a string) can be constructed.Combiner Combines imputed and inferred genotypes to give a final called genotypeCombinerOption Represents the combiner options to LinkImputeComparableDistribution<V extends java.lang.Comparable<V>> Represents a distribution of comparable discrete objects.ComparableDistributionCollector<V extends java.lang.Comparable<V>> Collector for use with streams that creates a ComparableDistribution from a stream of objectsCorrelation Calculates correlations.CountMap<V> Keeps counts of an objectDepthMapper Maps from a string representing read depths to an integer array of read depthsDepthMask Creates a mask where reads for some genotypes are masked to a given depthDepthMask.Method Represents the method to be used to select genotypes to be maskedDepthMaskFactory Utility class for easily creating multiple DepthMasks with the same parametersDescent Optimizes the input to a function of type MultipleIntegerValue using the descent methodDistribution<V> Represents a discrete distribution of objects.DistributionCollector<V> Collector for use with streams that creates a Distribution from a stream of objectsDotsProgress Draws and updates a progress bar to standard outDoubleMapper Maps from a text string to a doubleEM Calculates LD using the expectation maximization methodExtendedXMLConfiguration Extends XMLConfiguration so XML output is indented.GenoToByte Maps from a text string representing a genotype to a byte representing a genotypeGenotype Represents a single genotype in a VCF fileGenotypeChanger Changes a genotypeGoldenSection Optimizes the input to a function of type SingleDoubleValue using the Golden Section methodHasDepthFilter Filter positions that do not have depth dataImputationOption Represents the imputer options to LinkImputeImputer Represents an imputerINIException Exception for when there is a problem with a ini fileInput Represents the input to LinkImputeRIntegerMapper Maps from a text string to an integerKnniLDProb Class to perform standard LD-kNNi imputation using probabilitiesKnniLDProbOptimizedCalls Represents a KnniLDProb imputer that can be optimized to maximise the number of correctly called genotypedLinkImputeR Main classLog Very simple logger.Log.Level Represents different levels of message output.LogBiasedBinomialCaller A biased binomial caller, that is one where each read is not equally likely in the case of a hetrozygoteLogBinomialCaller Simple binomial callerMAFCalculator Calculates minor allele frequencyMAFFilter Filters positions based on minor allele frequencyMapper<M> Maps from string to objectMatrix Matrix utility functionsMaxDepthCombiner Combines called and imputed genotype probabilities, only using called genotypes above a given read depthMaxDepthCombinerOptimizedCalls Gets an optimized MaxDepthCombiner.MaxDepthNoReadsChanger Changes the genotype (the GT field) of genotype to unknown (./.) if the total number of reads is less than a thresholdMeta Represents the meta information in a VCFMinDepthMissingChanger Changes the genotype (the GT field) of genotype to unknown (./.) if the total number of reads is less than a thresholdMultipleIntegerValue Represents a function that can be optimized.MultipleTest Optimizes the input to a function of type SingleDoubleValue by testing multiple possible input valuesNotEnoughMaskableGenotypesException Exception for when there are not enough maskable genotypesOptimizeCombiner<C extends Combiner> Optimizes a combinerOptimizeImputer<I extends Imputer> Represents an imputer that can be optimizedOutput Represents the output options to LinkImputeROutputException Exception for when there is a problem with creating outputParalogHWFilter Filters a position based on a Hardy-Weinburg test.Pearson Calculates LD as a simple Pearson correlationPosition Represents a position in a VCF filePositionChanger Changes a positionPositionFilter Represents a position filterPositionMeta Represents the meta data for a positionPositionMissing Filters a position based on a maximum allowed amount of missing genotypesPrintStats Class used to print statsProbToCall Converts genotype probabilities to a called genotypeProbToCallMinDepth Converts genotype probabilities to a called genotypeProgrammerException Represents an exception an end user should never seeProgress A means for indicating progress to the userProgressFactory Factory for creating a progress indicatorProgressFactory.ProgressType Represents the types of progress indicatorsRenameFormatChanger Renames a formatSample Represents a sample in a VCF fileSampleFilter Represents a sample filterSampleMissing Filters a sample based on a maximum allowed amount of missing genotypesSilentProgress Dummy progress indicator that shows nothingSingleDoubleValue Represents a function that can be optimized.SingleGenotypeCall Represents a single genotype callSingleGenotypeMasked Represents a single masked genotypeSingleGenotypePosition Represents the position of a single genotypeSingleGenotypeProbability Represents the genotype probabilities for a single genotypeSingleGenotypeReads Represents the reads for a single genotypeSortByIndexDouble Comparator to sort integer indices based on the corresponding value in a double array.StandardizeCountsFormatChanger Changes readcounts included in two formats to the new single format (AD) specificationTextBarProgress Draws and updates a progress bar to standard outTextProgress Shows progress as a simple tex output showing" number complete / total number"TopQueue Queue that keeps only the entries with the top valuesVCF Represents the data from a VCF fileVCFDataException Exception for when there is a problem with data in the VCFVCFDataLineException Exception for when there is a problem reading in a data line of a VCFVCFException Exception for when there is a problem with the VCFVCFFilter Represents a VCF filter (either a position filter or a sample filter)VCFHeaderLineException Exception for when there is a problem reading in a header line of a VCFVCFInputException Exception for when there is a problem reading in a VCFVCFMissingFormatException Exception for when the vcf is missing a required formatVCFNoDataException Exception for when there is no data for a given formatVCFUnexpectedDataException Exception for when there is unexpected data for a given formatXMLException Exception for when there is a problem with a xml file