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samePosition(SingleGenotypePosition, SingleGenotypePosition) - Static method in class Utils.SingleGenotype.SingleGenotypePosition
Tests whether two positions represent the same genotype
samePositions(List<? extends SingleGenotypePosition>, List<? extends SingleGenotypePosition>) - Static method in class Utils.SingleGenotype.SingleGenotypePosition
Tests whether two lists represent the same genotypes in the same order
sample() - Method in class Utils.Distribution.Distribution
Get a sample from the distribution
Sample - Class in VCF
Represents a sample in a VCF file
SampleFilter - Class in VCF.Filters
Represents a sample filter
SampleFilter() - Constructor for class VCF.Filters.SampleFilter
 
SampleMissing - Class in VCF.Filters
Filters a sample based on a maximum allowed amount of missing genotypes
SampleMissing(double, int) - Constructor for class VCF.Filters.SampleMissing
Constructor
SampleMissing(HierarchicalConfiguration<ImmutableNode>) - Constructor for class VCF.Filters.SampleMissing
Constructor from a config (read in from a XML file)
samples() - Method in class VCF.Position
Get a stream of sample names for this position
sampleStream() - Method in class VCF.VCF
Returns a stream of samples in the VCF
set(ProgressFactory.ProgressType) - Static method in class Utils.Progress.ProgressFactory
Set the type of progress indicator the factory creates
SILENT - Utils.Progress.ProgressFactory.ProgressType
The silent indicator (SilentProgress)
SilentProgress - Class in Utils.Progress
Dummy progress indicator that shows nothing
SilentProgress() - Constructor for class Utils.Progress.SilentProgress
 
SingleDoubleValue - Interface in Utils.Optimize
Represents a function that can be optimized.
SingleGenotypeCall - Class in Utils.SingleGenotype
Represents a single genotype call
SingleGenotypeCall(int, int, byte) - Constructor for class Utils.SingleGenotype.SingleGenotypeCall
Constructor
SingleGenotypeMasked - Class in Utils.SingleGenotype
Represents a single masked genotype
SingleGenotypeMasked(int, int, int[], int[], double) - Constructor for class Utils.SingleGenotype.SingleGenotypeMasked
Constructor
SingleGenotypePosition - Class in Utils.SingleGenotype
Represents the position of a single genotype
SingleGenotypePosition(int, int) - Constructor for class Utils.SingleGenotype.SingleGenotypePosition
Constructor
SingleGenotypeProbability - Class in Utils.SingleGenotype
Represents the genotype probabilities for a single genotype
SingleGenotypeProbability(int, int, double[]) - Constructor for class Utils.SingleGenotype.SingleGenotypeProbability
Constructor
SingleGenotypeReads - Class in Utils.SingleGenotype
Represents the reads for a single genotype
SingleGenotypeReads(int, int, int[]) - Constructor for class Utils.SingleGenotype.SingleGenotypeReads
Constructor
singlePosition(PositionMeta) - Method in class VCF.VCF
Returns the data for a single position
singleSample(String) - Method in class VCF.VCF
Returns the data for a single sample
size() - Method in class Accuracy.DepthMask
Returns the number of genotypes masked
sort() - Method in class Utils.SortByIndexDouble
Produce a sorted list of indices for the entire array
SortByIndexDouble - Class in Utils
Comparator to sort integer indices based on the corresponding value in a double array.
SortByIndexDouble(double[]) - Constructor for class Utils.SortByIndexDouble
Constructor.
SortByIndexDouble(double[], boolean) - Constructor for class Utils.SortByIndexDouble
Constructor.
StandardizeCountsFormatChanger - Class in VCF.Changers
Changes readcounts included in two formats to the new single format (AD) specification
StandardizeCountsFormatChanger(String, String) - Constructor for class VCF.Changers.StandardizeCountsFormatChanger
Constructor
supplier() - Method in class Utils.Distribution.ComparableDistributionCollector
 
supplier() - Method in class Utils.Distribution.DistributionCollector
 
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