A B C D E F G H I K L M N O P R S T U V W X
All Classes All Packages
All Classes All Packages
All Classes All Packages
S
- 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
All Classes All Packages