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A

accept(E) - Method in interface blbutil.Filter
Returns true if the specified object is accepted and returns false if the specified object is rejected.
acceptAllFilter() - Static method in interface blbutil.Filter
Returns a filter that accepts all non-null objects.
add(E) - Method in class beagleutil.CenteredIntIntervalTree
 
add(E) - Method in interface beagleutil.IntIntervalTree
Adds the specified element to this interval tree, and returns true if the interval tree is changed as a result of the call.
add(int) - Method in class blbutil.IndexSet
Adds the specified element to the set.
add(int) - Method in class blbutil.IntList
Adds the specified integer to the end of this list.
add(int) - Method in class blbutil.IntSet
Adds the specified element to this set.
add(int, double[]) - Method in class main.BasicGenotypeValues
 
add(int, int, int, double) - Method in class main.BasicGenotypeValues
 
add(int, double[]) - Method in interface main.GenotypeValues
Adds the specified genotype values to the stored genotype values for the specified sample.
add(int, int, int, double) - Method in interface main.GenotypeValues
Adds the specified genotype value to the stored genotype value.
add(int, double[]) - Method in class main.RevGenotypeValues
 
add(int, int, int, double) - Method in class main.RevGenotypeValues
 
add(double[]) - Method in class main.SampleGenotypeValues
Adds the specified genotype values to this.
add(int, int, double) - Method in class main.SampleGenotypeValues
Adds the specified genotype value to this.
addRestrictedRefHapPairs(List<HapPair>) - Method in class main.CurrentData
Add the reference haplotype pairs that are restricted to the target data markers to the specified list.
addSampleData(double[]) - Method in class vcf.R2Estimator
Adds the specified allele dose probabilities for a genotype to the stored allele dose data.
addSampleData(double[]) - Method in class vcf.VcfRecBuilder
Adds the FORMAT field for a sample to the VCF record for the current marker.
addSampleData(double[], double[]) - Method in class vcf.VcfRecBuilder
Adds the FORMAT field for a sample to the VCF record for the current marker.
addToCompessedList(VcfEmission) - Method in class vcf.VcfEmissionCompressor
Attempts to add the specified VcfEmission object to the list of compressed VcfEmission objects, and returns true if the VcfEmission object was added.
adjustedIbdScale(int) - Method in class main.Par
Returns a sample-size-adjusted IBD scale parameter equal to Math.max(2.0f, (float) Math.sqrt(nSamples/100.0)) if this.ibdscale() == 0f, and returns this.ibdscale() otherwise.
advanceWindow(int, int) - Method in class vcf.AllData
 
advanceWindow(int, int) - Method in interface vcf.Data
Advances the sliding window of VCF records, and returns the advanced window.
advanceWindow(Markers) - Method in class vcf.RestrictedVcfWindow
Advances the sliding marker window, and returns the advanced window as a VcfEmission[] object.
advanceWindow(int, int) - Method in class vcf.TargetData
 
advanceWindow(int, int) - Method in class vcf.VcfWindow
Advances the sliding window of VCF records, and returns the advanced window as a VcfEmission[] object.
AL - Interface in vcf
Interface AL (Allele Likelihoods) represents allele likelihoods for a set of haplotypes.
al(int, int, int) - Method in interface vcf.AL
Returns the probability of the observed data if the specified allele is the true allele for the specified marker and haplotype.
al(int, int, int) - Method in class vcf.HbdAL
 
AllData - Class in vcf
Class AllData represents a sliding window of reference and target VCF records.
allData(SampleFileIt<VcfEmission>, SampleFileIt<? extends VcfEmission>) - Static method in class vcf.AllData
Constructs and returns a new AllData instance from VCF records returned by the specified SampleFileIt objects.
allele(int, int) - Method in class haplotype.BasicHapPairs
 
allele(int, int) - Method in class haplotype.BasicSampleHapPairs
 
allele(int, int) - Method in class haplotype.GLSampleHapPairs
 
allele(int, int) - Method in interface haplotype.HapPairs
Returns the allele for the specified marker and haplotype.
allele(int, int) - Method in class haplotype.RefHapPairs
 
allele(int, int) - Method in class haplotype.RevHapPairs
 
allele(int, int) - Method in class haplotype.RevSampleHapPairs
 
allele(int) - Method in class ibd.Haplotype
Returns the specified allele on the haplotype.
allele(int, int) - Method in interface main.HapAlleleProbs
Returns the specified allele probability.
allele(int, int) - Method in class main.LowMemHapAlleleProbs
 
allele(int, int) - Method in class sample.RefHapSeg
Return the specified reference haplotype allele.
allele(int, int, int) - Method in class sample.RefHapSegs
Return the specified reference haplotype allele.
allele(int, int) - Method in interface vcf.AL
Returns the allele on the specified haplotype if the allele emission probabilities are determined by a called allele, and returns -1 otherwise.
allele(int, int) - Method in class vcf.BasicGL
 
allele(int) - Method in class vcf.BasicMarker
 
allele(int) - Method in class vcf.BitSetGT
 
allele(int) - Method in class vcf.BitSetRefGT
 
allele(int) - Method in class vcf.ByteArrayRefGT
 
allele(int, int) - Method in class vcf.FuzzyGL
 
allele(int, int) - Method in interface vcf.GL
Returns the allele on the specified haplotype for the specified marker if the observed data include a non-missing allele, and returns -1 otherwise.
allele(int) - Method in interface vcf.HapsMarker
Returns the allele on the specified haplotype.
allele(int, int) - Method in class vcf.HbdAL
 
allele(int) - Method in class vcf.LowMafRefDiallelicGT
 
allele(int) - Method in class vcf.LowMafRefGT
 
allele(int) - Method in interface vcf.Marker
Returns the specified allele.
allele(int, int) - Method in class vcf.MaskedEndsGL
 
allele(int, int) - Method in class vcf.NoPhaseGL
 
allele(int, int) - Method in class vcf.RefGL
 
allele(int, int) - Method in class vcf.RevGL
 
allele(int) - Method in class vcf.SeqCodedRefGT
 
allele(int, int) - Method in class vcf.SplicedGL
 
allele(int) - Method in interface vcf.VcfEmission
Returns the allele on the specified haplotype or -1 if the allele is missing.
allele(int) - Method in class vcf.VcfRecord
 
allele1(int, int) - Method in class haplotype.BasicHapPairs
 
allele1(int, int) - Method in class haplotype.BasicSampleHapPairs
 
allele1(int) - Method in class haplotype.BitHapPair
 
allele1(int, int) - Method in class haplotype.GLSampleHapPairs
 
allele1(int) - Method in interface haplotype.HapPair
Returns the first allele for the specified marker.
allele1(int, int) - Method in interface haplotype.HapPairs
Returns the first allele for the specified marker and haplotype pair.
allele1(int, int) - Method in class haplotype.RefHapPairs
 
allele1(int) - Method in class haplotype.RevHapPair
 
allele1(int, int) - Method in class haplotype.RevHapPairs
 
allele1(int, int) - Method in class haplotype.RevSampleHapPairs
 
allele1(int) - Method in class haplotype.WrappedHapPair
 
allele1(int, int) - Method in interface main.AlleleProbs
Returns the marker allele with maximum probability for the first haplotype of the specified sample.
allele1(int, int) - Method in class main.BasicAlleleProbs
 
allele1(int, int) - Method in class main.ConstrainedAlleleProbs
 
allele1(int, int) - Method in class main.SampleHapPairAlleleProbs
 
allele1(int, int) - Method in class vcf.BasicGL
 
allele1(int) - Method in class vcf.BitSetGT
 
allele1(int) - Method in class vcf.BitSetRefGT
 
allele1(int) - Method in class vcf.ByteArrayRefGT
 
allele1(int, int) - Method in class vcf.FuzzyGL
 
allele1(int, int) - Method in interface vcf.GL
Returns the first allele for the specified marker and sample if the observed data include a non-missing allele, and returns -1 otherwise.
allele1(int) - Method in interface vcf.HapsMarker
Returns the first allele for the specified haplotype pair.
allele1(int) - Method in class vcf.LowMafRefDiallelicGT
 
allele1(int) - Method in class vcf.LowMafRefGT
 
allele1(int, int) - Method in class vcf.MaskedEndsGL
 
allele1(int, int) - Method in class vcf.NoPhaseGL
 
allele1(int, int) - Method in class vcf.RefGL
 
allele1(int, int) - Method in class vcf.RevGL
 
allele1(int) - Method in class vcf.SeqCodedRefGT
 
allele1(int, int) - Method in class vcf.SplicedGL
 
allele1(int) - Method in interface vcf.VcfEmission
Returns the first allele for the specified sample or -1 if the allele is missing.
allele1() - Method in class vcf.VcfRecGTParser
Returns the first allele of the genotype for the current sample.
allele1(int) - Method in class vcf.VcfRecord
 
allele2(int, int) - Method in class haplotype.BasicHapPairs
 
allele2(int, int) - Method in class haplotype.BasicSampleHapPairs
 
allele2(int) - Method in class haplotype.BitHapPair
 
allele2(int, int) - Method in class haplotype.GLSampleHapPairs
 
allele2(int) - Method in interface haplotype.HapPair
Returns the second allele for the specified marker.
allele2(int, int) - Method in interface haplotype.HapPairs
Returns the second allele for the specified marker and haplotype pair.
allele2(int, int) - Method in class haplotype.RefHapPairs
 
allele2(int) - Method in class haplotype.RevHapPair
 
allele2(int, int) - Method in class haplotype.RevHapPairs
 
allele2(int, int) - Method in class haplotype.RevSampleHapPairs
 
allele2(int) - Method in class haplotype.WrappedHapPair
 
allele2(int, int) - Method in interface main.AlleleProbs
Returns the marker allele with maximum probability for the second haplotype of the specified sample.
allele2(int, int) - Method in class main.BasicAlleleProbs
 
allele2(int, int) - Method in class main.ConstrainedAlleleProbs
 
allele2(int, int) - Method in class main.SampleHapPairAlleleProbs
 
allele2(int, int) - Method in class vcf.BasicGL
 
allele2(int) - Method in class vcf.BitSetGT
 
allele2(int) - Method in class vcf.BitSetRefGT
 
allele2(int) - Method in class vcf.ByteArrayRefGT
 
allele2(int, int) - Method in class vcf.FuzzyGL
 
allele2(int, int) - Method in interface vcf.GL
Returns the second allele for the specified marker and sample if the observed data include a non-missing allele, and returns -1 otherwise.
allele2(int) - Method in interface vcf.HapsMarker
Returns the second allele for the specified haplotype pair.
allele2(int) - Method in class vcf.LowMafRefDiallelicGT
 
allele2(int) - Method in class vcf.LowMafRefGT
 
allele2(int, int) - Method in class vcf.MaskedEndsGL
 
allele2(int, int) - Method in class vcf.NoPhaseGL
 
allele2(int, int) - Method in class vcf.RefGL
 
allele2(int, int) - Method in class vcf.RevGL
 
allele2(int) - Method in class vcf.SeqCodedRefGT
 
allele2(int, int) - Method in class vcf.SplicedGL
 
allele2(int) - Method in interface vcf.VcfEmission
Returns the second allele for the specified sample or -1 if the allele is missing.
allele2() - Method in class vcf.VcfRecGTParser
Returns the second allele of the genotype for the current sample.
allele2(int) - Method in class vcf.VcfRecord
 
alleleCount(int, int) - Method in class haplotype.BasicSampleHapPairs
 
alleleCount(int, int) - Method in class haplotype.GLSampleHapPairs
 
alleleCount(int, int) - Method in class haplotype.RefHapPairs
 
alleleCount(int, int) - Method in class haplotype.RevSampleHapPairs
 
alleleCount(int, int) - Method in interface haplotype.SampleHapPairs
Returns the number of haplotypes that carry the specified allele.
alleleCount(int) - Method in class vcf.BitSetGT
 
alleleCount(int) - Method in class vcf.BitSetRefGT
 
alleleCount(int) - Method in class vcf.ByteArrayRefGT
 
alleleCount(int) - Method in class vcf.LowMafRefDiallelicGT
 
alleleCount(int) - Method in class vcf.LowMafRefGT
 
alleleCount(int) - Method in class vcf.SeqCodedRefGT
 
alleleCount(int) - Method in interface vcf.VcfEmission
Returns the number of haplotypes that carry the specified allele.
alleleCount(int) - Method in class vcf.VcfRecord
 
alleleFreq() - Method in class vcf.GprobsStatistics
Returns an array of length this.marker().nAlleles() whose j-th element is the estimated sample frequency of allele j.
AlleleProbs - Interface in main
Interface AlleleProbs represents per-haplotype allele probabilities for a list of samples.
alleles() - Method in class vcf.BasicMarker
 
alleles() - Method in interface vcf.Marker
Returns the alleles.
alleleString(int, int) - Static method in class vcf.Bref
Returns an array that is obtained by taking the first length elements of the specified permutation of "A", "C", "G", and "T".
alleleWithMaxProb(int) - Method in interface main.HapAlleleProbs
Returns the allele with maximum posterior probability.
alleleWithMaxProb(int) - Method in class main.LowMemHapAlleleProbs
 
allelicR2() - Method in class vcf.GprobsStatistics
Returns the estimated squared correlation between the most probable ALT allele dose and the true ALT allele dose.
allelicR2() - Method in class vcf.R2Estimator
Returns the estimated squared correlation between the most probable ALT allele dose and the true ALT allele dose for the current genotype data.
allSamples() - Method in class main.CurrentData
Returns a list of all target and reference samples.
allSamples() - Method in class vcf.AllData
 
allSamples() - Method in interface vcf.Data
Returns a list of all target and reference samples.
allSamples() - Method in class vcf.TargetData
 
alProb1(int, int, int) - Method in interface main.AlleleProbs
Returns the probability that the specified marker allele is present on the first haplotype of the specified sample.
alProb1(int, int, int) - Method in class main.BasicAlleleProbs
 
alProb1(int, int, int) - Method in class main.ConstrainedAlleleProbs
 
alProb1(int, int, int) - Method in class main.SampleHapPairAlleleProbs
 
alProb2(int, int, int) - Method in interface main.AlleleProbs
Returns the probability that the specified marker allele is present on the second haplotype of the specified sample.
alProb2(int, int, int) - Method in class main.BasicAlleleProbs
 
alProb2(int, int, int) - Method in class main.ConstrainedAlleleProbs
 
alProb2(int, int, int) - Method in class main.SampleHapPairAlleleProbs
 
alProbs(int) - Method in class sample.HapBaumLevel
Returns the specified posterior allele probability.
appendRecords(GenotypeValues, int, int, PrintWriter) - Static method in class vcf.VcfWriter
Writes the specified genotype data as VCF records to the specified PrintWriter.
appendRecords(AlleleProbs, boolean[], int, int, boolean, boolean, PrintWriter) - Static method in class vcf.VcfWriter
Writes the data in alProbs for markers with index between start (inclusive) and end (exclusive) to the specified PrintWriter.
args() - Method in class main.Par
Returns the Beagle command line arguments.
argsToMap(String[], char) - Static method in class blbutil.Validate
Returns a map with one (key, value) pair for each element of the specified array.
asString() - Method in interface blbutil.IntArray
Returns a string representation of this IntArray by applying java.utils.Arrays.toString() to an equivalent int[] object.

B

backwardValue(int) - Method in class sample.DuoBaumLevel
Returns the normalized backward value for the specified HMM state with nonzero forward probability.
backwardValue(int) - Method in class sample.HapBaumLevel
Returns the normalized backward value for the specified HMM state with nonzero forward probability.
backwardValue(int) - Method in class sample.RecombSingleBaumLevel
Returns the normalized backward value for the specified HMM state with nonzero forward probability.
backwardValue(int) - Method in class sample.SingleBaumLevel
Returns the normalized backward value for the specified HMM state with nonzero forward probability.
backwardValuesSum() - Method in class sample.DuoBaumLevel
Returns the sum of the backward values at this level of the HMM when the backward values are computed using backward values from the next level that are normalized to sum to 1.
backwardValuesSum() - Method in class sample.HapBaumLevel
Returns the sum of the backward values at this level of the HMM when the backward values are computed using backward values from the next level that are normalized to sum to 1.
backwardValuesSum() - Method in class sample.RecombSingleBaumLevel
Returns the sum of the backward values at this level of the HMM when the backward values are computed using backward values from the next level that are normalized to sum to 1.
backwardValuesSum() - Method in class sample.SingleBaumLevel
Returns the sum of the backward values at this level of the HMM when the backward values are computed using backward values from the next level that are normalized to sum to 1.
basePos(int, double) - Method in interface main.GeneticMap
Returns the base position corresponding to the specified genetic map position.
basePos(int, double) - Method in class main.PlinkGeneticMap
 
basePos(int, double) - Method in class main.PositionMap
 
BasicAlleleProbs - Class in main
Class BasicAlleleProbs stores per-haplotype allele probabilities for a list of samples.
BasicAlleleProbs(HapAlleleProbs[]) - Constructor for class main.BasicAlleleProbs
Construct a new BasicAlleleProbs instance from the specified data.
BasicGenotypeValues - Class in main
Class BasicGenotypeValues stores values for each possible genotype for each sample at each marker.
BasicGenotypeValues(Markers, Samples) - Constructor for class main.BasicGenotypeValues
Constructs a new BasicGenotypeValues instance with initial value 0 for each possible genotype for each sample at each marker.
BasicGL - Class in vcf
Class BasicGL represents genotype emission probabilities for a set of samples.
BasicGL(Samples, VcfEmission[]) - Constructor for class vcf.BasicGL
Constructs a BasicGL instance.
BasicHapPairs - Class in haplotype
Class BasicHapPairs represents a list of haplotype pairs.
BasicHapPairs(List<HapPair>) - Constructor for class haplotype.BasicHapPairs
Constructs a new BasicHapPairs instance corresponding to the specified list of haplotype pairs.
BasicIntInterval - Class in beagleutil
Class BasicIntInterval represents an interval of consecutive integers.
BasicIntInterval(int, int) - Constructor for class beagleutil.BasicIntInterval
Constructs an SimpleIntInterval instance.
BasicMarker - Class in vcf
Class BasicMarker represents a genetic marker.
BasicMarker(int, int, String[], String[]) - Constructor for class vcf.BasicMarker
Constructs a new BasicMarker instance from the specified data.
BasicMarker(int, int, String[], String[], int) - Constructor for class vcf.BasicMarker
Constructs a new BasicMarker instance from the specified data.
BasicMarker(String) - Constructor for class vcf.BasicMarker
Constructs a new BasicMarker instance from the specified string VCF record.
BasicSampleHapPairs - Class in haplotype
Class BasicSampleHapPairs stores a list of samples and a haplotype pair for each sample.
BasicSampleHapPairs(Samples, List<HapPair>) - Constructor for class haplotype.BasicSampleHapPairs
Constructs a new BasicSampleHapPairs instance.
beagleutil - package beagleutil
 
BGZIPOutputStream - Class in blbutil
Class BGZIPOutputStream is an output stream filter that performs BGZIP compression.
BGZIPOutputStream(OutputStream, boolean) - Constructor for class blbutil.BGZIPOutputStream
Creates a new BGZIPOutputStream instance that writes to the specified output stream.
bgzipPrintWriter(File) - Static method in class blbutil.FileUtil
Returns a buffered java.io.PrintWriter that compresses data using the BGZIP algorithm and writes the compressed data to the specified file.
bgzipPrintWriter(File, boolean) - Static method in class blbutil.FileUtil
Returns a buffered java.io.PrintWriter that compresses data using the BGZIP algorithm and writes the compressed data to the specified file.
BitHapPair - Class in haplotype
Class BitHapPair represents a pair of haplotypes for a sample.
BitHapPair(Markers, Samples, int, int[], int[]) - Constructor for class haplotype.BitHapPair
Constructs a new BitHapPair instance.
BitSetGT - Class in vcf
Class BitSetGT represents genotype emission probabilities for a list of samples at a single marker.
BitSetGT(VcfHeader, String) - Constructor for class vcf.BitSetGT
Constructs a new BitSetGT instance representing the specified VCF record's GT format field data.
BitSetRefGT - Class in vcf
Class BitSetRefGT represents genotype emission probabilities for a list reference samples with phased, non-missing genotypes at a single marker.
BitSetRefGT(VcfHeader, String) - Constructor for class vcf.BitSetRefGT
Creates a new BitSetRefGT instance from a VCF record storing phased, non-missing reference genotypes.
BitSetRefGT(VcfRecGTParser) - Constructor for class vcf.BitSetRefGT
Creates a new VcfEmission instance from a VCF record containing phased, non-missing genotypes for a list of reference samples.
blbutil - package blbutil
 
blockedAppendRecords(AlleleProbs, boolean[], int, int, boolean, boolean, PrintWriter) - Static method in class vcf.VcfWriter
Writes the data in alProbs for markers with index between start (inclusive) and end (exclusive) to the specified PrintWriter.
booleanArg(String, Map<String, String>, boolean, boolean) - Static method in class blbutil.Validate
Removes the specified key from the specified map, and returns the boolean value corresponding to the specified key.
Bref - Class in vcf
Class Bref has methods for reading and writing phased, non-missing genotypes that are stored in a "bref" binary VCF file.
BrefIt - Class in vcf
Class BrefIt represents an iterator whose next() method returns an object storing data from a VCF record with phased, non-missing genotypes.
BrefIt(File) - Constructor for class vcf.BrefIt
Constructs a new BrefIt instance.
BrefIt(File, Filter<Marker>) - Constructor for class vcf.BrefIt
Constructs a new BrefIt instance.
buildNanos(long) - Method in class main.RunStats
Increases the cumulative time to build the DAG models by the specified number of nanoseconds.
burnin_its() - Method in class main.Par
Returns the burnin-its parameter.
ByteArrayRefGT - Class in vcf
Class ByteArrayRefGT represents phased, non-missing genotypes for a list of reference samples at a single marker.
ByteArrayRefGT(VcfHeader, String) - Constructor for class vcf.ByteArrayRefGT
Creates a new ByteArrayRefGT instance from the specified VcfHeader and string VCF record.
ByteArrayRefGT(VcfRecGTParser) - Constructor for class vcf.ByteArrayRefGT
Creates a new VcfEmission instance from a VCF record containing phased, non-missing genotypes for a list of reference samples.
ByteIndexArray - Class in blbutil
Class ByteIndexArray represents an immutable int[] array that is stored as a byte[] array.
ByteIndexArray(int[]) - Constructor for class blbutil.ByteIndexArray
Constructs a new ByteIndexArray instance.
ByteIndexArray(int[], int, int) - Constructor for class blbutil.ByteIndexArray
Constructs a new ByteIndexArray instance from the specified subarray.

C

canAdvanceWindow() - Method in class vcf.AllData
 
canAdvanceWindow() - Method in interface vcf.Data
Returns true if the sliding window of VCF records can advance and returns false otherwise.
canAdvanceWindow() - Method in class vcf.TargetData
 
canAdvanceWindow() - Method in class vcf.VcfWindow
Returns true if the sliding window of VCF records can advance and returns false otherwise.
capacity() - Method in class blbutil.IntSet
Returns the capacity of this set.
capacity() - Method in class sample.RecombSingleBaumLevel
Returns the current capacity of this level.
capacity() - Method in class vcf.VcfEmissionCompressor
Returns the maximum number of allele sequences that is permitted to exist in the list of compressed VcfEmission objects.
CenteredIntIntervalTree<E extends IntInterval & java.lang.Comparable<E>> - Class in beagleutil
Class CenteredIntIntervalTree implements a centered interval tree that stores IntInterval objects.
CenteredIntIntervalTree(int, int) - Constructor for class beagleutil.CenteredIntIntervalTree
Creates a new CenteredIntIntervalTree instance for the specified range.
CharIndexArray - Class in blbutil
Class CharIndexArray represents an immutable int[] array that is stored as a char[] array.
CharIndexArray(int[]) - Constructor for class blbutil.CharIndexArray
Constructs a new CharIndexArray instance.
CharIndexArray(int[], int, int) - Constructor for class blbutil.CharIndexArray
Constructs a new CharIndexArray instance from the specified subarray.
childNode(int, int) - Method in interface dag.Dag
Returns the index of the specified child node in the DAG.
childNode(int) - Method in interface dag.DagLevel
Returns the index of the child node of the specified edge at this level of the DAG.
childNode(int) - Method in class dag.HighCapacityDagLevel
 
childNode(int, int) - Method in class dag.ImmutableDag
 
childNode(int, int) - Method in class dag.LinkageEquilibriumDag
 
childNode(int) - Method in class dag.LowCapacityDagLevel
 
childNode(int) - Method in class dag.MergeableDagLevel
Returns the child node of the specified edge or -1 if the edge does not exist
childNode(int) - Method in class sample.HapBaumLevel
Returns the child node of the specified HMM state with nonzero forward probability.
childNode1(int) - Method in class sample.RecombSingleBaumLevel
Returns the child node of the first edge of the specified HMM state with nonzero forward probability.
childNode1(int) - Method in class sample.SingleBaumLevel
Returns the child node of the first edge of the specified HMM state with nonzero forward probability.
childNode2(int) - Method in class sample.RecombSingleBaumLevel
Returns the child node of the second edge of the specified HMM state with nonzero forward probability.
childNode2(int) - Method in class sample.SingleBaumLevel
Returns the child node of the second edge of the specified HMM state with nonzero forward probability.
childNodeA2(int) - Method in class sample.DuoBaumLevel
Returns the child node of the second edge of the specified HMM state with nonzero forward probability.
childNodeAB1(int) - Method in class sample.DuoBaumLevel
Returns the child node of the first edge of the specified HMM state with nonzero forward probability.
childNodeB2(int) - Method in class sample.DuoBaumLevel
Returns the child node of the third edge of the specified HMM state with nonzero forward probability.
chrom() - Method in class beagleutil.ChromInterval
Returns the chromosome identifier.
chrom() - Method in class main.Par
Returns the chrom parameter or null if no chrom parameter was specified.
chrom() - Method in class vcf.BasicMarker
 
chrom() - Method in interface vcf.Marker
Returns the chromosome.
ChromIds - Class in beagleutil
Class ChromIds is a singleton class that represents a list of chromosome identifiers.
chromIndex() - Method in class beagleutil.ChromInterval
Returns the chromosome index.
chromIndex() - Method in class vcf.BasicMarker
 
chromIndex() - Method in interface vcf.Marker
Returns the chromosome index.
ChromInterval - Class in beagleutil
Class ChromInterval represents a chromosome interval whose end points are genome coordinates.
ChromInterval(Marker, Marker) - Constructor for class beagleutil.ChromInterval
Constructs a new ChromInterval instance.
ChromInterval(String, int, int) - Constructor for class beagleutil.ChromInterval
Constructs a new ChromInterval instance.
clear() - Method in class beagleutil.CenteredIntIntervalTree
 
clear() - Method in interface beagleutil.IntIntervalTree
Removes all of the elements from this interval tree.
clear() - Method in class blbutil.IndexMap
Removes all key-value pairs from the map.
clear() - Method in class blbutil.IndexSet
Removes all elements from the set.
clear() - Method in class blbutil.IntList
Removes all elements from this list.
clear() - Method in class blbutil.IntSet
Removes all elements from this set.
clear() - Method in class sample.DuoNodes
Sets the value of each node trio to 0.
clear() - Method in class sample.HapNodes
Sets the value of each node to 0.
clear() - Method in class sample.RecombSingleNodes
Sets the value of each ordered node pair to 0.
clear() - Method in class sample.SingleNodes
Sets the value of each ordered node pair to 0.
clear() - Method in class vcf.R2Estimator
Clears all genotype data and sets the number of genotype with allele dose data to 0.
clear() - Method in class vcf.VcfEmissionCompressor
Clears the list of compressed VcfEmission objects.
close() - Method in class blbutil.BGZIPOutputStream
 
close() - Method in interface blbutil.FileIt
Terminates the iteration and releases any system resources that are held by this object.
close() - Method in class blbutil.InputIt
 
close() - Method in class haplotype.HapsMarkerIterator
 
close() - Method in class main.WindowWriter
 
close() - Method in class vcf.AllData
 
close() - Method in class vcf.BrefIt
 
close() - Method in interface vcf.Data
Releases any I/O resources controlled by this object.
close() - Method in class vcf.IntervalVcfIt
 
close() - Method in class vcf.RefIt
 
close() - Method in class vcf.RestrictedVcfWindow
Releases any I/O resources controlled by this object.
close() - Method in class vcf.TargetData
 
close() - Method in class vcf.VcfIt
 
close() - Method in class vcf.VcfWindow
Releases any I/O resources controlled by this object.
closestIndex(int, int) - Method in class main.PlinkGeneticMap
Returns the index of the genetic map position that is closest to the specified base position.
cluster() - Method in class main.Par
Returns the cluster parameter.
colon - Static variable in class blbutil.Const
The colon character: ':'
comma - Static variable in class blbutil.Const
The comma character: ','
command - Static variable in class main.Main
 
compareTo(BasicIntInterval) - Method in class beagleutil.BasicIntInterval
Compares the specified BasicIntInterval with this for order, and returns a negative integer, zero, or a positive integer as this is less than, equal to, or greater than the specified BasicIntInterval object.
compareTo(ChromInterval) - Method in class beagleutil.ChromInterval
Compares this ChromInteval with the specified ChromInterval instance for order, and returns -1, 0, or 1 depending on whether this is less than, equal or greater than the specified instance.
compareTo(IntPair) - Method in class blbutil.IntPair
Returns -1, 0, or 1 depending on whether this is less than, equal, or greater than the specified IntPair object.
compareTo(Score) - Method in class dag.Score
Returns -1, 0, or 1 depending on whether this Score is less than, equal to, or greater than the specified Score.
compareTo(HapSegment) - Method in class ibd.HapSegment
Compares this object with the specified object for order.
compareTo(Marker) - Method in class vcf.BasicMarker
 
compareTo(Marker) - Method in interface vcf.Marker
Compares this marker with the specified marker for order, and returns a negative integer, 0, or a positive integer depending on whether this marker is less than, equal to, or greater than the specified marker.
condEdgeProb(int, int) - Method in interface dag.Dag
Returns the ratio of the sum of the weights of the sequences that pass through the specified edge of the DAG and the sum of the weights of the sequences that pass through the parent node of the specified edge of the DAG.
condEdgeProb(int) - Method in interface dag.DagLevel
Returns the conditional edge probability, which is defined to be the ratio of the sum of the weights of the sequences that pass through the specified edge at this level of the DAG and the sum of the weights of the sequences that pass through the parent node of the specified edge.
condEdgeProb(int) - Method in class dag.HighCapacityDagLevel
 
condEdgeProb(int, int) - Method in class dag.ImmutableDag
 
condEdgeProb(int, int) - Method in class dag.LinkageEquilibriumDag
 
condEdgeProb(int) - Method in class dag.LowCapacityDagLevel
 
confirmEmptyMap(Map<String, String>) - Static method in class blbutil.Validate
Checks whether the specified map of key-value pairs is empty.
ConsensusPhaser - Class in haplotype
Class ConsensusPhaser contains a static method for calculating a consensus phasing from multiple estimated haplotype pairs for an individual.
Const - Class in blbutil
Class Const provides public static final fields with string and character constants.
ConstrainedAlleleProbs - Class in main
Class ConstrainedAlleleProbs is a wrapper for an AlleleProbs instance that changes the wrapped haplotype allele probabilities for a subset of markers.
ConstrainedAlleleProbs(SampleHapPairs, AlleleProbs, int[]) - Constructor for class main.ConstrainedAlleleProbs
Construct a new ConstrainedAlleleProbs instance.
ConsumeSingleSamples - Class in sample
Class ConsumeSingleSamples samples haplotype pairs conditional on the observed genotype data and a haplotype frequency model.
ConsumeSingleSamples(boolean, SingleBaumInterface, BlockingQueue<Integer>, List<HapPair>) - Constructor for class sample.ConsumeSingleSamples
Constructs a new ConsumeSingleSample instance.
ConsumeSingleSamples(boolean, SingleBaumInterface, BlockingQueue<Integer>, List<HapPair>, GenotypeValues) - Constructor for class sample.ConsumeSingleSamples
Constructs a new ConsumeSingleSample instance.
contains(E) - Method in class beagleutil.CenteredIntIntervalTree
 
contains(E) - Method in interface beagleutil.IntIntervalTree
Returns true if the interval tree contains the specified element, and returns false otherwise.
contains(int) - Method in class blbutil.IndexSet
Returns true if the set contains the specified element, and returns false otherwise.
contains(int) - Method in class blbutil.IntSet
Returns true if the set contains the specified element, and returns false otherwise.
contains(Marker) - Method in class vcf.Markers
Returns true if the specified marker is not null and is an element in the list of markers represented by this, and returns false otherwise.
copyright - Static variable in class main.Main
The copyright string.
countFields(String, char) - Static method in class blbutil.StringUtil
Returns the number of delimited fields in the specified string.
countFields(String, char, int) - Static method in class blbutil.StringUtil
Returns Math.min(countFields(s, delimiter), max).
countFields(String) - Static method in class blbutil.StringUtil
Returns the number of white-space delimited fields in the specified string.
create(int[], int, int) - Static method in interface blbutil.IntArray
Returns a new IntArray instance that has the same sequence of nonnegative integers as the specified array.
create(Marker[]) - Static method in class vcf.Markers
Construct and return a new Markers instance that represents the specified list of markers.
create(FileIt<String>) - Static method in class vcf.RefIt
Create and returns a new RefIt instance from the specified iterator.
create(FileIt<String>, Filter<String>, Filter<Marker>, int) - Static method in class vcf.RefIt
Create and returns a new RefIt instance from the specified objects.
create(FileIt<String>, BiFunction<VcfHeader, String, R>) - Static method in class vcf.VcfIt
Create and returns a new VcfIt instance from the specified objects.
create(FileIt<String>, Filter<String>, BiFunction<VcfHeader, String, R>) - Static method in class vcf.VcfIt
Create and returns a new VcfIt instance from the specified objects.
create(FileIt<String>, Filter<String>, Filter<Marker>, BiFunction<VcfHeader, String, R>) - Static method in class vcf.VcfIt
Create and returns a new VcfIt instance from the specified objects.
create(FileIt<String>, Filter<String>, Filter<Marker>, BiFunction<VcfHeader, String, R>, int) - Static method in class vcf.VcfIt
Create and returns a new VcfIt instance from the specified objects.
cumMarkerCnt() - Method in class vcf.RestrictedVcfWindow
Returns the number of VCF records in the union of the current window and all previous windows.
cumMarkerCnt() - Method in class vcf.VcfWindow
Returns the number of distinct VCF records in the union of the current window and all previous windows.
CurrentData - Class in main
Class CurrentData represents input data for the current marker window.
CurrentData(Par, GeneticMap, Data, SampleHapPairs, NuclearFamilies) - Constructor for class main.CurrentData
Constructs a new CurrentData instance from the specified data.
currentSample() - Method in class vcf.VcfRecGTParser
Returns the index of the current sample, or -1 if this.nextSample() has not yet been invoked.

D

dag - package dag
 
Dag - Interface in dag
Interface Dag represents a leveled directed acyclic graph (DAG).
dag(HapPairs, float[], float, int) - Static method in class dag.MergeableDag
Constructs and returns a new Dag instance from the specified data.
dag() - Method in class dag.MergeableDag
Returns the constructed DAG.
dag() - Method in class ibd.IbdBaum
Returns the directed acyclic graph that determines the transition probabilities.
dag() - Method in class main.Par
Returns the dag parameter or null if no ref parameter was specified.
dag() - Method in class sample.DuoBaumLevel
Returns the directed acyclic graph that determines the transition probabilities.
dag() - Method in class sample.HapBaumLevel
Returns the directed acyclic graph that determines the transition probabilities.
dag() - Method in class sample.RecombSingleBaum
 
dag() - Method in class sample.RecombSingleBaumLevel
Returns the directed acyclic graph that determines the transition probabilities.
dag() - Method in class sample.RestrictedDag
Returns the DAG.
dag() - Method in class sample.SingleBaum
 
dag() - Method in interface sample.SingleBaumInterface
Returns the directed acyclic graph that determines the transition probabilities.
dag() - Method in class sample.SingleBaumLevel
Returns the directed acyclic graph that determines the transition probabilities.
DagLevel - Interface in dag
Interface DagLevel represents a level of a leveled directed acyclic graph (DAG).
dagStats(Dag) - Static method in class dag.DagUtil
Return a string description of the specified DAG object.
DagUtil - Class in dag
Class DagUtil contains static, thread-safe methods for removing elements of an array that have a specified value and for creating a string representation of a DAG.
Data - Interface in vcf
Interface Data represents a sliding window of target VCF records or a sliding window of reference and target VCF records.
decrementAndGet(int) - Method in class blbutil.IntList
Decrements by one the element at the specified position in this list.
DEFAULT_BUFFER_SIZE - Static variable in class blbutil.InputIt
The default buffer size, which is 4,194,304 bytes.
DEFAULT_BUFFER_SIZE - Static variable in class vcf.VcfIt
The default number of VCF records stored in a buffer, which is 1000.
DEFAULT_EM_BUFFER_SIZE - Static variable in class vcf.RefIt
The default number of VcfEmission objects that are stored in a buffer.
DEFAULT_INIT_CAPACITY - Static variable in class beagleutil.ThreadSafeIndexer
The default initial capacity, which is 500.
DEFAULT_INIT_CAPACITY - Static variable in class blbutil.IntList
The default initial capacity of an IntList, which is 10.
DEFAULT_INIT_SIZE - Static variable in class vcf.VcfRecBuilder
The default initial size for the string buffer, which is 50 characters.
DELIMITER - Static variable in class vcf.VcfMetaInfo
The VCF meta-information line key-value delimiter: '='
DiploidStates - Interface in sample
Class DiploidStates represents a list of iterators (one iterator for each marker) that iterate over a subset of diploid HMM states at a marker.
doseR2() - Method in class vcf.GprobsStatistics
Returns the estimated squared correlation between the estimated ALT allele dose and the true ALT allele dose.
doseR2() - Method in class vcf.R2Estimator
Returns the estimated squared correlation between the expected ALT allele dose and the true ALT allele dose for the current genotype data.
doubleArg(String, Map<String, String>, boolean, double, double, double) - Static method in class blbutil.Validate
Removes the specified key from the specified map, and returns the double value corresponding to the specified key.
DuoBaumLevel - Class in sample
Class DuoBaumLevel computes forward and backward Baum values at a level of a hidden Markov model (HMM) whose states are ordered edge trios of a leveled directed acyclic graph (DAG).
DuoBaumLevel(Dag, GL) - Constructor for class sample.DuoBaumLevel
Constructs a new DuoBaumLevel instance from the specified data.
DuoNodes - Class in sample
Class DuoNodes stores ordered node trios and associated values.
DuoNodes() - Constructor for class sample.DuoNodes
Creates a new instance of DuoNodes that has an initial value of 0 for each ordered node trio.
duoOffspring(int) - Method in class main.NuclearFamilies
Returns the sample index of the offspring of the specified parent-offspring duo.
duoParent(int) - Method in class main.NuclearFamilies
Returns the sample index of the parent of the specified parent-offspring duo.
duoPrint(PrintWriter, CharSequence) - Static method in class blbutil.Utilities
Prints the specified string to the specified PrintWriter and to standard out.
duoPrintln(PrintWriter, CharSequence) - Static method in class blbutil.Utilities
Prints the specified string to the specified PrintWriter and to standard out.

E

edge(int) - Method in class sample.HapBaumLevel
Returns the edge of the specified HMM state with nonzero forward probability.
edge1() - Method in interface sample.DiploidStates
Returns the first edge of the edge pair that is the current element in the iterations, or returns -1 if this.next() has not been invoked since the most recent invocation of this.setMarker().
edge1(int) - Method in class sample.RecombSingleBaumLevel
Returns the first edge of the specified HMM state with nonzero forward probability.
edge1(int) - Method in class sample.SingleBaumLevel
Returns the first edge of the specified HMM state with nonzero forward probability.
edge2() - Method in interface sample.DiploidStates
Returns the second edge of the edge pair that is the current element in the iteration, or returns -1 if this.next() has not been invoked since the most recent invocation of this.setMarker().
edge2(int) - Method in class sample.RecombSingleBaumLevel
Returns the second edge of the specified HMM state with nonzero forward probability.
edge2(int) - Method in class sample.SingleBaumLevel
Returns the second edge of the specified HMM state with nonzero forward probability.
edgeA2(int) - Method in class sample.DuoBaumLevel
Returns the second edge of the specified HMM state with nonzero forward probability.
edgeAB1(int) - Method in class sample.DuoBaumLevel
Returns the first edge of the specified HMM state with nonzero forward probability.
edgeB2(int) - Method in class sample.DuoBaumLevel
Returns the third edge of the specified HMM state with nonzero forward probability.
edgeCount(int) - Method in class dag.MergeableDagLevel
Returns the sum of weights for the sequences that pass through the specified edge or 0 if the edge does not exist.
edgeProb(int, int) - Method in interface dag.Dag
Returns the ratio of the sum of the weights of the sequences that pass through the specified edge of the DAG and the sum of the weights of all sequences.
edgeProb(int) - Method in interface dag.DagLevel
Returns the edge probability, which is defined to be the ratio of the sum of the weights of the sequences that pass through the specified edge at this level of the DAG and the sum of the weights of the sequences that pass through any edge at this level of the DAG.
edgeProb(int) - Method in class dag.HighCapacityDagLevel
 
edgeProb(int, int) - Method in class dag.ImmutableDag
 
edgeProb(int, int) - Method in class dag.LinkageEquilibriumDag
 
edgeProb(int) - Method in class dag.LowCapacityDagLevel
 
edgeWeight(int, int) - Method in interface dag.Dag
Returns the sum of the weights of the sequences that pass through the specified edge of the DAG.
edgeWeight(int) - Method in interface dag.DagLevel
Returns the sum of weights for the sequences that pass through the specified edge at this level of the DAG.
edgeWeight(int) - Method in class dag.HighCapacityDagLevel
 
edgeWeight(int, int) - Method in class dag.ImmutableDag
 
edgeWeight(int, int) - Method in class dag.LinkageEquilibriumDag
 
edgeWeight(int) - Method in class dag.LowCapacityDagLevel
 
elapsedNanos(long) - Static method in class blbutil.Utilities
Returns a string representation of the specified elapsed time in the format "H hours M minutes S seconds".
elementWithIndex(int) - Method in class blbutil.IntSet
Returns the specified element.
emissions() - Method in class sample.HapBaumLevel
Returns the emission probabilities.
end() - Method in class beagleutil.BasicIntInterval
 
end() - Method in class beagleutil.CenteredIntIntervalTree
 
end() - Method in class beagleutil.ChromInterval
Returns the last genome coordinate in this chromosome interval.
end() - Method in interface beagleutil.IntInterval
Returns the end of the interval (inclusive).
end() - Method in interface beagleutil.IntIntervalTree
Returns the maximum end (inclusive) of an interval that can be stored in this interval tree.
end() - Method in class ibd.HapSegment
Returns the end marker index (inclusive).
end() - Method in class ibd.IbdSegment
Returns the ending marker (inclusive).
end() - Method in class sample.RefHapSeg
Returns the ending marker index (exclusive) of this segment.
end() - Method in class vcf.BasicMarker
 
end() - Method in interface vcf.Marker
Returns the INFO END field, or -1 if there is no INFO END field.
endIndex() - Method in class ibd.IbdSegment
Returns the ending marker index (inclusive) or -1 if the ending marker index is unknown.
enumeratedKey(int) - Method in class blbutil.IndexMap
Returns the specified key in an enumeration of the keys in the map.
enumeratedValue(int) - Method in class blbutil.IndexMap
Returns the value associated with the specified key in an enumeration of the keys in the map.
enumeratedValue(int) - Method in class blbutil.IndexSet
Returns the specified element in an enumeration of the elements in the set.
enumNode(int) - Method in class sample.HapNodes
Returns the specified node in a list of nodes with non-zero value.
enumNode1(int) - Method in class sample.RecombSingleNodes
Returns the first node of the specified node pair in the list of node pairs with non-zero value.
enumNode1(int) - Method in class sample.SingleNodes
Returns the first node of the specified node pair in the list of node pairs with non-zero value.
enumNode2(int) - Method in class sample.RecombSingleNodes
Returns the second node of the specified node pair in a list of node pairs with non-zero value.
enumNode2(int) - Method in class sample.SingleNodes
Returns the second node of the specified node pair in a list of node pairs with non-zero value.
enumNodeA2(int) - Method in class sample.DuoNodes
Returns the second node of the specified node trio in a list of node trios with non-zero value.
enumNodeAB1(int) - Method in class sample.DuoNodes
Returns the first node of the specified node trio in a list of node trios with non-zero value.
enumNodeB2(int) - Method in class sample.DuoNodes
Returns the third node of the specified node trio in a list of node trios with non-zero value.
enumValue(int) - Method in class sample.DuoNodes
Returns the value of the specified ordered node trio in a list of node trios with non-zero value.
enumValue(int) - Method in class sample.HapNodes
Returns the value of the specified node in a list of nodes with non-zero value.
enumValue(int) - Method in class sample.RecombSingleNodes
Returns the value of the specified node pair in a list of node pairs with non-zero value.
enumValue(int) - Method in class sample.SingleNodes
Returns the value of the specified node pair in a list of node pairs with non-zero value.
EOF - Static variable in class vcf.Bref
The end of file character for a bref file.
equals(Object) - Method in class beagleutil.BasicIntInterval
Returns true if the specified object is an BasicIntInterval instance and this.start() == ((BasicIntInterval) obj).start(), and this.end() == ((BasicIntInterval) obj).end(), and returns false otherwise.
equals(Object) - Method in class beagleutil.ChromInterval
Returns true if the specified object is a ChromInterval instance representing the same interval of genome coordinates as this, and returns false otherwise.
equals(Object) - Method in class beagleutil.Samples
Returns true if the specified object is a Samples object which represents the same ordered list of samples as this, and returns false otherwise.
equals(Object) - Method in class blbutil.IntPair
Compares the specified object with this IntPair for equality.
equals(Object) - Method in class dag.Score
Compares the specified object with this Score for equality.
equals(Object) - Method in class ibd.Haplotype
Compares the specified object with this Haplotype for equality.
equals(Object) - Method in class ibd.HapSegment
Compares the specified object with this HapSegment for equality.
equals(Object) - Method in class ibd.IbdSegment
Compares the specified object with this IbdSegment for equality.
equals(Object) - Method in class vcf.BasicMarker
 
equals(Object) - Method in interface vcf.Marker
Returns true if the specified object is a Marker with the same chromosome, position, allele lists, and INFO END field, and returns false otherwise.
equals(Object) - Method in class vcf.Markers
Returns true if the specified object is a Markers instance which represents the same list of markers as this, and returns false otherwise.
err() - Method in class main.Par
Returns the err parameter.
err() - Method in class sample.SamplerData
Returns the allele error rate
errProb(int) - Method in class sample.ImputationData
Returns the specified allele error probability.
errProb() - Method in interface vcf.AL
Returns the allelic error probability.
errProb() - Method in class vcf.HbdAL
 
excludeFilter(Collection<E>) - Static method in interface blbutil.Filter
Returns a filter that accepts all non-null objects that are not contained in the specified collection.
excludemarkers() - Method in class main.Par
Returns the excludemarkers parameter or null if no excludemarkers parameter was specified.
excludesamples() - Method in class main.Par
Returns the excludesamples parameter or null if no excludesamples parameter was specified.
exit(String, Throwable) - Static method in class blbutil.Utilities
Prints the specified exception, its stack trace, and the specified string to standard out and then terminates the Java virtual machine.
exit(String) - Static method in class blbutil.Utilities
Prints the specified string to standard out and then terminates the Java virtual machine.

F

families() - Method in class haplotype.Weights
Returns the parent-offspring relationships.
families() - Method in class main.CurrentData
Returns the parent-offspring relationships.
father(int) - Method in class main.NuclearFamilies
Returns the sample index of the father of the specified sample, or returns -1 if the father is unknown or is not present in the list of samples.
file() - Method in interface blbutil.FileIt
Returns the file from which the data are read, or null if the data are read from standard input or are computed data.
file() - Method in class blbutil.InputIt
 
file() - Method in class haplotype.HapsMarkerIterator
 
file() - Method in class vcf.BrefIt
 
file() - Method in class vcf.IntervalVcfIt
 
file() - Method in class vcf.RefIt
 
file() - Method in class vcf.RestrictedVcfWindow
Returns the file from which VCF records are read, or returns null if the source is standard input.
file() - Method in class vcf.VcfHeader
Returns the file from which data are read, or returns null if the source is standard input.
file() - Method in class vcf.VcfIt
 
file() - Method in class vcf.VcfWindow
Returns the file from which VCF records are read, or returns null if the source is standard input.
fileInputStream(File) - Static method in class blbutil.FileUtil
Returns an unbuffered java.io.FileInputStream reading from the specified file.
FileIt<E> - Interface in blbutil
An iterator for data elements in a file.
fileOutputStream(File) - Static method in class blbutil.FileUtil
Returns an unbuffered java.io.FileOutputStream.
fileOutputStream(File, boolean) - Static method in class blbutil.FileUtil
Returns an unbuffered java.io.FileOutputStream.
FileUtil - Class in blbutil
Class FileUtil contains static methods for working with files.
Filter<E> - Interface in blbutil
A filter for accepting or rejecting objects.
filter() - Method in class vcf.VcfRecord
Returns the FILTER field.
filteredFind(int) - Method in class ibd.IbsHapSegments
Returns a list of haplotype segments for other haplotypes that are IBS with the specified haplotype and that have length greater than or equal to this.minIbsLength().
FilterUtil - Class in vcf
Class FilterUtil contains static methods for constructing marker filters.
find(int) - Method in class ibd.IbsHapSegments
Returns the list of haplotype segments for other haplotypes that are IBS with the specified haplotype and have length greater than or equal to this.minIbsLength().
first() - Method in class blbutil.IntPair
Returns the first integer in the ordered pair of integers.
flipStrand(Marker) - Static method in class vcf.BasicMarker
Constructs and returns a new marker obtained from the specified marker by changing the marker's non-symbolic alleles to the alleles on the opposite chromosome strand.
floatArg(String, Map<String, String>, boolean, float, float, float) - Static method in class blbutil.Validate
Removes the specified key from the specified map, and returns the float value corresponding to the specified key.
flush() - Method in class blbutil.BGZIPOutputStream
 
format() - Method in class vcf.VcfRecord
Returns the FORMAT field.
formatData(String) - Method in class vcf.VcfRecord
Returns an array of length this.nSamples() containing the specified FORMAT subfield data for each sample.
formatIndex(String) - Method in class vcf.VcfRecord
Returns the index of the specified FORMAT subfield if the specified subfield is defined for this VCF record, and returns -1 otherwise.
formatSubfield(int) - Method in class vcf.VcfRecord
Returns the specified FORMAT subfield.
forwardValue(int) - Method in class sample.DuoBaumLevel
Returns the normalized forward value for the specified HMM state with nonzero forward probability.
forwardValue(int) - Method in class sample.HapBaumLevel
Returns the normalized forward value for the specified HMM state with nonzero forward probability.
forwardValue(int) - Method in class sample.RecombSingleBaumLevel
Returns the normalized forward value for the specified HMM state with nonzero forward probability.
forwardValue(int) - Method in class sample.SingleBaumLevel
Returns the normalized forward value for the specified HMM state with nonzero forward probability.
forwardValuesSum() - Method in class sample.DuoBaumLevel
Returns the sum of the forward values at this level of the HMM when the forward values are computed using forward values from the previous level that are normalized to sum to 1.
forwardValuesSum() - Method in class sample.HapBaumLevel
Returns the sum of the forward values at this level of the HMM when the forward values are computed using forward values from the previous level that are normalized to sum to 1.
forwardValuesSum() - Method in class sample.RecombSingleBaumLevel
Returns the sum of the forward values at this level of the HMM when the forward values are computed using forward values from the previous level that are normalized to sum to 1.
forwardValuesSum() - Method in class sample.SingleBaumLevel
Returns the sum of the forward values at this level of the HMM when the forward values are computed using forward values from the previous level that are normalized to sum to 1.
freqLod(int, int, int, HapPairs, Dag) - Static method in class ibd.IbdBaum
Returns the estimated frequency of the haplotype segment on the LOD (-Math.log10) scale.
fromGL(VcfHeader, String, float) - Static method in class vcf.VcfRecord
Constructs and returns a new VcfRecord instance from a VCF record and its GL or PL format subfield data.
fromGT(VcfHeader, String) - Static method in class vcf.VcfRecord
Constructs and returns a new VcfRecord instance from a VCF record and its GT format subfield data
fromGTGL(VcfHeader, String, float) - Static method in class vcf.VcfRecord
Constructs and returns a new VcfRecord instance from a VCF record and its GT, GL, and PL format subfield data.
fromGzipFile(File) - Static method in class blbutil.InputIt
Constructs and returns an InputIt instance with the default buffer size that iterates through lines of the specified compressed or uncompressed text file.
fromGzipFile(File, int) - Static method in class blbutil.InputIt
Constructs and returns an InputIt instance with the specified buffer size that iterates through lines of the specified compressed or uncompressed text file.
fromIds(String[]) - Static method in class beagleutil.Samples
Constructs and returns a Samples instance corresponding to the specified list of sample identifiers.
fromPlinkMapFile(File) - Static method in class main.PlinkGeneticMap
Constructs and returns a new PlinkGeneticMap instance from the data in the specified file.
fromPlinkMapFile(File, String) - Static method in class main.PlinkGeneticMap
Constructs and returns a new PlinkGeneticMap instance from the data in the specified file.
fromStdIn() - Static method in class blbutil.InputIt
Constructs and returns an InputIt instance with the default buffer size that iterates through lines of text read from standard input.
fromStdIn(int) - Static method in class blbutil.InputIt
Constructs and returns an InputIt instance with the specified buffer size that iterates through lines of text read from standard input.
fromTextFile(File) - Static method in class blbutil.InputIt
Constructs and returns an InputIt instance with the default buffer size that iterates through lines of the specified text file.
fromTextFile(File, int) - Static method in class blbutil.InputIt
Constructs and returns an InputIt instance with the specified buffer size that iterates through lines of the specified text file.
FuzzyGL - Class in vcf
Class FuzzyGL is a wrapper for a GL instance that incorporates a fixed error rate for the observed (emitted) allele to differ from the true allele.
FuzzyGL(GL, float) - Constructor for class vcf.FuzzyGL
Constructs a FuzzyGL instance.

G

GeneticMap - Interface in main
Interface GeneticMap represents a genetic map for one or more chromosomes.
genotype(int, int) - Static method in class vcf.BasicGL
Returns the genotype index corresponding to the specified unordered alleles.
GenotypeCorrection - Class in haplotype
Class GenotypeCorrection removes any inconsistencies between haplotype pairs and genotypes that determine genotype likelihoods.
GenotypeValues - Interface in main
Interface GenotypeValues represents a value for each possible genotype for each sample at each marker.
genPos(Marker) - Method in interface main.GeneticMap
Returns the genetic map position of the specified marker.
genPos(int, int) - Method in interface main.GeneticMap
Returns the genetic map position of the specified genome coordinate.
genPos(Markers) - Method in interface main.GeneticMap
Returns the an array of length hapPairs.nMarkers() whose whose j-th element is the genetic map position of the j-th marker.
genPos(Marker) - Method in class main.PlinkGeneticMap
 
genPos(int, int) - Method in class main.PlinkGeneticMap
 
genPos(Marker) - Method in class main.PositionMap
 
genPos(int, int) - Method in class main.PositionMap
 
get(int) - Method in class blbutil.ByteIndexArray
 
get(int) - Method in class blbutil.CharIndexArray
 
get(int) - Method in class blbutil.IndexMap
Returns the value associated with the specified key, or this.nil() if the specified key is not contained in the map.
get(int) - Method in interface blbutil.IntArray
Returns the specified array element.
get(int) - Method in class blbutil.IntList
Returns the element at the specified position in this list.
get(int) - Method in class blbutil.ShiftedByteIndexArray
 
get(int) - Method in class blbutil.WrappedIntArray
 
get(HapPairs) - Method in class haplotype.Weights
Returns an array of length haps.nHaps() with per-haplotype weights.
getAndDecrement(int) - Method in class blbutil.IntList
Decrements by one the element at the specified position in this list.
getAndIncrement(int) - Method in class blbutil.IntList
Increments by one the element at the specified position in this list.
getCompressedList() - Method in class vcf.VcfEmissionCompressor
Returns the list of compressed VcfEmission objects.
getFields(String, char) - Static method in class blbutil.StringUtil
Returns an array obtained by splitting the specified string around the specified delimiter.
getFields(String, char, int) - Static method in class blbutil.StringUtil
Returns an array obtained by splitting the specified string around the first (limit - 1) occurrences of the specified delimiter.
getFields(String) - Static method in class blbutil.StringUtil
Returns an array obtained by trimming white-space from the beginning and end of the specified string, and splitting the resulting string around white space.
getFields(String, int) - Static method in class blbutil.StringUtil
Returns an array obtained by trimming white-space from the beginning and end of the specified string, and splitting the resulting string around the first (limit-1) white-space delimiters.
getFile(String) - Static method in class blbutil.Validate
Returns a File object corresponding to the specified filename or null if filename == null
getIndex(String) - Method in class beagleutil.ChromIds
Returns the index of the specified chromosome identifier.
getIndex(String) - Method in class beagleutil.SampleIds
Returns the index of the specified sample identifier.
getIndex(T) - Method in class beagleutil.ThreadSafeIndexer
Returns the index of the specified object.
getIndexIfIndexed(String) - Method in class beagleutil.ChromIds
Returns the index of the specified chromosome identifier, or returns -1 if the specified chromosome identifier is not indexed.
getIndexIfIndexed(String) - Method in class beagleutil.SampleIds
Returns the index of the specified sampled identifier, or returns -1 if the specified sample identifier is not indexed.
getIndexIfIndexed(T) - Method in class beagleutil.ThreadSafeIndexer
Returns the index of the specified object, or returns -1 if the specified object is not indexed.
giga - Static variable in class blbutil.Const
The value 1,000,000,000
gl() - Method in class ibd.IbdBaum
Returns the HMM emission probabilities.
gl() - Method in class main.Par
Returns the gl parameter or null if no gl parameter was specified.
gl() - Method in class sample.DuoBaumLevel
Returns the emission probabilities.
gl() - Method in class sample.RecombSingleBaum
 
gl() - Method in class sample.RecombSingleBaumLevel
Returns the emission probabilities.
gl() - Method in class sample.SamplerData
Returns the genotype likelihoods for the target samples at the target data markers.
gl() - Method in class sample.SingleBaum
 
gl() - Method in interface sample.SingleBaumInterface
Returns the emission probabilities.
gl() - Method in class sample.SingleBaumLevel
Returns the emission probabilities.
gl(int, int, int, int) - Method in class vcf.BasicGL
 
gl(int, int, int) - Method in class vcf.BitSetGT
 
gl(int, int, int) - Method in class vcf.BitSetRefGT
 
gl(int, int, int) - Method in class vcf.ByteArrayRefGT
 
gl(int, int, int, int) - Method in class vcf.FuzzyGL
 
GL - Interface in vcf
Interface GL (Genotype Likelihoods) represents genotype likelihoods for a set of samples.
gl(int, int, int, int) - Method in interface vcf.GL
Returns the probability of the observed data for the specified marker and sample if the specified pair of ordered alleles is the true ordered genotype.
gl(int, int, int) - Method in class vcf.LowMafRefDiallelicGT
 
gl(int, int, int) - Method in class vcf.LowMafRefGT
 
gl(int, int, int, int) - Method in class vcf.MaskedEndsGL
 
gl(int, int, int, int) - Method in class vcf.NoPhaseGL
 
gl(int, int, int, int) - Method in class vcf.RefGL
 
gl(int, int, int, int) - Method in class vcf.RevGL
 
gl(int, int, int) - Method in class vcf.SeqCodedRefGT
 
gl(int, int, int, int) - Method in class vcf.SplicedGL
 
gl(int, int, int) - Method in interface vcf.VcfEmission
Returns the probability of the observed data if the specified pair of ordered alleles is the true genotype in the specified sample.
gl(int, int, int) - Method in class vcf.VcfRecord
 
GL_FORMAT - Static variable in class vcf.VcfRecord
The VCF FORMAT code for log-scaled genotype likelihood data: "GL".
GLSampleHapPairs - Class in haplotype
Class GLSampleHapPairs wraps a GL instance that stores phased, non-missing genotypes.
GLSampleHapPairs(GL) - Constructor for class haplotype.GLSampleHapPairs
Constructs a new GLSampleHapPairs instance from the specified data.
gprobs() - Method in class main.Par
Returns the gprobs parameter.
gprobs(int) - Method in class sample.RecombSingleBaumLevel
Returns the specified posterior genotype probability.
GprobsStatistics - Class in vcf
Class GprobsStatistics has methods for computing statistics from posterior genotype probabilities.
GprobsStatistics(GenotypeValues, int) - Constructor for class vcf.GprobsStatistics
Constructs a new GprobsStatistics instance from the specified scaled genotype probabilities.
GprobsStatistics(AlleleProbs, int) - Constructor for class vcf.GprobsStatistics
Constructs a new GprobsStatistics instance from the specified allele probabilities.
gt() - Method in class main.Par
Returns the gt parameter or null if no gt parameter was specified.
GT_FORMAT - Static variable in class vcf.BitSetGT
The VCF FORMAT code for genotype data: "GT".
gtgl() - Method in class main.Par
Returns the gtgl parameter or null if no gtgl parameter was specified.
gtIndex(int, int) - Static method in class vcf.VcfRecord
Returns the VCF genotype index for the specified pair of alleles.
gtProb(int, int, int, int) - Method in interface main.AlleleProbs
Returns the phased genotype probability, equal to (this.allele1(marker, sample, allele1) * this.allele2(marker, sample, allele2)).
gtProb(int, int, int, int) - Method in class main.BasicAlleleProbs
 
gtProb(int, int, int, int) - Method in class main.ConstrainedAlleleProbs
 
gtProb(int, int, int, int) - Method in class main.SampleHapPairAlleleProbs
 
gtProbs(int) - Method in class sample.SingleBaumLevel
Returns the specified posterior genotype probability.
gtProbsA(int) - Method in class sample.DuoBaumLevel
Returns the specified posterior genotype probability for the parent.
gtProbsB(int) - Method in class sample.DuoBaumLevel
Returns the specified posterior genotype probability for the offspring.
gzipPrintWriter(File) - Static method in class blbutil.FileUtil
Returns a buffered java.io.PrintWriter writing to the specified file.

H

hap() - Method in class ibd.HapSegment
Returns the first haplotype index.
hap1() - Method in class ibd.IbdSegment
Returns the first haplotype index.
hap2() - Method in class ibd.IbdSegment
Returns the second haplotype index.
HapAlleleProbs - Interface in main
Interface HapAlleleProbs stores allele probabilities for a haplotype.
HapBaumLevel - Class in sample
Class HapBaumLevel computes forward and backward Baum values for a haploid hidden Markov model (HMM) whose states are edges of a leveled directed acyclic graph (DAG).
HapBaumLevel(Dag, AL) - Constructor for class sample.HapBaumLevel
Constructs a new HapBaumLevel instance from the specified data.
hapIndex(int, int, int) - Method in class haplotype.BasicSampleHapPairs
 
hapIndex(int, int, int) - Method in class haplotype.GLSampleHapPairs
 
hapIndex(int, int, int) - Method in class haplotype.RefHapPairs
 
hapIndex(int, int, int) - Method in class haplotype.RevSampleHapPairs
 
hapIndex(int, int, int) - Method in interface haplotype.SampleHapPairs
Returns index of the haplotype that carries the specified copy of the specified allele.
hapIndex() - Method in class ibd.Haplotype
Returns the index of the haplotype.
hapIndex() - Method in interface main.HapAlleleProbs
Returns the haplotype index.
hapIndex() - Method in class main.LowMemHapAlleleProbs
 
hapIndex(int, int) - Method in class vcf.BitSetGT
 
hapIndex(int, int) - Method in class vcf.BitSetRefGT
 
hapIndex(int, int) - Method in class vcf.ByteArrayRefGT
 
hapIndex(int, int) - Method in class vcf.LowMafRefDiallelicGT
 
hapIndex(int, int) - Method in class vcf.LowMafRefGT
 
hapIndex(int, int) - Method in class vcf.SeqCodedRefGT
 
hapIndex(int, int) - Method in interface vcf.VcfEmission
Returns index of the haplotype that carries the specified copy of the specified allele.
hapIndex(int, int) - Method in class vcf.VcfRecord
 
HaploidIbd - Class in ibd
Class HaploidIbd implements the Refined IBD algorithm.
HaploidIbd(int, float) - Constructor for class ibd.HaploidIbd
Constructs a new HaploidIbd instance from the specified data.
haplotype - package haplotype
 
Haplotype - Class in ibd
Class Haplotype represents a haplotype segment.
Haplotype(SampleHapPairs, int) - Constructor for class ibd.Haplotype
Constructs a new Haplotype instance.
Haplotype(SampleHapPairs, int, int, int) - Constructor for class ibd.Haplotype
Constructs a new Haplotype instance.
HaplotypeCoder - Class in sample
Class HaplotypeCoder indexes the observed allele sequences in reference and target haplotype pairs for a list of consecutive markers.
HaplotypeCoder(SampleHapPairs, SampleHapPairs) - Constructor for class sample.HaplotypeCoder
Constructs a new HaplotypeCoder instance from the specified data.
HapNodes - Class in sample
Class HapNodes stores nodes and associated values.
HapNodes() - Constructor for class sample.HapNodes
Creates a new instance of HapNodes that has an initial value of 0 for each node.
HapPair - Interface in haplotype
Interface HapPair represents a pair of haplotypes for a sample.
hapPair() - Method in class ibd.IbdSegment
Returns the ordered pair of haplotype indices.
HapPairs - Interface in haplotype
Interface HapPairs represents a list of haplotype pairs.
HapPairSampler - Class in main
Class HapPairSampler samples haplotype pairs and estimates posterior genotype probabilities.
HapPairSampler(Par, RunStats) - Constructor for class main.HapPairSampler
Constructs a new HapPairSampler instance from the specified data.
haps() - Method in class ibd.IbsHapSegments
Returns the sample haplotype pairs.
HapSegment - Class in ibd
Class HapSegment represents a marker interval for a haplotype.
HapSegment(int, int, int) - Constructor for class ibd.HapSegment
Constructs a new HapSegment instance.
HapsMarker - Interface in vcf
Interface HapsMarker represents marker alleles for a list of haplotype pairs.
HapsMarkerIterator - Class in haplotype
Class HapsMarkerIterator represents a file iterator whose next() method returns HapsMarker objects.
HapsMarkerIterator(HapPairs) - Constructor for class haplotype.HapsMarkerIterator
Constructs a new HapsMarkerIterator instance that iterates through the markers of the specified HapPairs object.
hapToSeq() - Method in class vcf.VcfEmissionCompressor
Returns an array of length 2*this.samples().nSamples(), whose j-th element is the index of the allele sequence carried by the j-th haplotype in the list of compressed VcfEmission objects.
hasFormat(String) - Method in class vcf.VcfRecord
Returns true if the specified FORMAT subfield is present, and returns false otherwise.
hashCode() - Method in class beagleutil.BasicIntInterval
Returns a hash code value for the object.
hashCode() - Method in class beagleutil.ChromInterval
Returns a hash code value for the object.
hashCode() - Method in class beagleutil.Samples
Returns a hash code value for the object.
hashCode() - Method in class blbutil.IntPair
Returns a hash code value for the object.
hashCode() - Method in class dag.Score
Returns the hash code value for this object.
hashCode() - Method in class ibd.Haplotype
Returns a hash code value for the object.
hashCode() - Method in class ibd.HapSegment
Returns the hash code value for this object.
hashCode() - Method in class ibd.IbdSegment
Returns the hash code value for this object.
hashCode() - Method in class vcf.BasicMarker
 
hashCode() - Method in interface vcf.Marker
Returns the hash code value for this object.
hashCode() - Method in class vcf.Markers
Returns a hash code value for the object.
hasNext() - Method in class blbutil.InputIt
Returns true if the iteration has more elements.
hasNext() - Method in class haplotype.HapsMarkerIterator
Returns true if the iteration has more elements, and returns false otherwise.
hasNext() - Method in interface sample.DiploidStates
Returns true if the iteration of the ordered edge pairs has more elements, and returns false otherwise.
hasNext() - Method in class vcf.BrefIt
Returns true if the iteration has more elements, and returns false otherwise.
hasNext() - Method in class vcf.IntervalVcfIt
Returns true if the iteration has more elements.
hasNext() - Method in class vcf.RefIt
Returns true if the iteration has more elements, and returns false otherwise.
hasNext() - Method in class vcf.VcfIt
Returns true if the iteration has more elements, and returns false otherwise.
hasSibling(int) - Method in class dag.MergeableDagLevel
Returns true if the specified parent node has a sibling and returns false otherwise.
HbdAL - Class in vcf
Class HbdAL represents allele emission probabilities for a set of haplotype pairs under a homozygosity by descent (HBD) model.
HbdAL(GL) - Constructor for class vcf.HbdAL
Constructs an HbdAL instance.
hbdLod(int, int, int) - Method in class ibd.IbdBaum
Returns the homozygosity-by-descent (HBD) LOD score.
HEADER_PREFIX - Static variable in class vcf.VcfHeader
A string equal to the first nine tab-delimited fields of a VCF header line that contains sample data.
headerLine() - Method in class vcf.VcfHeader
Returns the VCF header line.
HighCapacityDagLevel - Class in dag
Class HighCapacityDagLevel represents a level of a leveled directed acyclic graph (DAG) that can contain up to Integer.MAX_VALUE edges.
HighCapacityDagLevel(int[], int[], int[], float[]) - Constructor for class dag.HighCapacityDagLevel
Constructs a new HighCapacityDagLevel instance from the specified data.
hweDoseR2() - Method in class vcf.GprobsStatistics
Returns the estimated squared correlation between the estimated ALT allele dose and the true ALT allele dose where the variance of the true ALT allele dose is estimated from the estimated ALT allele frequency.
hyphen - Static variable in class blbutil.Const
The hyphen character: '-'

I

ibd - package ibd
 
ibd() - Method in class main.Par
Returns the ibd parameter.
IbdBaum - Class in ibd
Class IbdBaum estimates LOD scores for an IBD versus a non-IBD model, and it estimates LOD scores for an HBD versus a non-HBD model.
IbdBaum(Dag, GL) - Constructor for class ibd.IbdBaum
Creates a new IbdBaum instance from the specified data.
ibdextend() - Method in class main.Par
Returns the ibdextend parameter.
ibdlength() - Method in class main.Par
Returns the ibdlength parameter.
ibdLod(int, int, int, int) - Method in class ibd.IbdBaum
Returns the identity-by-descent (IBD) LOD score.
ibdlod() - Method in class main.Par
Returns the ibdlod parameter.
ibdNanos(long) - Method in class main.RunStats
Increases the cumulative time for detecting identity-by-descent by the specified number of nanoseconds.
ibdscale() - Method in class main.Par
Returns the ibdscale parameter.
IbdSegment - Class in ibd
Class IbdSegment represents a pair of IBD haplotype segments.
IbdSegment(IntPair, Marker, Marker, float, int, int) - Constructor for class ibd.IbdSegment
Constructs an new IbdSegment instance from the specified data.
ibdtrim() - Method in class main.Par
Returns the ibdtrim parameter.
IbsHapSegments - Class in ibd
Class IbsHapSegments identifies IBS haplotype segments in a list of sample halotype pairs.
IbsHapSegments(SampleHapPairs, double[], double) - Constructor for class ibd.IbsHapSegments
Constructs a new IbsHapSegments object from the specified data.
IbsHapSegments(SampleHapPairs, int) - Constructor for class ibd.IbsHapSegments
Constructs a new IbsHapSegments object with marker positions defined to be marker indices.
id(int) - Method in class beagleutil.ChromIds
Returns the chromosome identifier with the specified index.
id(int) - Method in class beagleutil.SampleIds
Returns the sample identifier with the specified index.
id(int) - Method in class beagleutil.Samples
Returns the identifier for the sample with the specified index in this list of samples.
id(int) - Method in class vcf.BasicMarker
 
id() - Method in class vcf.BasicMarker
 
id(int) - Method in interface vcf.Marker
Returns the specified marker identifier.
id() - Method in interface vcf.Marker
Returns the first marker identifier if there is at least one identifier in the VCF record ID field, and returns this.chr() + ":" + this.pos() otherwise.
idFilter(Collection<String>) - Static method in class vcf.FilterUtil
Returns a filter that accepts all markers which do not have an identifier or chromomsome position present in the specified collection.
idIndex(int) - Method in class beagleutil.Samples
Returns the sample identifier index corresponding to the sample with the specified index in this list of samples.
ids() - Method in class beagleutil.ChromIds
Returns the list of chromosome identifiers as an array.
ids() - Method in class beagleutil.SampleIds
Returns the list of indexed sample identifiers as an array.
ids() - Method in class beagleutil.Samples
Returns this list of samples as an array of sample identifiers.
idSet(File) - Static method in class blbutil.Utilities
Returns a set of identifiers found in a text file that has one identifier per line.
ImmutableDag - Class in dag
Class ImmutableDag represents a leveled Directed Acyclic Graph (DAG).
ImmutableDag(Markers, DagLevel[]) - Constructor for class dag.ImmutableDag
Constructs a new ImmutableDag instance from the specified data.
ImputationData - Class in sample
Class ImputationData contains the input data that is required for imputation of ungenotyped markers in the imputation target.
ImputationData(Par, CurrentData, SampleHapPairs, GeneticMap) - Constructor for class sample.ImputationData
Constructs a new ImputationData instance from the specified data.
imputationData() - Method in class sample.LSHapBaum
Returns the input data for genotype imputation.
imputationNanos(long) - Method in class main.RunStats
Stores the time for imputing ungenotyped marker and increases the cumulative imputation time by the specified number of nanoseconds.
impute() - Method in class main.Par
Returns the impute parameter.
includeFilter(Collection<E>) - Static method in interface blbutil.Filter
Returns a filter that accepts all non-null objects that are contained in the specified collection.
incrementAndGet(int) - Method in class blbutil.IntList
Increments by one the element at the specified position in this list.
index(int) - Method in class beagleutil.Samples
Returns the index of the sample that corresponds to the specified sample identifier index, or returns -1 if there is no corresponding sample in this list of samples.
index(String) - Method in class beagleutil.Samples
Returns the index of the sample that corresponds to the specified sample identifier, or returns -1 if there is no corresponding sample in this list of samples.
index() - Method in class dag.MergeableDagLevel
Returns the marker index.
index2BasePos(int, int) - Method in class main.PlinkGeneticMap
Returns the specified base position
index2GenPos(int, int) - Method in class main.PlinkGeneticMap
Returns the specified genetic map position
IndexMap - Class in blbutil
Class IndexMap is a map whose keys are a bounded set of non-negative integers and whose values are integers.
IndexMap(int, int) - Constructor for class blbutil.IndexMap
Creates a new instance of IndexMap whose nil() method will return the specified nil value.
IndexSet - Class in blbutil
Class IndexSet is a set that stores non-negative indices that are less than or equal to a specified maximum value.
IndexSet(int) - Constructor for class blbutil.IndexSet
Creates a new instance of IndexSet that can contain non-negative integer indices that are less than or equal to the specified maximum value.
inEdge(int, int, int) - Method in interface dag.Dag
Returns the index of the specified edge in the DAG.
inEdge(int, int) - Method in interface dag.DagLevel
Returns the index of the specified edge at this level of the DAG.
inEdge(int, int) - Method in class dag.HighCapacityDagLevel
 
inEdge(int, int, int) - Method in class dag.ImmutableDag
 
inEdge(int, int, int) - Method in class dag.LinkageEquilibriumDag
 
inEdge(int, int) - Method in class dag.LowCapacityDagLevel
 
info() - Method in class vcf.VcfRecord
Returns the INFO field.
initHaps() - Method in class main.CurrentData
Returns the target data haplotype pairs in the segment of the current marker window preceding the splice point with the previous marker window: this.targetMarkers().restrict(0, this.prevTargetSplice())
INITIAL_NUMBER - Static variable in class vcf.Bref
The initial long in a bref file created with this bref version.
initialHaps(CurrentData) - Method in class main.HapPairSampler
Returns a list of sampled haplotype pairs.
InputIt - Class in blbutil
Class InputIt is a buffered iterator whose next() method returns lines of a text input stream.
instance() - Static method in class beagleutil.ChromIds
Returns the singleton ChromIds instance.
instance() - Static method in class beagleutil.SampleIds
Returns the singleton SampleIds instance.
intArg(String, Map<String, String>, boolean, int, int, int) - Static method in class blbutil.Validate
Removes the specified key from the specified map, and returns the integer value corresponding to the specified key.
IntArray - Interface in blbutil
Interface IntArray represents an immutable int[] array.
intersect(int, Collection<E>) - Method in class beagleutil.CenteredIntIntervalTree
 
intersect(int, Collection<E>) - Method in interface beagleutil.IntIntervalTree
Adds the elements in this interval tree that intersect the specified point to the specified collection.
intersectAll(int, int, Collection<E>) - Method in class beagleutil.CenteredIntIntervalTree
 
intersectAll(int, int, Collection<E>) - Method in interface beagleutil.IntIntervalTree
Adds the elements in this interval tree that contain the specified interval to the specified collection.
intersectPart(int, int, Collection<E>) - Method in class beagleutil.CenteredIntIntervalTree
 
intersectPart(int, int, Collection<E>) - Method in interface beagleutil.IntIntervalTree
Adds the elements in this interval tree that intersect any part of the specified interval to the specified collection.
IntervalVcfIt<E extends MarkerContainer> - Class in vcf
Class IntervalVcfIterator is a sample file iterator whose next() method returns a marker container.
IntervalVcfIt(SampleFileIt<E>, ChromInterval) - Constructor for class vcf.IntervalVcfIt
Constructs a new IntervalVcfIterator instance.
IntInterval - Interface in beagleutil
Interface IntInterval represents an interval of consecutive integers.
IntIntervalTree<E extends IntInterval> - Interface in beagleutil
Interface IntIntervalTree represents an interval tree whose elements are IntInterval objects.
IntList - Class in blbutil
Class IntList represents a list of integers.
IntList() - Constructor for class blbutil.IntList
Constructs an IntList object with the default initial capacity.
IntList(int) - Constructor for class blbutil.IntList
Constructs an IntList object with the specified initial capacity.
IntPair - Class in blbutil
Class IntPair represents an ordered pair of integers.
IntPair(int, int) - Constructor for class blbutil.IntPair
Constructs an IntPair instance that represents the specified ordered pair of integers.
IntSet - Class in blbutil
Class IntSet represents an indexed set of integers.
IntSet(int) - Constructor for class blbutil.IntSet
Creates a new IntSet instance.
isChildOf(int, int, int) - Method in interface dag.Dag
Returns true if the child node of the specified parent edge equals the parent node of the specified child edge and returns false otherwise.
isChildOf(int, int, int) - Method in class dag.ImmutableDag
 
isChildOf(int, int, int) - Method in class dag.LinkageEquilibriumDag
 
isEmpty() - Method in class beagleutil.CenteredIntIntervalTree
 
isEmpty() - Method in interface beagleutil.IntIntervalTree
Returns true if this interval tree contains no elements.
isEmpty() - Method in class blbutil.IntList
Returns true if this list has no elements, and returns false otherwise.
isImputed(int) - Method in class main.ConstrainedAlleleProbs
Returns true if the specified marker is not present in the input data and returns false otherwise.
isMergeable() - Method in class dag.Score
Returns true if the two trees may be merged, and returns false otherwise.
isPhased(int, int) - Method in class vcf.BasicGL
 
isPhased(int) - Method in class vcf.BitSetGT
 
isPhased(int) - Method in class vcf.BitSetRefGT
 
isPhased(int) - Method in class vcf.ByteArrayRefGT
 
isPhased(int, int) - Method in class vcf.FuzzyGL
 
isPhased(int, int) - Method in interface vcf.GL
Returns true if the observed data for the specified marker and sample includes a phased genotype, and returns false otherwise.
isPhased(int) - Method in class vcf.LowMafRefDiallelicGT
 
isPhased(int) - Method in class vcf.LowMafRefGT
 
isPhased(int, int) - Method in class vcf.MaskedEndsGL
 
isPhased(int, int) - Method in class vcf.NoPhaseGL
 
isPhased(int, int) - Method in class vcf.RefGL
 
isPhased(int, int) - Method in class vcf.RevGL
 
isPhased(int) - Method in class vcf.SeqCodedRefGT
 
isPhased(int, int) - Method in class vcf.SplicedGL
 
isPhased(int) - Method in interface vcf.VcfEmission
Returns true if the genotype emission probabilities for the specified sample are determined by a phased, nonmissing genotype, and returns false otherwise.
isPhased() - Method in class vcf.VcfRecGTParser
Returns true if the genotype for the current sample is phased, and returns false otherwise.
isPhased(int) - Method in class vcf.VcfRecord
 
isRefData() - Method in class vcf.BasicGL
 
isRefData() - Method in class vcf.BitSetGT
 
isRefData() - Method in class vcf.BitSetRefGT
 
isRefData() - Method in class vcf.ByteArrayRefGT
 
isRefData() - Method in class vcf.FuzzyGL
 
isRefData() - Method in interface vcf.GL
Returns true if the observed data for each marker and sample includes a phased genotype that has no missing alleles, and returns false otherwise.
isRefData() - Method in class vcf.LowMafRefDiallelicGT
 
isRefData() - Method in class vcf.LowMafRefGT
 
isRefData() - Method in class vcf.MaskedEndsGL
 
isRefData() - Method in class vcf.NoPhaseGL
 
isRefData() - Method in class vcf.RefGL
 
isRefData() - Method in class vcf.RevGL
 
isRefData() - Method in class vcf.SeqCodedRefGT
 
isRefData() - Method in class vcf.SplicedGL
 
isRefData() - Method in interface vcf.VcfEmission
Returns true if the genotype emission probabilities for each sample are determined by a phased called genotype that has no missing alleles, and returns false otherwise.
isRefData() - Method in class vcf.VcfRecord
 
item(int) - Method in class beagleutil.ThreadSafeIndexer
Returns the object with the specified index.
items() - Method in class beagleutil.ThreadSafeIndexer
Returns an listed of indexed objects.

K

key() - Method in class vcf.VcfMetaInfo
Returns the VCF meta-information line key.

L

lastWindowOnChrom() - Method in class vcf.AllData
 
lastWindowOnChrom() - Method in interface vcf.Data
Returns true if the current window of VCF records is the last window for the chromosome and returns false otherwise.
lastWindowOnChrom() - Method in class vcf.TargetData
 
lastWindowOnChrom() - Method in class vcf.VcfWindow
Returns true if the sliding window of VCF Records is the last window for the chromosome and returns false otherwise.
length() - Method in class ibd.Haplotype
Returns the number of alleles in this haplotype segment.
LiAndStephensHapSampler - Class in main
Class LiAndStephensHapSampler estimates posterior allele probabilities.
LiAndStephensHapSampler(Par, GeneticMap) - Constructor for class main.LiAndStephensHapSampler
Constructs a LiAndStephensHapSampler instance from the specified data.
LinkageEquilibriumDag - Class in dag
Class LinkageEquilibriumDag represents a leveled DAG with one parent node at each level.
LinkageEquilibriumDag(GL, float) - Constructor for class dag.LinkageEquilibriumDag
Constructs a new LinkageEquilibriumDag instance that represents markers in linkage equilibrium, with one level per marker, one parent node per level, one edge per allele at each level, and edge count equal to the estimated allele frequency.
longArg(String, Map<String, String>, boolean, long, long, long) - Static method in class blbutil.Validate
Removes the specified key from the specified map, and returns the long value corresponding to the specified key.
LowCapacityDagLevel - Class in dag
Class LowCapacityDagLevel represents a level of a leveled directed acyclic graph (DAG) that can contain up to Character.MAX_VALUE edges.
LowCapacityDagLevel(char[], char[], char[], float[]) - Constructor for class dag.LowCapacityDagLevel
Constructs a new LowCapacityDagLevel instance from the specified data.
LowMafRefDiallelicGT - Class in vcf
Class LowMafRefDiallelicGT represent represents phased, non-missing genotypes for a list of reference samples at a single diallelic marker.
LowMafRefDiallelicGT(Marker, Samples, int, int[]) - Constructor for class vcf.LowMafRefDiallelicGT
Constructs a new LowMafRefDiallelicGT instance with phased non-missing genotypes from the specified marker, samples, and haplotype indices.
LowMafRefGT - Class in vcf
Class LowMafRefGT represent represents phased, non-missing genotypes for a list of reference samples at a single marker.
LowMafRefGT(Marker, Samples, int[][]) - Constructor for class vcf.LowMafRefGT
Constructs a new LowMafRefGT instance with phased, non-missing genotypes from the specified marker, samples, and haplotype indices.
lowmem() - Method in class main.Par
Returns the lowmem parameter.
LowMemHapAlleleProbs - Class in main
Class LowMemHapAlleleProbs stores allele probabilities for a haplotype.
LowMemHapAlleleProbs(Markers, Samples, int, float[]) - Constructor for class main.LowMemHapAlleleProbs
Constructs a new LowMemHapAlleleProbs instance.
LSHapBaum - Class in sample
Class LSHapBaum implements the Baum hidden Markov model forward and backward algorithms for imputing missing alleles on a target haplotype.
LSHapBaum(ImputationData, boolean) - Constructor for class sample.LSHapBaum
Creates a LSHapBaum instance from the specified data.

M

main - package main
 
main(String[]) - Static method in class blbutil.BGZIPOutputStream
Applies BGZIP compression on the specified files.
Main - Class in main
Class Main is the entry class for the Beagle program.
main(String[]) - Static method in class main.Main
Entry point to Beagle program.
main(String[]) - Static method in class vcf.Bref
The main() method is the entry point to the bref program.
MainHelper - Class in main
Class MainHelper is an auxiliary class with methods called by the main.Main class.
majorAllele(int) - Method in class haplotype.BasicSampleHapPairs
 
majorAllele(int) - Method in class haplotype.GLSampleHapPairs
 
majorAllele(int) - Method in class haplotype.RefHapPairs
 
majorAllele(int) - Method in class haplotype.RevSampleHapPairs
 
majorAllele(int) - Method in interface haplotype.SampleHapPairs
Returns the index of the major allele.
majorAllele() - Method in class vcf.BitSetGT
 
majorAllele() - Method in class vcf.BitSetRefGT
 
majorAllele() - Method in class vcf.ByteArrayRefGT
 
majorAllele() - Method in class vcf.LowMafRefDiallelicGT
 
majorAllele() - Method in class vcf.LowMafRefGT
 
majorAllele() - Method in class vcf.SeqCodedRefGT
 
majorAllele() - Method in interface vcf.VcfEmission
Returns the index of the major allele.
majorAllele() - Method in class vcf.VcfRecord
 
map() - Method in class main.Par
Returns the map parameter.
mapscale() - Method in class main.Par
Returns the mapscale parameter.
marker(int) - Method in class haplotype.BasicHapPairs
 
marker(int) - Method in class haplotype.BasicSampleHapPairs
 
marker(int) - Method in class haplotype.BitHapPair
 
marker(int) - Method in class haplotype.GLSampleHapPairs
 
marker(int) - Method in interface haplotype.HapPair
Returns the specified marker.
marker(int) - Method in interface haplotype.HapPairs
Returns the specified marker.
marker(int) - Method in class haplotype.RefHapPairs
 
marker(int) - Method in class haplotype.RevHapPair
 
marker(int) - Method in class haplotype.RevHapPairs
 
marker(int) - Method in class haplotype.RevSampleHapPairs
 
marker(int) - Method in class haplotype.WrappedHapPair
 
marker(int) - Method in class ibd.Haplotype
Returns the specified marker.
marker(int) - Method in interface main.AlleleProbs
Returns the specified marker.
marker(int) - Method in class main.BasicAlleleProbs
 
marker(int) - Method in class main.BasicGenotypeValues
 
marker(int) - Method in class main.ConstrainedAlleleProbs
 
marker(int) - Method in interface main.GenotypeValues
Returns the specified marker.
marker(int) - Method in interface main.HapAlleleProbs
Returns the specified marker.
marker(int) - Method in class main.LowMemHapAlleleProbs
 
marker(int) - Method in class main.RevGenotypeValues
 
marker(int) - Method in class main.SampleGenotypeValues
Returns the specified marker.
marker(int) - Method in class main.SampleHapPairAlleleProbs
 
marker() - Method in interface sample.DiploidStates
Returns the current marker index.
marker() - Method in class sample.DuoBaumLevel
Return the level of the HMM.
marker() - Method in class sample.HapBaumLevel
Return the level of the HMM.
marker() - Method in class sample.RecombSingleBaumLevel
Return the level of the HMM.
marker() - Method in class sample.SingleBaumLevel
Return the level of the HMM.
marker(int) - Method in interface vcf.AL
Returns the specified marker.
marker(int) - Method in class vcf.BasicGL
 
marker() - Method in class vcf.BitSetGT
 
marker() - Method in class vcf.BitSetRefGT
 
marker() - Method in class vcf.ByteArrayRefGT
 
marker(int) - Method in class vcf.FuzzyGL
 
marker(int) - Method in interface vcf.GL
Returns the specified marker.
marker() - Method in class vcf.GprobsStatistics
Returns the marker.
marker() - Method in interface vcf.HapsMarker
Returns the marker.
marker(int) - Method in class vcf.HbdAL
 
marker() - Method in class vcf.LowMafRefDiallelicGT
 
marker() - Method in class vcf.LowMafRefGT
 
Marker - Interface in vcf
Interface Marker represents a genetic marker.
marker() - Method in interface vcf.MarkerContainer
Returns the marker.
marker(int) - Method in class vcf.Markers
Returns the specified marker.
marker(int) - Method in class vcf.MaskedEndsGL
 
marker(int) - Method in class vcf.NoPhaseGL
 
marker(int) - Method in class vcf.RefGL
 
marker(int) - Method in class vcf.RevGL
 
marker() - Method in class vcf.SeqCodedRefGT
 
marker(int) - Method in class vcf.SplicedGL
 
marker(int) - Method in class vcf.VcfEmissionCompressor
Returns the specified marker.
marker() - Method in class vcf.VcfRecBuilder
Returns the current marker.
marker() - Method in class vcf.VcfRecGTParser
Returns the marker.
marker() - Method in class vcf.VcfRecord
 
MarkerContainer - Interface in vcf
Interface MarkerContainer represents an object that stores a unique vcf.Marker instance.
markerFilter(File) - Static method in class vcf.FilterUtil
Returns a filter that excludes markers that have an identifier or genome coordinates that matches a line of the specified file, or returns null if the excludeMarkersFile parameter is null.
markerIndex(int) - Method in class main.CurrentData
Returns the index of the specified marker in the reference data markers.
markerIndex(int) - Method in class vcf.AllData
 
markerIndex(int) - Method in interface vcf.Data
Returns the marker index corresponding to the specified target data marker.
markerIndex(int) - Method in class vcf.TargetData
 
markerIndices() - Method in class main.CurrentData
Returns an array of length this.nTargetMarkers() which maps the k-th marker in the list of target data markers to the index of the marker in the list of reference data markers.
markerIsInSet(Marker, Set<String>) - Static method in class vcf.FilterUtil
Returns true if the specified marker has an identifier is in the specified set, or if ("marker.chrom()" + ":" + "marker.pos()") is in the specified set, and returns false otherwise.
markers() - Method in interface dag.Dag
Returns the markers represented by this DAG.
markers() - Method in class dag.ImmutableDag
 
markers() - Method in class dag.LinkageEquilibriumDag
 
markers() - Method in class haplotype.BasicHapPairs
 
markers() - Method in class haplotype.BasicSampleHapPairs
 
markers() - Method in class haplotype.BitHapPair
 
markers() - Method in class haplotype.GLSampleHapPairs
 
markers() - Method in interface haplotype.HapPair
Returns the markers.
markers() - Method in interface haplotype.HapPairs
Returns the markers.
markers() - Method in class haplotype.RefHapPairs
 
markers() - Method in class haplotype.RevHapPair
 
markers() - Method in class haplotype.RevHapPairs
 
markers() - Method in class haplotype.RevSampleHapPairs
 
markers() - Method in class haplotype.WrappedHapPair
 
markers() - Method in interface main.AlleleProbs
Returns the list of markers.
markers() - Method in class main.BasicAlleleProbs
 
markers() - Method in class main.BasicGenotypeValues
 
markers() - Method in class main.ConstrainedAlleleProbs
 
markers() - Method in class main.CurrentData
Returns the list of reference data markers.
markers() - Method in interface main.GenotypeValues
Returns the list of markers.
markers() - Method in interface main.HapAlleleProbs
Returns the list of markers.
markers() - Method in class main.LowMemHapAlleleProbs
 
markers() - Method in class main.RevGenotypeValues
 
markers() - Method in class main.SampleGenotypeValues
Returns the list of markers.
markers() - Method in class main.SampleHapPairAlleleProbs
 
markers() - Method in class sample.SamplerData
returns the list of markers.
markers() - Method in interface vcf.AL
Returns the list of markers.
markers() - Method in class vcf.AllData
 
markers() - Method in class vcf.BasicGL
 
markers() - Method in interface vcf.Data
Returns the list of markers in the current window.
markers() - Method in class vcf.FuzzyGL
 
markers() - Method in interface vcf.GL
Returns the list of markers.
markers() - Method in class vcf.HbdAL
 
Markers - Class in vcf
Class Markers represent a list of markers in chromosome order.
markers() - Method in class vcf.Markers
Returns the list of markers.
markers() - Method in class vcf.MaskedEndsGL
 
markers() - Method in class vcf.NoPhaseGL
 
markers() - Method in class vcf.RefGL
 
markers() - Method in class vcf.RevGL
 
markers() - Method in class vcf.SplicedGL
 
markers() - Method in class vcf.TargetData
 
markersAreReversed() - Method in class sample.SamplerData
Returns true if the order of markers is reversed, and false otherwise
MaskedEndsGL - Class in vcf
Class MaskedEndsGL is a wrapper for a GL instance that masks the genotype emission probabilities for a user-specified number of starting and ending markers.
MaskedEndsGL(GL, int, int) - Constructor for class vcf.MaskedEndsGL
Constructs a new MaskedEndsGL instance.
maxEdges() - Method in interface dag.Dag
Returns the maximum number of edges at any level of the DAG.
maxEdges() - Method in class dag.ImmutableDag
 
maxEdges() - Method in class dag.LinkageEquilibriumDag
 
maxKey() - Method in class blbutil.IndexMap
Returns the maximum key.
maxlr() - Method in class main.Par
Returns the maxlr parameter.
maxNodes() - Method in interface dag.Dag
Returns the maximum number of parent nodes at any level of the DAG.
maxNodes() - Method in class dag.ImmutableDag
 
maxNodes() - Method in class dag.LinkageEquilibriumDag
 
maxPermittedElement() - Method in class blbutil.IndexSet
Returns the maximum permitted element in the set.
mega - Static variable in class blbutil.Const
The value 1,000,000
merge(ChromInterval, ChromInterval) - Static method in class beagleutil.ChromInterval
Returns the union of the specified overlapping chromosome intervals.
MergeableDag - Class in dag
Class MergeableDag contains a static, thread-safe factory method that constructs a Directed Acyclic Graph (DAG) from sequence data.
MergeableDagLevel - Class in dag
Class MergeableDagLevel represents a level of a leveled directed acyclic graph (DAG).
MergeableDagLevel(HapsMarker) - Constructor for class dag.MergeableDagLevel
Constructs a new MergeableDagLevel instance from the specified phased genotype data.
MergeableDagLevel(HapsMarker, float[]) - Constructor for class dag.MergeableDagLevel
Constructs a new MergeableDagLevel instance from the specified phased genotype data and haplotype weights.
MergeableDagLevel(MergeableDagLevel, HapsMarker) - Constructor for class dag.MergeableDagLevel
Constructs a new MergeableDagLevel instance with the specified previous MergeableDagLevel and the specified phased genotype data.
mergeParentNodes(int, int) - Method in class dag.MergeableDagLevel
Merges the two specified parent nodes and assigns the specified retainedNode index to the merged node.
metaInfoLine(int) - Method in class vcf.VcfHeader
Returns the specified VCF meta-information line.
minIbsLength() - Method in class ibd.IbsHapSegments
Returns the minimum length of an IBS segment.
MISSING_DATA_CHAR - Static variable in class blbutil.Const
The VCF missing-data symbol as a character: '.'
MISSING_DATA_STRING - Static variable in class blbutil.Const
The VCF missing-data symbol as a string: "."
modelscale() - Method in class main.Par
Returns the modelscale parameter.
mother(int) - Method in class main.NuclearFamilies
Returns the sample index of the mother of the specified sample, or returns -1 if the mother is unknown or is not present in the list of samples.

N

nAlleles() - Method in class dag.MergeableDagLevel
Returns the number of alleles.
nAlleles(int) - Method in class haplotype.BasicSampleHapPairs
 
nAlleles(int) - Method in class haplotype.GLSampleHapPairs
 
nAlleles(int) - Method in class haplotype.RefHapPairs
 
nAlleles(int) - Method in class haplotype.RevSampleHapPairs
 
nAlleles(int) - Method in interface haplotype.SampleHapPairs
Returns the number of marker alleles.
nAlleles() - Method in class sample.HapBaumLevel
Return the number of possible alleles at this level of the HMM.
nAlleles() - Method in class vcf.BasicMarker
 
nAlleles() - Method in class vcf.BitSetGT
 
nAlleles() - Method in class vcf.BitSetRefGT
 
nAlleles() - Method in class vcf.ByteArrayRefGT
 
nAlleles() - Method in class vcf.LowMafRefDiallelicGT
 
nAlleles() - Method in class vcf.LowMafRefGT
 
nAlleles() - Method in interface vcf.Marker
Returns the number of alleles for the marker, including the REF allele.
nAlleles() - Method in class vcf.SeqCodedRefGT
 
nAlleles() - Method in interface vcf.VcfEmission
Returns the number of marker alleles.
nAlleles() - Method in class vcf.VcfRecord
 
nAllSamples() - Method in class main.CurrentData
Returns the number of reference and target samples.
nAllSamples() - Method in class vcf.AllData
 
nAllSamples() - Method in interface vcf.Data
Returns the total number of reference and target samples.
nAllSamples() - Method in class vcf.TargetData
 
nChildNodes(int) - Method in interface dag.Dag
Returns the number of child nodes at the specified level of the DAG.
nChildNodes() - Method in interface dag.DagLevel
Returns the number of child nodes at this level of the DAG.
nChildNodes() - Method in class dag.HighCapacityDagLevel
 
nChildNodes(int) - Method in class dag.ImmutableDag
 
nChildNodes(int) - Method in class dag.LinkageEquilibriumDag
 
nChildNodes() - Method in class dag.LowCapacityDagLevel
 
nClusters() - Method in class sample.ImputationData
Return the number of target marker clusters.
nDuos() - Method in class main.NuclearFamilies
Returns the number of parent-offspring duos in the list of samples.
ne() - Method in class main.Par
Returns the ne parameter
nEdges(int) - Method in interface dag.Dag
Returns the number of edges at the specified level of the DAG.
nEdges() - Method in interface dag.Dag
Returns the number of edges in the DAG.
nEdges() - Method in interface dag.DagLevel
Returns the number of edges at this level of the DAG.
nEdges() - Method in class dag.HighCapacityDagLevel
 
nEdges(int) - Method in class dag.ImmutableDag
 
nEdges() - Method in class dag.ImmutableDag
 
nEdges(int) - Method in class dag.LinkageEquilibriumDag
 
nEdges() - Method in class dag.LinkageEquilibriumDag
 
nEdges() - Method in class dag.LowCapacityDagLevel
 
next() - Method in class blbutil.InputIt
Returns the next element in the iteration.
next() - Method in class dag.MergeableDagLevel
Returns the next DAG level or null if no next level is stored.
next() - Method in class haplotype.HapsMarkerIterator
Returns the next element in the iteration.
next() - Method in interface sample.DiploidStates
Advances the iteration of ordered edge pairs to the next element.
next() - Method in class vcf.BrefIt
Returns the next element in the iteration.
next() - Method in class vcf.IntervalVcfIt
Returns the next element in the iteration.
next() - Method in class vcf.RefIt
Returns the next element in the iteration.
next() - Method in class vcf.VcfIt
Returns the next element in the iteration.
nextOverlapStart() - Method in class main.CurrentData
Returns the first marker index in the overlap between this marker window and the next marker window, or returns this.nMarkers() there is no overlap.
nextSample() - Method in class vcf.VcfRecGTParser
Increases the current sample index by one.
nextSpliceStart() - Method in class main.CurrentData
Returns the first marker index after the splice point between this marker window and the next marker window, or returns this.nMarkers() if there is no overlap or if there are no markers after the splice point.
nextTargetOverlapStart() - Method in class main.CurrentData
Returns the first target marker index in the overlap between this marker window and the next marker window, or returns this.nMarkers() if there is no overlap or if there are no target markers in the overlap.
nextTargetSpliceStart() - Method in class main.CurrentData
Returns the first target marker index after the splice point between this marker window and the next marker window, or returns this.nTargetMarkers() if there is no overlap or if there are no target markers after the splice point
nFormatSubfields() - Method in class vcf.VcfRecord
Returns the number of FORMAT subfields.
nGenotypes() - Method in class sample.DuoBaumLevel
Return the number of possible genotypes at this level of the HMM.
nGenotypes() - Method in class sample.RecombSingleBaumLevel
Return the number of possible genotypes at this level of the HMM.
nGenotypes() - Method in class sample.SingleBaumLevel
Return the number of possible genotypes at this level of the HMM.
nGenotypes() - Method in class vcf.BasicMarker
 
nGenotypes() - Method in interface vcf.Marker
Returns the number of distinct genotypes, which equals this.nAlleles()*(1 + this.nAlleles())/2.
nGenotypes() - Method in class vcf.R2Estimator
Returns the current number of genotypes with allele dose data.
nHapPairs() - Method in class haplotype.BasicHapPairs
 
nHapPairs() - Method in class haplotype.BasicSampleHapPairs
 
nHapPairs() - Method in class haplotype.GLSampleHapPairs
 
nHapPairs() - Method in interface haplotype.HapPairs
Returns the number of haplotype pairs.
nHapPairs() - Method in class haplotype.RefHapPairs
 
nHapPairs() - Method in class haplotype.RevHapPairs
 
nHapPairs() - Method in class haplotype.RevSampleHapPairs
 
nHapPairs() - Method in class vcf.BitSetGT
 
nHapPairs() - Method in class vcf.BitSetRefGT
 
nHapPairs() - Method in class vcf.ByteArrayRefGT
 
nHapPairs() - Method in interface vcf.HapsMarker
Returns the number of haplotype pairs.
nHapPairs() - Method in class vcf.LowMafRefDiallelicGT
 
nHapPairs() - Method in class vcf.LowMafRefGT
 
nHapPairs() - Method in class vcf.SeqCodedRefGT
 
nHapPairs() - Method in class vcf.VcfRecord
 
nHaps() - Method in class dag.MergeableDagLevel
Returns the number of sequences used to construct the DAG.
nHaps() - Method in class haplotype.BasicHapPairs
 
nHaps() - Method in class haplotype.BasicSampleHapPairs
 
nHaps() - Method in class haplotype.GLSampleHapPairs
 
nHaps() - Method in interface haplotype.HapPairs
Returns the number of haplotypes.
nHaps() - Method in class haplotype.RefHapPairs
 
nHaps() - Method in class haplotype.RevHapPairs
 
nHaps() - Method in class haplotype.RevSampleHapPairs
 
nHaps() - Method in class sample.SamplerData
Returns the number of haplotypes.
nHaps() - Method in interface vcf.AL
Returns the number of haplotypes.
nHaps() - Method in class vcf.BasicGL
 
nHaps() - Method in class vcf.BitSetGT
 
nHaps() - Method in class vcf.BitSetRefGT
 
nHaps() - Method in class vcf.ByteArrayRefGT
 
nHaps() - Method in class vcf.FuzzyGL
 
nHaps() - Method in interface vcf.GL
Returns the number of haplotypes.
nHaps() - Method in interface vcf.HapsMarker
Returns the number of haplotypes.
nHaps() - Method in class vcf.HbdAL
 
nHaps() - Method in class vcf.LowMafRefDiallelicGT
 
nHaps() - Method in class vcf.LowMafRefGT
 
nHaps() - Method in class vcf.MaskedEndsGL
 
nHaps() - Method in class vcf.NoPhaseGL
 
nHaps() - Method in class vcf.RefGL
 
nHaps() - Method in class vcf.RevGL
 
nHaps() - Method in class vcf.SeqCodedRefGT
 
nHaps() - Method in class vcf.SplicedGL
 
nHaps() - Method in class vcf.VcfRecord
 
nHeaderFields() - Method in class vcf.VcfHeader
Returns the number of fields in the VCF header line before sample exclusions.
nIds() - Method in class vcf.BasicMarker
 
nIds() - Method in interface vcf.Marker
Returns the number of marker identifiers.
nil() - Method in class blbutil.IndexMap
Returns the value that is returned by this.get() if a key has no assigned value.
nInEdges(int, int) - Method in interface dag.Dag
Returns the number of ingoing edges for the specified node of the DAG.
nInEdges(int) - Method in interface dag.DagLevel
Returns the number of ingoing edges for the specified child node at this level of the DAG.
nInEdges(int) - Method in class dag.HighCapacityDagLevel
 
nInEdges(int, int) - Method in class dag.ImmutableDag
 
nInEdges(int, int) - Method in class dag.LinkageEquilibriumDag
 
nInEdges(int) - Method in class dag.LowCapacityDagLevel
 
niterations() - Method in class main.Par
Returns the niterations parameter.
nl - Static variable in class blbutil.Const
The system-dependent string representing a new line-line: System.getProperty("line.separator")
nLevels() - Method in interface dag.Dag
Returns the number of markers.
nLevels() - Method in class dag.ImmutableDag
 
nLevels() - Method in class dag.LinkageEquilibriumDag
 
nMapPositions(int) - Method in class main.PlinkGeneticMap
Returns the number of mapped loci in this genetic map.
nMarkers() - Method in class haplotype.BasicHapPairs
 
nMarkers() - Method in class haplotype.BasicSampleHapPairs
 
nMarkers() - Method in class haplotype.BitHapPair
 
nMarkers() - Method in class haplotype.GLSampleHapPairs
 
nMarkers() - Method in interface haplotype.HapPair
Returns the number of markers.
nMarkers() - Method in interface haplotype.HapPairs
Returns the number of markers.
nMarkers() - Method in class haplotype.RefHapPairs
 
nMarkers() - Method in class haplotype.RevHapPair
 
nMarkers() - Method in class haplotype.RevHapPairs
 
nMarkers() - Method in class haplotype.RevSampleHapPairs
 
nMarkers() - Method in class haplotype.WrappedHapPair
 
nMarkers() - Method in interface main.AlleleProbs
Returns the number of markers.
nMarkers() - Method in class main.BasicAlleleProbs
 
nMarkers() - Method in class main.BasicGenotypeValues
 
nMarkers() - Method in class main.ConstrainedAlleleProbs
 
nMarkers() - Method in class main.CurrentData
Returns the number of reference data markers.
nMarkers() - Method in interface main.GenotypeValues
Returns the number of markers.
nMarkers() - Method in interface main.HapAlleleProbs
Returns the number of markers.
nMarkers() - Method in class main.LowMemHapAlleleProbs
 
nMarkers() - Method in class main.RevGenotypeValues
 
nMarkers() - Method in class main.SampleGenotypeValues
Returns the number of markers.
nMarkers() - Method in class main.SampleHapPairAlleleProbs
 
nMarkers() - Method in interface sample.DiploidStates
Returns the number of markers.
nMarkers(int) - Method in class sample.RefHapSegs
Return the number of markers in the specified chromosome segment.
nMarkers() - Method in class sample.SamplerData
Returns the number of markers.
nMarkers() - Method in interface vcf.AL
Returns the number of markers.
nMarkers() - Method in class vcf.AllData
 
nMarkers() - Method in class vcf.BasicGL
 
nMarkers() - Method in interface vcf.Data
Returns the number of markers in the current window.
nMarkers() - Method in class vcf.FuzzyGL
 
nMarkers() - Method in interface vcf.GL
Returns the number of markers.
nMarkers() - Method in class vcf.HbdAL
 
nMarkers() - Method in class vcf.Markers
Returns the number of markers.
nMarkers() - Method in class vcf.MaskedEndsGL
 
nMarkers() - Method in class vcf.NoPhaseGL
 
nMarkers() - Method in class vcf.RefGL
 
nMarkers() - Method in class vcf.RevGL
 
nMarkers() - Method in class vcf.SplicedGL
 
nMarkers() - Method in class vcf.TargetData
 
nMarkersSoFar() - Method in class vcf.AllData
 
nMarkersSoFar() - Method in interface vcf.Data
Returns the number of markers in the union of the current window and all previous windows.
nMarkersSoFar() - Method in class vcf.TargetData
 
nMetaInfoLines() - Method in class vcf.VcfHeader
Returns the number of VCF meta-information lines.
nNodes() - Method in interface dag.Dag
Returns the number of nodes in the DAG.
nNodes() - Method in class dag.ImmutableDag
 
nNodes() - Method in class dag.LinkageEquilibriumDag
 
nNodes() - Method in class sample.RecombSingleNodes
Returns the number of nodes.
nodeA() - Method in class dag.Score
Returns the root node index for the first tree.
nodeB() - Method in class dag.Score
Returns the root node index for the second tree.
nodeCount(int) - Method in class dag.MergeableDagLevel
Returns the sum of weights for the sequences that pass through the specified parent node or 0 if the parent node does not exist.
noErrProb(int) - Method in class sample.ImputationData
Returns (1f - this.errProb(marker)).
nonBufferedPrintWriter(File, boolean) - Static method in class blbutil.FileUtil
Returns an unbuffered java.io.PrintWriter writing to the specified file.
nonRefWt() - Method in class haplotype.Weights
Returns the non-reference sample weight.
NoPhaseGL - Class in vcf
Class NoPhaseGL is a wrapper for a GL instance that hides all genotype phase data in the wrapped object.
NoPhaseGL(GL) - Constructor for class vcf.NoPhaseGL
Constructs a new NoPhaseGL instance.
nOutEdges(int, int) - Method in interface dag.Dag
Returns the number of outgoing edges for the specified node of the DAG.
nOutEdges(int) - Method in interface dag.DagLevel
Returns the number of outgoing edges of the specified parent node at this level of the DAG.
nOutEdges(int) - Method in class dag.HighCapacityDagLevel
 
nOutEdges(int, int) - Method in class dag.ImmutableDag
 
nOutEdges(int, int) - Method in class dag.LinkageEquilibriumDag
 
nOutEdges(int) - Method in class dag.LowCapacityDagLevel
 
nParentNodes(int) - Method in interface dag.Dag
Returns the number of parent nodes at the specified level of the DAG.
nParentNodes() - Method in interface dag.DagLevel
Returns the number of parent nodes at this level of the DAG.
nParentNodes() - Method in class dag.HighCapacityDagLevel
 
nParentNodes(int) - Method in class dag.ImmutableDag
 
nParentNodes(int) - Method in class dag.LinkageEquilibriumDag
 
nParentNodes() - Method in class dag.LowCapacityDagLevel
 
nRefSamples() - Method in class main.CurrentData
Returns the number of reference samples.
nRefSamples() - Method in class vcf.AllData
 
nRefSamples() - Method in interface vcf.Data
Returns the number of reference samples.
nRefSamples() - Method in class vcf.TargetData
 
nSamples() - Method in class beagleutil.Samples
Returns the number of samples in this list.
nSamples() - Method in class haplotype.BasicSampleHapPairs
 
nSamples() - Method in class haplotype.GLSampleHapPairs
 
nSamples() - Method in class haplotype.RefHapPairs
 
nSamples() - Method in class haplotype.RevSampleHapPairs
 
nSamples() - Method in interface haplotype.SampleHapPairs
Returns the number of samples.
nSamples() - Method in interface main.AlleleProbs
Returns the number of samples.
nSamples() - Method in class main.BasicAlleleProbs
 
nSamples() - Method in class main.BasicGenotypeValues
 
nSamples() - Method in class main.ConstrainedAlleleProbs
 
nSamples() - Method in interface main.GenotypeValues
Returns the number of samples.
nSamples() - Method in class main.NuclearFamilies
Returns the number of samples.
nsamples() - Method in class main.Par
Return the nsamples parameter.
nSamples() - Method in class main.RevGenotypeValues
 
nSamples() - Method in class main.SampleHapPairAlleleProbs
 
nSamples() - Method in class sample.SamplerData
Returns the number of samples.
nSamples() - Method in interface vcf.AL
Returns the number of samples.
nSamples() - Method in class vcf.BasicGL
 
nSamples() - Method in class vcf.BitSetGT
 
nSamples() - Method in class vcf.BitSetRefGT
 
nSamples() - Method in class vcf.ByteArrayRefGT
 
nSamples() - Method in class vcf.FuzzyGL
 
nSamples() - Method in interface vcf.GL
Returns the number of samples.
nSamples() - Method in class vcf.HbdAL
 
nSamples() - Method in class vcf.LowMafRefDiallelicGT
 
nSamples() - Method in class vcf.LowMafRefGT
 
nSamples() - Method in class vcf.MaskedEndsGL
 
nSamples() - Method in class vcf.NoPhaseGL
 
nSamples() - Method in class vcf.RefGL
 
nSamples() - Method in class vcf.RestrictedVcfWindow
Returns the number of samples.
nSamples() - Method in class vcf.RevGL
 
nSamples() - Method in class vcf.SeqCodedRefGT
 
nSamples() - Method in class vcf.SplicedGL
 
nSamples() - Method in interface vcf.VcfEmission
Returns the number of samples.
nSamples() - Method in class vcf.VcfHeader
Returns the number of samples after sample exclusions.
nSamples() - Method in class vcf.VcfRecGTParser
Returns the number of samples.
nSamples() - Method in class vcf.VcfRecord
 
nSamples() - Method in class vcf.VcfWindow
Returns the number of samples.
nSamplesPerIndividual() - Method in class sample.RecombSingleBaum
 
nSamplesPerIndividual() - Method in class sample.SingleBaum
 
nSamplesPerIndividual() - Method in interface sample.SingleBaumInterface
Returns the number of haplotype pairs that are sampled for each individual.
nSegs() - Method in class sample.RefHapSegs
Returns the number of marker segments..
nSeq() - Method in class sample.RefHapSeg
Return the number of reference allele sequences in this segment.
nSeq(int) - Method in class sample.RefHapSegs
Return the number of distinct reference allele sequences in the specified chromosome segment.
nSeq() - Method in class vcf.VcfEmissionCompressor
Returns the number of distinct allele sequences in the list of compressed VcfEmission objects.
nSingles() - Method in class main.NuclearFamilies
Returns the number of single individuals in the list of samples.
nTargetMarkers() - Method in class main.CurrentData
Returns the number of target data markers.
nTargetMarkers() - Method in class vcf.AllData
 
nTargetMarkers() - Method in interface vcf.Data
Returns the number of target data markers in the current window.
nTargetMarkers() - Method in class vcf.TargetData
 
nTargetMarkersSoFar() - Method in class vcf.AllData
 
nTargetMarkersSoFar() - Method in interface vcf.Data
Returns the number of target VCF records in the union of the current window and all previous windows.
nTargetMarkersSoFar() - Method in class vcf.TargetData
 
nTargetSamples() - Method in class main.CurrentData
Returns the number of target samples.
nTargetSamples() - Method in class vcf.AllData
 
nTargetSamples() - Method in interface vcf.Data
Returns the number of target samples.
nTargetSamples() - Method in class vcf.TargetData
 
nthreads() - Method in class main.Par
Returns the nthreads parameter.
nTrios() - Method in class main.NuclearFamilies
Returns the number of parent-offspring trios in the list of samples.
NuclearFamilies - Class in main
Class NuclearFamilies stores parent-offspring relationships in a list of samples.
NuclearFamilies(Samples, File) - Constructor for class main.NuclearFamilies
Constructs a new NuclearFamilies instance.
nUnfilteredSamples() - Method in class vcf.VcfHeader
Returns the number of samples before sample exclusions.

O

out() - Method in class main.Par
Returns the out parameter.
outEdge(int, int, int) - Method in interface dag.Dag
Returns the index of the specified edge in the DAG.
outEdge(int, int) - Method in interface dag.DagLevel
Returns the index of the specified edge at this level of the DAG.
outEdge(int, int) - Method in class dag.HighCapacityDagLevel
 
outEdge(int, int, int) - Method in class dag.ImmutableDag
 
outEdge(int, int, int) - Method in class dag.LinkageEquilibriumDag
 
outEdge(int, int) - Method in class dag.LowCapacityDagLevel
 
outEdge(int, int) - Method in class dag.MergeableDagLevel
Returns the edge that is the outgoing edge of the specified parent parent node having the specified symbol, or returns -1 if no such edge exists.
outEdgeBySymbol(int, int, int) - Method in interface dag.Dag
Returns the index of the specified edge at the specified level of the DAG or -1 if no such edge exists.
outEdgeBySymbol(int, int) - Method in interface dag.DagLevel
Returns the index of the specified edge at this level of the DAG or -1 if no such edge exists.
outEdgeBySymbol(int, int) - Method in class dag.HighCapacityDagLevel
 
outEdgeBySymbol(int, int, int) - Method in class dag.ImmutableDag
 
outEdgeBySymbol(int, int, int) - Method in class dag.LinkageEquilibriumDag
 
outEdgeBySymbol(int, int) - Method in class dag.LowCapacityDagLevel
 
outPrefix() - Method in class main.WindowWriter
Returns the output file prefix.
overlap(ChromInterval, ChromInterval) - Static method in class beagleutil.ChromInterval
Returns true if the specified chromosome intervals have non-empty intersection and returns false otherwise.
overlap() - Method in class main.Par
Return the overlap parameter.
overlap() - Method in class vcf.AllData
 
overlap() - Method in interface vcf.Data
Returns the number of VCF records in the overlap between the current window and the previous window.
overlap() - Method in class vcf.RestrictedVcfWindow
Returns the number of VCF records in the overlap between the current window and the previous window.
overlap() - Method in class vcf.TargetData
 
overlap() - Method in class vcf.VcfWindow
Returns the number of VCF records in the overlap between the current window and the previous window.

P

Par - Class in main
Class Parameters represents the parameters for a Beagle analysis.
Par(String[]) - Constructor for class main.Par
Constructs a new Parameters instance from the specified command line arguments.
par() - Method in class sample.SamplerData
Returns the analysis parameters.
parentNode(int, int) - Method in interface dag.Dag
Returns the index of the specified parent node in the DAG.
parentNode(int) - Method in interface dag.DagLevel
Returns the index of the parent node of the specified edge at this level of the DAG.
parentNode(int) - Method in class dag.HighCapacityDagLevel
 
parentNode(int, int) - Method in class dag.ImmutableDag
 
parentNode(int, int) - Method in class dag.LinkageEquilibriumDag
 
parentNode(int) - Method in class dag.LowCapacityDagLevel
 
parentNode(int) - Method in class dag.MergeableDagLevel
Returns the parent node of the specified edge or -1 if the edge does not exist.
parentNode(int) - Method in class sample.HapBaumLevel
Returns the parent node of the specified HMM state with nonzero forward probability.
parentNode1(int) - Method in class sample.RecombSingleBaumLevel
Returns the parent node of the first edge of the specified HMM state with nonzero forward probability.
parentNode1(int) - Method in class sample.SingleBaumLevel
Returns the parent node of the first edge of the specified HMM state with nonzero forward probability.
parentNode2(int) - Method in class sample.RecombSingleBaumLevel
Returns the parent node of the second edge of the specified HMM state with nonzero forward probability.
parentNode2(int) - Method in class sample.SingleBaumLevel
Returns the parent node of the second edge of the specified HMM state with nonzero forward probability.
parentNodeA2(int) - Method in class sample.DuoBaumLevel
Returns the parent node of the second edge of the specified HMM state with nonzero forward probability.
parentNodeAB1(int) - Method in class sample.DuoBaumLevel
Returns the parent node of the first edge of the specified HMM state with nonzero forward probability.
parentNodeArray() - Method in class dag.MergeableDagLevel
Returns an array of parent node indices.
parentNodeB2(int) - Method in class sample.DuoBaumLevel
Returns the parent node of the third edge of the specified HMM state with nonzero forward probability.
parentProb(int, int) - Method in interface dag.Dag
Returns the ratio of the sum of the weights of the sequences that pass through the specified parent node of the DAG and the sum of the weights of all sequences.
parentProb(int) - Method in interface dag.DagLevel
Returns the parent node probability, which is defined to be the ratio of the sum of the weights of the sequences that pass through the specified parent node at this level of the DAG and the sum of the weights of the sequences that pass through any parent node at this level of the DAG.
parentProb(int) - Method in class dag.HighCapacityDagLevel
 
parentProb(int, int) - Method in class dag.ImmutableDag
 
parentProb(int, int) - Method in class dag.LinkageEquilibriumDag
 
parentProb(int) - Method in class dag.LowCapacityDagLevel
 
parentWeight(int, int) - Method in interface dag.Dag
Returns the sum of the weights of the sequences that pass through the specified node of the DAG.
parentWeight(int) - Method in interface dag.DagLevel
Returns the sum of weights for the sequences that pass through the specified node at this level of the DAG.
parentWeight(int) - Method in class dag.HighCapacityDagLevel
 
parentWeight(int, int) - Method in class dag.ImmutableDag
 
parentWeight(int, int) - Method in class dag.LinkageEquilibriumDag
 
parentWeight(int) - Method in class dag.LowCapacityDagLevel
 
parse(String) - Static method in class beagleutil.ChromInterval
Returns a ChromInterval instance corresponding to the specified string, or returns null if the specified string does not represent a valid chromosome interval or if the specified string is null.
ped() - Method in class main.Par
Returns the ped parameter or null if no ped parameter was specified.
Phase - Enum in beagleutil
Class Phase represents the equivalence of two phased genotypes for a marker or for a set of markers.
phase_its() - Method in class main.Par
Returns the phase-its parameter.
phasedSep - Static variable in class blbutil.Const
The phased allele separator: '|'
PL_FORMAT - Static variable in class vcf.VcfRecord
The VCF FORMAT code for phred-scaled genotype likelihood data: "PL".
PlinkGeneticMap - Class in main
Class PlinkGeneticMap represents a genetic map derived from a PLINK map file with map positions in cM units for one or more chromosomes.
POISON - Static variable in class sample.ConsumeSingleSamples
A sentinel Integer.
pos() - Method in class ibd.IbsHapSegments
Returns an array of non-decreasing marker positions whose j-th element is the position of marker this.haps().marker(j).
pos() - Method in class vcf.BasicMarker
 
pos() - Method in interface vcf.Marker
Returns the chromosome position coordinate.
posArray() - Method in interface dag.Dag
Returns an array of length this.nMarkers() whose j-th element is the distance from the root node to the child node at level j of the DAG.
posArray() - Method in class dag.ImmutableDag
 
posArray() - Method in class dag.LinkageEquilibriumDag
 
PositionMap - Class in main
Class PositionMap represents a genetic map obtained by multiplying chromosome position by a scale factor.
PositionMap(double) - Constructor for class main.PositionMap
Constructs a new PositionMap instance.
pRecomb(Markers, int, float) - Method in interface main.GeneticMap
Returns the an array of length hapPairs.nMarkers() whose whose j-th element for j > 0 is the probability of recombination between marker j - 1 and marker j, and whose initial element is 0.
pRecomb(int) - Method in class sample.ImputationData
Return the probability of recombination between the specified marker and the previous marker, or returns 0 if (marker == 0).
pRecomb(int) - Method in class sample.SamplerData
Returns the probability of recombination between (marker - 1) and marker.
PREFIX - Static variable in class vcf.VcfMetaInfo
The VCF meta-information line prefix: "##"
previous() - Method in class dag.MergeableDagLevel
Returns the previous DAG level or null if no previous level is stored.
prevSpliceStart() - Method in class main.CurrentData
Returns the first marker index after the splice point with the previous marker window.
prevTargetSpliceStart() - Method in class main.CurrentData
Returns the first target marker index after the splice point with the previous marker window.
print(AlleleProbs, boolean[], int, int, boolean, boolean, int) - Method in class main.WindowWriter
Prints the data in alProbs for markers with index between cd.lastSplice() (inclusive) and cd.nextSplice() (exclusive) to the output VCF file: this.outPrefix() + ".vcf.gz".
printDS() - Method in class vcf.VcfRecBuilder
Returns true if the FORMAT field in the VCF record for this marker includes a DS subfield, and false otherwise
printFixedFieldsGT(Marker, PrintWriter) - Static method in class vcf.VcfWriter
Prints the first 9 VCF record fields for the specified marker to the specified PrintWriter.
printGP() - Method in class vcf.VcfRecBuilder
Returns true if the FORMAT field in the VCF record for this marker includes a GP subfield, and false otherwise
printGV(CurrentData, GenotypeValues) - Method in class main.WindowWriter
Prints VCF records with GT and GP format fields for markers with index between cd.lastSplice() (inclusive) and cd.nextSplice() (exclusive).
printIbd(CurrentData, Map<IntPair, List<IbdSegment>>) - Method in class main.WindowWriter
Prints IBD segments that end between the markers with index between cd.lastSplice() (inclusive) and cd.nextSplice() (exclusive).
printImputationUpdate() - Method in class main.RunStats
Prints run time for most recent imputation to a log file and to standard output.
printIterationUpdate(int, int) - Method in class main.RunStats
Prints information about the specified iteration.
println(String) - Method in class main.RunStats
Prints the specified string to the log file and to standard out.
printMemoryUse(String) - Static method in class blbutil.Utilities
Prints a summary of memory use at the time of method invocation to standard output.
printRefinedIbdUpdate(float, Dag, long) - Method in class main.RunStats
Prints information about the Refined IBD analysis to a log file and to standard output.
printSampleSummary(NuclearFamilies, Data) - Method in class main.RunStats
Prints information about the samples to a log file and to standard output.
printStartInfo() - Method in class main.RunStats
Prints initial information about the analysis to a log file and to standard output.
printSummaryAndClose(int, int) - Method in class main.RunStats
Prints information about the complete analysis to a log file and to standard output, and closes the log file.
printWindowUpdate(Data) - Method in class main.RunStats
Prints information about the marker window to a log file and to standard output.
printWriter(File) - Static method in class blbutil.FileUtil
Returns a buffered java.io.PrintWriter writing to the specified file.
printWriter(File, boolean) - Static method in class blbutil.FileUtil
Returns a buffered java.io.PrintWriter writing to the specified file.
program - Static variable in class main.Main
The program name and version.
put(int, int) - Method in class blbutil.IndexMap
Adds the specified key and value to the map.

Q

qual() - Method in class vcf.VcfRecord
Returns the QUAL field.

R

R2Estimator - Class in vcf
Class R2Estimator estimates the correlation between the estimated allele dose and true allele dose for a set of genotypes.
R2Estimator() - Constructor for class vcf.R2Estimator
Constructs a new R2Estimator instance.
randomHapSample(int) - Method in class sample.LSHapBaum
Estimates and returns allele probabilities for the specified target haplotype.
randomSample(int) - Method in class sample.RecombSingleBaum
 
randomSample(int, double[]) - Method in class sample.RecombSingleBaum
 
randomSample(int) - Method in class sample.SingleBaum
 
randomSample(int, double[]) - Method in class sample.SingleBaum
 
randomSample(int) - Method in interface sample.SingleBaumInterface
Returns a list of this.nSamplesPerIndividual() sampled haplotype pairs for the specified individual.
randomSample(int, double[]) - Method in interface sample.SingleBaumInterface
Returns a list of this.nSamplesPerIndividual() sampled haplotype pairs for the specified individual.
rdag() - Method in class sample.SamplerData
Returns the DAG model.
RecombHapPairSampler - Class in main
Class RecombHapPairSamples samples haplotype pairs and estimates posterior genotype probabilities using a haplotype frequency model that permits transitions between any two states at adjacent markers.
RecombHapPairSampler(Par, RunStats) - Constructor for class main.RecombHapPairSampler
Constructs a new RecombHapPairSampler instance from the specified data.
recombRate() - Method in class main.CurrentData
Returns an array whose initial element is 0 and whose j-th element for j > 0 is the recombination rate between the target markers with indices (j - 1) and j.
RecombSingleBaum - Class in sample
Class RestrictedSingleBaum implements the Baum forward and backward algorithms for a hidden Markov model (HMM) of an individual's genotype data.
RecombSingleBaum(SamplerData, long, int, boolean) - Constructor for class sample.RecombSingleBaum
Creates a new RestrictedSingleBaum instance from the specified data.
RecombSingleBaumLevel - Class in sample
Class RestrictedSingleBaumLevel computes forward and backward Baum values at a level of a hidden Markov model (HMM) whose states are ordered edge pairs of a leveled directed acyclic graph (DAG).
RecombSingleBaumLevel(SamplerData) - Constructor for class sample.RecombSingleBaumLevel
Constructs a new RecombSingleBaumLevel instance from the specified data.
RecombSingleNodes - Class in sample
Class RecombSingleNodes stores ordered node pairs and associated values.
RecombSingleNodes(int) - Constructor for class sample.RecombSingleNodes
Creates a new instance of RecombSingleNodes that has an initial value of 0 for each ordered node pair.
ref() - Method in class main.Par
Returns the ref parameter or null if no ref parameter was specified.
refAllele(int, int) - Method in class sample.ImputationData
Returns the specified reference allele.
RefGL - Class in vcf
Class RefGL represents genotype emission probabilities for a reference panel of phased, non-missing genotypes.
RefGL(Samples, VcfEmission[]) - Constructor for class vcf.RefGL
Constructs a RefGL instance.
RefHapPairs - Class in haplotype
Class RefHapPairs stores a list of samples and a haplotype pair for each sample.
RefHapPairs(Markers, Samples, VcfEmission[]) - Constructor for class haplotype.RefHapPairs
Constructs a new RefHapPairs instance.
refHapPairs() - Method in class sample.HaplotypeCoder
Returns the reference haplotype pairs used to construct this.
refHapPairs() - Method in class sample.ImputationData
Return the reference haplotype pairs.
refHapPairs() - Method in class sample.RefHapSeg
Returns the reference haplotype pairs.
refHapPairs() - Method in class sample.RefHapSegs
Returns the reference haplotype pairs.
refHapPairs() - Method in class vcf.AllData
 
refHapPairs() - Method in interface vcf.Data
Returns a list of the reference haplotype pairs for the current window.
refHapPairs() - Method in class vcf.TargetData
 
RefHapSeg - Class in sample
Class RefHapSeg represents a chromosome segment of reference haplotypes.
RefHapSeg(SampleHapPairs, int, int) - Constructor for class sample.RefHapSeg
Constructs a new RefHapSegs instance from the specified data.
refHapSegs() - Method in class sample.ImputationData
Return the reference haplotype segments.
RefHapSegs - Class in sample
Class RefHapSegs represents reference haplotypes that span segments determined by non-overlapping clusters of markers.
RefHapSegs(SampleHapPairs, int[], int[]) - Constructor for class sample.RefHapSegs
Constructs a new RefHapSegs instance from the specified data.
RefIt - Class in vcf
Class RefIt represents an iterator whose next() method returns an object storing data from a VCF record with phased, non-missing genotypes.
refSampleHapPairs() - Method in class main.CurrentData
Returns a list of reference haplotype pairs, or returns null if there are no reference samples.
refSampleHapPairs() - Method in class vcf.AllData
 
refSampleHapPairs() - Method in interface vcf.Data
Returns the reference haplotype pairs for the current window.
refSampleHapPairs() - Method in class vcf.TargetData
 
refSamples() - Method in class main.CurrentData
Returns the list of reference samples, or null if there are no reference samples.
refSamples() - Method in class vcf.AllData
 
refSamples() - Method in interface vcf.Data
Returns the list of reference samples, or null if there are no reference samples.
refSamples() - Method in class vcf.TargetData
 
remove(E) - Method in class beagleutil.CenteredIntIntervalTree
 
remove(E) - Method in interface beagleutil.IntIntervalTree
Removes the specified element from this interval tree if the specified element is found in the interval tree.
remove() - Method in class blbutil.InputIt
The remove method is not supported by this iterator.
remove(int) - Method in class blbutil.IntSet
Removes the specified element from this set.
remove() - Method in class haplotype.HapsMarkerIterator
The remove method is not supported by this iterator.
remove() - Method in class vcf.BrefIt
The remove method is not supported by this iterator.
remove() - Method in class vcf.IntervalVcfIt
The remove method is not supported by this iterator.
remove() - Method in class vcf.RefIt
The remove method is not supported by this iterator.
remove() - Method in class vcf.VcfIt
The remove method is not supported by this iterator.
removeValues(int[], int) - Static method in class dag.DagUtil
Returns an array obtained by removing all elements in the specified array that equal the specified value.
removeValues(float[], float) - Static method in class dag.DagUtil
Returns an array obtained by removing all elements in the specified array that equal the specified value.
reset(int) - Method in class sample.RecombSingleBaumLevel
Resets the size of this level to 0 and resets the capacity of this level to the specified value.
reset(Marker, boolean, boolean) - Method in class vcf.VcfRecBuilder
Clears existing data, and sets the current marker to the specified marker.
restrict(int, int) - Method in class ibd.Haplotype
Returns a new Haplotype instance that is obtained by restricting this haplotype to the specified marker interval.
restrict(int, int) - Method in class vcf.Markers
Returns a Markers instance that represents the specified range of marker indices.
RestrictedDag - Class in sample
Class RestrictedDag is a wrapper for a Dag object that stores segments of identity by descent.
RestrictedDag(SampleHapPairs, float[], int, float, double, double) - Constructor for class sample.RestrictedDag
Constructs a RestrictedDag instance.
restrictedRefHapPairs() - Method in class vcf.AllData
 
restrictedRefHapPairs() - Method in interface vcf.Data
Returns a list of reference haplotype pairs that are restricted to the target data markers in the current window.
restrictedRefHapPairs() - Method in class vcf.TargetData
 
restrictedRefSampleHapPairs() - Method in class main.CurrentData
Returns a list of reference haplotype pairs that are restricted to the target data markers, or returns null if there are no reference samples.
RestrictedVcfWindow - Class in vcf
Class RestrictedVcfWindow represents a sliding window of VCF records.
RestrictedVcfWindow(SampleFileIt<? extends VcfEmission>) - Constructor for class vcf.RestrictedVcfWindow
Construct a new RestrictedVcfWindow instance.
reverse() - Method in class vcf.Markers
Constructs and returns a new Markers instance that is obtained by reversing the order of markers in this.
RevGenotypeValues - Class in main
Class RevGenotypeValues is a wrapper for a GenotypeValues instance.
RevGenotypeValues(GenotypeValues) - Constructor for class main.RevGenotypeValues
Constructs a new RevGenotypeValues instance from the specified data.
RevGL - Class in vcf
Class RevGL is wrapper for a GL instance.
RevGL(GL) - Constructor for class vcf.RevGL
Constructs a new RevGL instance.
RevHapPair - Class in haplotype
Class RevHapPair is a wrapper for a HapPair instance.
RevHapPair(HapPair) - Constructor for class haplotype.RevHapPair
Creates a new RevHapPair instance from the specified data.
RevHapPairs - Class in haplotype
Class RevHapPairs is a wrapper for a HapPairs instance.
RevHapPairs(HapPairs) - Constructor for class haplotype.RevHapPairs
Creates a new RevSampleHapPairs instance from the specified data.
RevSampleHapPairs - Class in haplotype
Class RevSampleHapPairs is a wrapper for a SampleHapPairs instance.
RevSampleHapPairs(SampleHapPairs) - Constructor for class haplotype.RevSampleHapPairs
Creates a new RevSampleHapPairs instance from the specified data.
run(List<HapPair>) - Static method in class haplotype.ConsensusPhaser
Returns a list of consensus haplotype pairs (one pair per individual) sorted in order of increasing sample index.
run(List<HapPair>, GL, long) - Static method in class haplotype.GenotypeCorrection
Removes any inconsistencies between the specified list of haplotype pairs and the genotypes determined by the allele1() and allele2() methods of the specified genotype likelihoods.
run(List<HapPair>, GL, long, File, boolean) - Static method in class haplotype.GenotypeCorrection
Removes any inconsistencies between the specified list of haplotype pairs and the genotypes determined by the allele1() and allele2() methods of the specified genotype likelihoods.
run(GL, Dag, SampleHapPairs, int) - Method in class ibd.HaploidIbd
Runs the Refined IBD algorithm, and returns a map whose keys are ordered pairs of haplotype indices and whose values are thread-safe lists of IBD segments for each haplotype pair.
run() - Method in class sample.ConsumeSingleSamples
Takes sample indices from the thread-safe work-queue specified at time of construction and samples haplotype pairs for each sample.
run(int, int) - Method in class sample.HaplotypeCoder
Returns a two element array whose first element maps each reference haplotype index to the index of the allele sequence carried by that reference haplotype, and whose second element maps each target haplotype index to the index of the allele sequence carried by that target haplotype.
RunStats - Class in main
Class RunStats contains methods for storing and printing statistics describing a Beagle analysis.

S

sample - package sample
 
sample(CurrentData, List<HapPair>, boolean, GenotypeValues) - Method in class main.HapPairSampler
Returns a list of sampled haplotype pairs.
sample(CurrentData, SampleHapPairs) - Method in class main.LiAndStephensHapSampler
Returns estimated allele probabilities for each target sample.
sample(CurrentData, List<HapPair>, boolean, GenotypeValues) - Method in class main.RecombHapPairSampler
Returns a list of sampled haplotype pairs.
sampleData(int) - Method in class vcf.VcfRecord
Returns the data for the specified sample.
sampleData(int, String) - Method in class vcf.VcfRecord
Returns the specified data for the specified sample.
sampleData(int, int) - Method in class vcf.VcfRecord
Returns the specified data for the specified sample.
SampleFileIt<E> - Interface in blbutil
An iterator for records in a file.
sampleFilter(File) - Static method in class vcf.FilterUtil
Returns a filter that excludes samples that have an identifier that matches a line of the specified file, or returns null if the excludeSamplesFile parameter is null
SampleGenotypeValues - Class in main
Class SampleGenotypeValues stores a value for each possible genotype at each marker for one sample.
SampleGenotypeValues(Markers, Samples, int) - Constructor for class main.SampleGenotypeValues
Constructs a SampleGenotypeValues instance for the specified markers and sample with initial value 0 for each possible genotype at each marker.
SampleHapPairAlleleProbs - Class in main
Class SampleHapPairAlleleProbs is a wrapper for a SampleHapPairs instance.
SampleHapPairAlleleProbs(SampleHapPairs) - Constructor for class main.SampleHapPairAlleleProbs
Constructs a new SampleHapPairAlleleProbs instance that wraps the specified SampleHapPairs object.
SampleHapPairs - Interface in haplotype
Interface SampleHapPairs represents a list of samples and a haplotype pair for each sample.
sampleHapPairs() - Method in class ibd.Haplotype
Returns the sample haplotype pairs.
sampleHaps() - Method in class sample.RestrictedDag
Returns the haplotypes used to construct this.
SampleIds - Class in beagleutil
Class SampleIds is a singleton class that represents a list of sample identifiers.
sampleIds() - Method in class vcf.VcfHeader
Returns this.sample().ids().
sampleIndex(int) - Method in class haplotype.BasicHapPairs
 
sampleIndex(int) - Method in class haplotype.BasicSampleHapPairs
 
sampleIndex() - Method in class haplotype.BitHapPair
 
sampleIndex(int) - Method in class haplotype.GLSampleHapPairs
 
sampleIndex() - Method in interface haplotype.HapPair
Returns the index of the sample associated with this haplotype pair in the list of samples returned by this.samples().
sampleIndex(int) - Method in interface haplotype.HapPairs
Returns the index of the sample associated with the specified haplotype pair in the list of samples returned by this.samples().
sampleIndex(int) - Method in class haplotype.RefHapPairs
 
sampleIndex() - Method in class haplotype.RevHapPair
 
sampleIndex(int) - Method in class haplotype.RevHapPairs
 
sampleIndex(int) - Method in class haplotype.RevSampleHapPairs
 
sampleIndex() - Method in class haplotype.WrappedHapPair
 
sampleIndex() - Method in class main.SampleGenotypeValues
Returns the sample index.
sampleNanos(long) - Method in class main.RunStats
Stores the time for sampling new haplotypes and increases the cumulative sampling time by the specified number of nanoseconds.
SamplerData - Class in sample
Class SamplerData contains immutable input data for the current marker window.
SamplerData(Par, CurrentData, List<HapPair>, boolean, RunStats) - Constructor for class sample.SamplerData
Constructs a new SamplerData instance from the specified data.
Samples - Class in beagleutil
Class Samples stores a list of samples.
Samples(int[]) - Constructor for class beagleutil.Samples
Constructs a new instance of Samples corresponding to the specified list of sample identifier indices.
samples() - Method in interface blbutil.SampleFileIt
Returns the list of samples.
samples(int) - Method in class haplotype.BasicHapPairs
 
samples() - Method in class haplotype.BasicSampleHapPairs
 
samples(int) - Method in class haplotype.BasicSampleHapPairs
 
samples() - Method in class haplotype.BitHapPair
 
samples() - Method in class haplotype.GLSampleHapPairs
 
samples(int) - Method in class haplotype.GLSampleHapPairs
 
samples() - Method in interface haplotype.HapPair
Returns the list of samples containing the sample associated with this haplotype pair.
samples(int) - Method in interface haplotype.HapPairs
Returns a list of samples containing the sample associated with the specified haplotype pair
samples() - Method in class haplotype.RefHapPairs
 
samples(int) - Method in class haplotype.RefHapPairs
 
samples() - Method in class haplotype.RevHapPair
 
samples(int) - Method in class haplotype.RevHapPairs
 
samples() - Method in class haplotype.RevSampleHapPairs
 
samples(int) - Method in class haplotype.RevSampleHapPairs
 
samples() - Method in interface haplotype.SampleHapPairs
Returns the samples.
samples() - Method in class haplotype.WrappedHapPair
 
samples() - Method in interface main.AlleleProbs
Returns the list of samples.
samples() - Method in class main.BasicAlleleProbs
 
samples() - Method in class main.BasicGenotypeValues
 
samples() - Method in class main.ConstrainedAlleleProbs
 
samples() - Method in interface main.GenotypeValues
Returns the list of samples.
samples() - Method in interface main.HapAlleleProbs
Returns the list of samples.
samples() - Method in class main.LowMemHapAlleleProbs
 
samples() - Method in class main.NuclearFamilies
Returns the list of samples.
samples() - Method in class main.RevGenotypeValues
 
samples() - Method in class main.SampleGenotypeValues
Returns the list of samples.
samples() - Method in class main.SampleHapPairAlleleProbs
 
samples() - Method in class main.WindowWriter
Returns the samples whose data is written by this.
samples() - Method in interface vcf.AL
Returns the list of samples.
samples() - Method in class vcf.BasicGL
 
samples() - Method in class vcf.BitSetGT
 
samples() - Method in class vcf.BitSetRefGT
Returns the samples.
samples() - Method in class vcf.BrefIt
 
samples() - Method in class vcf.ByteArrayRefGT
Returns the samples.
samples() - Method in class vcf.FuzzyGL
 
samples() - Method in interface vcf.GL
Returns the list of samples.
samples() - Method in class vcf.HbdAL
 
samples() - Method in class vcf.IntervalVcfIt
 
samples() - Method in class vcf.LowMafRefDiallelicGT
 
samples() - Method in class vcf.LowMafRefGT
 
samples() - Method in class vcf.MaskedEndsGL
 
samples() - Method in class vcf.NoPhaseGL
 
samples() - Method in class vcf.RefGL
 
samples() - Method in class vcf.RefIt
 
samples() - Method in class vcf.RestrictedVcfWindow
Returns the list of samples.
samples() - Method in class vcf.RevGL
 
samples() - Method in class vcf.SeqCodedRefGT
 
samples() - Method in class vcf.SplicedGL
 
samples() - Method in interface vcf.VcfEmission
Returns the list of samples.
samples() - Method in class vcf.VcfEmissionCompressor
Returns the list of samples whose phased genotype data will be compressed.
samples() - Method in class vcf.VcfHeader
Return the list of samples after sample exclusions.
samples() - Method in class vcf.VcfIt
 
samples() - Method in class vcf.VcfRecGTParser
Returns the list of samples.
samples() - Method in class vcf.VcfRecord
 
samples() - Method in class vcf.VcfWindow
Returns the list of samples.
scaleFactor() - Method in class main.PositionMap
Returns the scale factor that is multiplied by the chromosome position to obtain the corresponding genetic map position
Score - Class in dag
Class Score represents a similarity score for a pair of trees.
Score(int, int, float, boolean) - Constructor for class dag.Score
Constructs a new Score instance.
score() - Method in class dag.Score
Returns the similarity score for the two trees.
score() - Method in class ibd.IbdSegment
Returns the IBD segment score.
second() - Method in class blbutil.IntPair
Returns the second integer in the ordered pair of integers.
seed() - Method in class main.Par
Returns the seed parameter.
seed() - Method in class sample.RecombSingleBaum
 
seed() - Method in class sample.SingleBaum
 
seed() - Method in interface sample.SingleBaumInterface
Returns the initial random seed.
segEnd(int) - Method in class sample.RefHapSegs
Returns the index of the last marker (exclusive) in the specified marker segment.
segStart(int) - Method in class sample.RefHapSegs
Returns the index of the first marker (inclusive) in the specified marker segment.
semicolon - Static variable in class blbutil.Const
The semicolon character: ';'
seq(int) - Method in class sample.RefHapSeg
Return the index of the reference allele sequence in this segment for the specified reference haplotype.
seq(int, int) - Method in class sample.RefHapSegs
Return the index of the allele sequence in the specified chromosome segment for the specified reference haplotype.
SeqCodedRefGT - Class in vcf
Class SeqCodedRefGT represents phased, non-missing genotypes for a list of reference samples at a single marker.
SeqCodedRefGT(Marker, Samples, IntArray, IntArray) - Constructor for class vcf.SeqCodedRefGT
Creates a new SeqCodedRefGT instance with phased, non-missing genotypes from the specified marker, samples, and haplotype alleles.
seqToAllele(int) - Method in class vcf.VcfEmissionCompressor
Returns an array of length this.nSeq() whose j-th element is the allele carried by the j-th distinct allele sequence at this.marker(index).
set(int, int) - Method in class blbutil.IntList
Replaces the element at the specified position in this list with the specified element.
setBackwardValues(DuoNodes) - Method in class sample.DuoBaumLevel
Sets the Baum backward algorithm values for this level of the HMM and stores the parent node trio values in the specified nodes parameter.
setBackwardValues(HapNodes) - Method in class sample.HapBaumLevel
Sets the Baum backward algorithm values for this level of the HMM and stores the parent node values in the specified nodes parameter.
setBackwardValues(RecombSingleNodes) - Method in class sample.RecombSingleBaumLevel
Sets the Baum backward algorithm values for this level of the HMM and stores the parent node pair values in the specified nodes parameter.
setBackwardValues(SingleNodes) - Method in class sample.SingleBaumLevel
Sets the Baum backward algorithm values for this level of the HMM and stores the parent node pair values in the specified nodes parameter.
setCapacity(int) - Method in class blbutil.IntSet
Sets the capacity of this list to the specified value.
setChildNodes(DuoNodes) - Method in class sample.DuoBaumLevel
Stores the Baum forward algorithm child node trio values for this level of the HMM in the specified DuoNodes object.
setChildNodes(HapNodes) - Method in class sample.HapBaumLevel
Stores the Baum forward algorithm child node values for this level of the HMM in the specified HapNodes object.
setChildNodes(RecombSingleNodes) - Method in class sample.RecombSingleBaumLevel
Stores the Baum forward algorithm child node pair values for this level of the HMM in the specified SingleNodes object.
setChildNodes(SingleNodes) - Method in class sample.SingleBaumLevel
Stores the Baum forward algorithm child node pair values for this level of the HMM in the specified SingleNodes object.
setDagStats(Dag) - Method in class main.RunStats
Stores statistics for the DAG model used to sample single individuals.
setForwardValues(DuoNodes, int, int, int) - Method in class sample.DuoBaumLevel
Sets the Baum forward algorithm values for this level of the HMM and records the child node trio values in the specified nodes parameter.
setForwardValues(HapNodes, int, int) - Method in class sample.HapBaumLevel
Sets the Baum forward algorithm values for this level of the HMM and records the child node values in the specified nodes parameter.
setForwardValues(RecombSingleNodes, DiploidStates, int, int) - Method in class sample.RecombSingleBaumLevel
Sets the Baum forward algorithm values for this level of the HMM and records the child node pair values in the specified nodes parameter.
setForwardValues(SingleNodes, int, int) - Method in class sample.SingleBaumLevel
Sets the Baum forward algorithm values for this level of the HMM and records the child node pair values in the specified nodes parameter.
setInitialBackwardValues(RecombSingleNodes) - Method in class sample.RecombSingleBaumLevel
Initializes the node pair values for the Baum backward algorithm.
setMarker(int) - Method in interface sample.DiploidStates
Initializes the iteration of permitted ordered edge pairs for the specified marker.
setNextLevel(MergeableDagLevel) - Method in class dag.MergeableDagLevel
Sets the next level to the specified MergeableDagLevel.
setPreviousToNull() - Method in class dag.MergeableDagLevel
Sets the previous DAG level to null, and returns the previous DAG level that existed immediately prior to the invocation of this method.
ShiftedByteIndexArray - Class in blbutil
Class ShiftedByteIndexArray represents an immutable int[] array that is stored as a byte[] array.
ShiftedByteIndexArray(int[]) - Constructor for class blbutil.ShiftedByteIndexArray
Constructs a new ShiftedByteIndexArray instance.
ShiftedByteIndexArray(int[], int, int) - Constructor for class blbutil.ShiftedByteIndexArray
Constructs a new ShiftedByteIndexArray instance from the specified subarray.
shortHelp - Static variable in class main.Main
The program name and a brief help message.
single(int) - Method in class main.NuclearFamilies
Returns the sample index of the specified single individual.
SingleBaum - Class in sample
Class SingleBaum implements the Baum forward and backward algorithms for a hidden Markov model (HMM) of an individual's genotype data.
SingleBaum(Dag, GL, long, int, boolean) - Constructor for class sample.SingleBaum
Creates a new SingleBaum instance from the specified data.
SingleBaumInterface - Interface in sample
Interface SingleBaumInterface has methods for sampling haplotype pairs.
SingleBaumLevel - Class in sample
Class SingleBaumLevel computes forward and backward Baum values at a level of a hidden Markov model (HMM) whose states are ordered edge pairs of a leveled directed acyclic graph (DAG).
SingleBaumLevel(Dag, GL) - Constructor for class sample.SingleBaumLevel
Constructs a new SingleBaumLevel instance from the specified data.
SingleNodes - Class in sample
Class SingleNodes stores ordered node pairs and associated values.
SingleNodes() - Constructor for class sample.SingleNodes
Creates a new instance of SingleNodes that has an initial value of 0 for each ordered node pair.
singleStates(int) - Method in class sample.RestrictedDag
Returns the permitted states for the specified sample.
size() - Method in class beagleutil.CenteredIntIntervalTree
 
size() - Method in class beagleutil.ChromIds
Returns the number of indexed chromosomes identifiers.
size() - Method in interface beagleutil.IntIntervalTree
Returns the number of elements in this interval tree.
size() - Method in class beagleutil.SampleIds
Returns the number of indexed sample identifiers.
size() - Method in class beagleutil.ThreadSafeIndexer
Returns the number of indexed objects.
size() - Method in class blbutil.ByteIndexArray
 
size() - Method in class blbutil.CharIndexArray
 
size() - Method in class blbutil.IndexMap
Returns the number of key-value pairs in the map.
size() - Method in class blbutil.IndexSet
Returns the number of elements in this set.
size() - Method in interface blbutil.IntArray
Returns the number of elements.
size() - Method in class blbutil.IntList
Returns the number of elements in this list.
size() - Method in class blbutil.IntSet
Returns the number of elements in this set.
size() - Method in class blbutil.ShiftedByteIndexArray
 
size() - Method in class blbutil.WrappedIntArray
 
size() - Method in class sample.DuoBaumLevel
Return the number of states with nonzero forward probability at this level of the HMM.
size() - Method in class sample.DuoNodes
Returns the number of node trios with non-zero value.
size() - Method in class sample.HapBaumLevel
Return the number of states with nonzero forward probability at this level of the HMM.
size() - Method in class sample.HapNodes
Returns the number of nodes with non-zero value.
size() - Method in class sample.RecombSingleBaumLevel
Return the number of states with nonzero forward probability at this level of the HMM.
size() - Method in class sample.RecombSingleNodes
Returns the number of node pairs with non-zero value.
size() - Method in class sample.SingleBaumLevel
Return the number of states with nonzero forward probability at this level of the HMM.
size() - Method in class sample.SingleNodes
Returns the number of node pairs with non-zero value.
size() - Method in class vcf.VcfEmissionCompressor
Returns the size of the list of compressed VcfEmission objects.
size() - Method in class vcf.VcfWindow
Returns the number of VCF records in the current window.
SplicedGL - Class in vcf
Class SplicedGL represents genotype emission probabilities for a set of samples.
SplicedGL(SampleHapPairs, GL) - Constructor for class vcf.SplicedGL
Constructs a new SplicedGL instance.
start() - Method in class beagleutil.BasicIntInterval
 
start() - Method in class beagleutil.CenteredIntIntervalTree
 
start() - Method in class beagleutil.ChromInterval
Returns the first genome coordinate in this chromosome interval.
start() - Method in interface beagleutil.IntInterval
Returns the start of the interval (inclusive).
start() - Method in interface beagleutil.IntIntervalTree
Returns the minimum start (inclusive) of an interval that can be stored in this interval tree.
start() - Method in class ibd.HapSegment
Returns the start marker index (inclusive).
start() - Method in class ibd.IbdSegment
Returns the starting marker (inclusive).
start() - Method in class sample.RefHapSeg
Returns the starting marker index (inclusive) of this segment.
startIndex() - Method in class ibd.IbdSegment
Returns the starting marker index (inclusive) or -1 if the starting marker index is unknown.
stdOutPrintWriter() - Static method in class blbutil.FileUtil
Returns a java.io.PrintWriter that writes to standard out.
storesNonMajorIndices(int) - Method in class haplotype.BasicSampleHapPairs
 
storesNonMajorIndices(int) - Method in class haplotype.GLSampleHapPairs
 
storesNonMajorIndices(int) - Method in class haplotype.RefHapPairs
 
storesNonMajorIndices(int) - Method in class haplotype.RevSampleHapPairs
 
storesNonMajorIndices(int) - Method in interface haplotype.SampleHapPairs
Returns true if this object stores the indices of haplotypes that carry non-major alleles, and returns false otherwise.
storesNonMajorIndices() - Method in class vcf.BitSetGT
 
storesNonMajorIndices() - Method in class vcf.BitSetRefGT
 
storesNonMajorIndices() - Method in class vcf.ByteArrayRefGT
 
storesNonMajorIndices() - Method in class vcf.LowMafRefDiallelicGT
 
storesNonMajorIndices() - Method in class vcf.LowMafRefGT
 
storesNonMajorIndices() - Method in class vcf.SeqCodedRefGT
 
storesNonMajorIndices() - Method in interface vcf.VcfEmission
Returns true if this instance stores the indices of haplotypes that carry non-major alleles, and returns false otherwise.
storesNonMajorIndices() - Method in class vcf.VcfRecord
 
stringArg(String, Map<String, String>, boolean, String, String[]) - Static method in class blbutil.Validate
Removes the specified key from the specified map, and returns the string value corresponding to the specified key.
StringUtil - Class in blbutil
Class StringUtil is a utility class with static methods for counting and returning delimited fields in a string.
sumAlleles(int) - Method in class vcf.Markers
Returns the sum of the number of alleles for the markers with index less than the specified index.
sumAlleles() - Method in class vcf.Markers
Returns this.sumAlleles(this.nMarkers()).
sumGenotypes(int) - Method in class vcf.Markers
Returns the sum of the number of possible genotypes for the markers with index less than the specified index.
sumGenotypes() - Method in class vcf.Markers
Returns this.sumGenotypes(this.nMarkers()).
sumHaplotypeBits(int) - Method in class vcf.Markers
Returns the number of bits requires to store a haplotype for the markers with index less than the specified index.
sumHaplotypeBits() - Method in class vcf.Markers
Returns this.sumHaplotypeBits(this.nMarkers()).
sumNode1Value(int) - Method in class sample.RecombSingleNodes
Returns the sum of the values of the node pairs that have the specified first node
sumNode2Value(int) - Method in class sample.RecombSingleNodes
Returns the sum of the values of the node pairs that have the specified second node.
sumUpdate(int, int, int, float) - Method in class sample.DuoNodes
Adds the specified value to the stored value of the specified node trio.
sumUpdate(int, float) - Method in class sample.HapNodes
Adds the specified value to the stored value of the specified node.
sumUpdate(int, int, float) - Method in class sample.RecombSingleNodes
Adds the specified positive value to the stored value of the specified node pair.
sumUpdate(int, int, float) - Method in class sample.SingleNodes
Adds the specified positive value to the stored value of the specified node pair.
sumValue() - Method in class sample.RecombSingleNodes
Returns the sum of the values of all node pairs.
symbol(int, int) - Method in interface dag.Dag
Returns the symbol labeling the specified edge of the DAG.
symbol(int) - Method in interface dag.DagLevel
Returns the symbol labeling the specified edge at this level of the DAG.
symbol(int) - Method in class dag.HighCapacityDagLevel
 
symbol(int, int) - Method in class dag.ImmutableDag
 
symbol(int, int) - Method in class dag.LinkageEquilibriumDag
 
symbol(int) - Method in class dag.LowCapacityDagLevel
 
symbol(int) - Method in class sample.HapBaumLevel
Returns the symbol of the specified HMM state with nonzero forward probability.
symbol1(int) - Method in class sample.RecombSingleBaumLevel
Returns the symbol for the first edge of the specified HMM state with nonzero forward probability.
symbol1(int) - Method in class sample.SingleBaumLevel
Returns the symbol for the first edge of the specified HMM state with nonzero forward probability.
symbol2(int) - Method in class sample.RecombSingleBaumLevel
Returns the symbol for the second edge of the specified HMM state with nonzero forward probability.
symbol2(int) - Method in class sample.SingleBaumLevel
Returns the symbol for the second edge of the specified HMM state with nonzero forward probability.
symbolA2(int) - Method in class sample.DuoBaumLevel
Returns the symbol for the second edge of the specified HMM state with nonzero forward probability.
symbolAB1(int) - Method in class sample.DuoBaumLevel
Returns the symbol for the first edge of the specified HMM state with nonzero forward probability.
symbolB2(int) - Method in class sample.DuoBaumLevel
Returns the symbol for the third edge of the specified HMM state with nonzero forward probability.

T

tab - Static variable in class blbutil.Const
The tab character: '\t'
targetAllele(int, int) - Method in class sample.ImputationData
Returns the specified target allele.
TargetData - Class in vcf
Class TargetData represents a sliding window of target VCF records.
targetData(SampleFileIt<? extends VcfEmission>) - Static method in class vcf.TargetData
Constructs and returns a new TargetData instance from VcfRecords returned by the specified SampleFileIt objects.
targetGL() - Method in class main.CurrentData
Returns the genotype likelihoods for the target samples at the target data markers.
targetGL() - Method in class vcf.AllData
 
targetGL() - Method in interface vcf.Data
Returns the genotype likelihoods for the target samples restricted to the target data markers in the current window.
targetGL() - Method in class vcf.TargetData
 
targetHapPairs() - Method in class sample.HaplotypeCoder
Returns the target haplotype pairs used to construct this.
targetMarkerIndex(int) - Method in class main.CurrentData
Returns the index of the specified marker in the target data, or returns -1 if the marker is not present in the target data.
targetMarkerIndex(int) - Method in class vcf.AllData
 
targetMarkerIndex(int) - Method in interface vcf.Data
Returns the target data marker index corresponding to the specified marker, or returns -1 if no corresponding target data marker exists.
targetMarkerIndex(int) - Method in class vcf.TargetData
 
targetMarkerIndices() - Method in class main.CurrentData
Returns an array of length this.nMarkers() whose k-th element is the index of the k-th marker in the list of target markers or is -1 if the marker is not present in the target data.
targetMarkers() - Method in class main.CurrentData
Returns the list of target data markers.
targetMarkers() - Method in class vcf.AllData
 
targetMarkers() - Method in interface vcf.Data
Returns the list of target data markers in the current window.
targetMarkers() - Method in class vcf.TargetData
 
targetOverlap() - Method in class vcf.AllData
 
targetOverlap() - Method in interface vcf.Data
Returns the number of target data markers in the overlap between the current marker window and the previous marker window.
targetOverlap() - Method in class vcf.TargetData
 
targetSamples() - Method in class main.CurrentData
Returns the list of target samples.
targetSamples() - Method in class sample.ImputationData
Returns the list of target samples.
targetSamples() - Method in class vcf.AllData
 
targetSamples() - Method in interface vcf.Data
Returns the list of target samples.
targetSamples() - Method in class vcf.TargetData
 
targHapPairs() - Method in class sample.ImputationData
Return the target haplotype pairs.
tempFile(String) - Static method in class blbutil.FileUtil
Returns a temporary File that will be deleted when the Java virtual machine exits.
ThreadSafeIndexer<T> - Class in beagleutil
Class ThreadSafeIndexer indexes objects.
ThreadSafeIndexer() - Constructor for class beagleutil.ThreadSafeIndexer
Creates a new ThreadSafeIndexer instance with the default initial capacity.
ThreadSafeIndexer(int) - Constructor for class beagleutil.ThreadSafeIndexer
Creates a new ThreadSafeIndexerinstance with the specified initial capacity.
timeStamp() - Static method in class blbutil.Utilities
Returns the current local time as a string.
toArray() - Method in class beagleutil.CenteredIntIntervalTree
 
toArray() - Method in interface beagleutil.IntIntervalTree
Returns an array containing all of the elements of this interval tree.
toArray() - Method in class blbutil.IndexSet
Returns an array containing the elements in this set.
toArray() - Method in class blbutil.IntList
Returns an integer array containing the sequence of elements in this list.
toArray() - Method in class blbutil.IntSet
Returns an array containing the elements in this set.
toBitSetGT - Static variable in class vcf.VcfIt
A function mapping a string VCF record with GT format fields to a VcfEmission object.
toDagLevel() - Method in class dag.MergeableDagLevel
Returns an immutable DagLevel corresponding to this.
toGLRec - Static variable in class vcf.VcfIt
A function mapping a string VCF record with GL format fields to a VcfRecord object.
toGTGLRec - Static variable in class vcf.VcfIt
A function mapping a string VCF record with GT or GL format fields to a VcfRecord object.
toRef - Static variable in class vcf.RefIt
 
toString() - Method in class beagleutil.BasicIntInterval
Returns a string representation of this.
toString() - Method in class beagleutil.CenteredIntIntervalTree
Returns a string representation of this.
toString() - Method in class beagleutil.ChromIds
Returns java.util.Arrays.toString(this.ids()).
toString() - Method in class beagleutil.ChromInterval
Returns the string: this.chrom() + ":" + this.start() + "-" + this.end()
toString() - Method in class beagleutil.SampleIds
Returns java.util.Arrays.toString(this.ids()).
toString() - Method in class beagleutil.Samples
Returns java.util.Arrays.toString(this.ids()).
toString() - Method in class beagleutil.ThreadSafeIndexer
Returns this.items().toString().
toString() - Method in class blbutil.ByteIndexArray
 
toString() - Method in class blbutil.CharIndexArray
 
toString() - Method in interface blbutil.FileIt
Returns a string representation of this.
toString() - Method in class blbutil.IndexMap
Returns a string representation of this.
toString() - Method in class blbutil.IndexSet
Returns java.util.Arrays.toString(this.toArray()).
toString() - Method in class blbutil.InputIt
Returns a string representation of this iterator.
toString() - Method in interface blbutil.IntArray
Returns a string representation of this IntArray by applying java.utils.Arrays.toString() to an equivalent int[] object.
toString() - Method in class blbutil.IntList
Returns java.util.Arrays.toString(this.toArray())
toString() - Method in class blbutil.IntPair
Returns a string representation of this.
toString() - Method in class blbutil.IntSet
Returns java.util.Arrays.toString(this.toArray()).
toString() - Method in class blbutil.ShiftedByteIndexArray
 
toString() - Method in class blbutil.WrappedIntArray
 
toString(int, int) - Method in interface dag.Dag
Returns a description of the specified levels of the DAG.
toString() - Method in interface dag.Dag
Returns a string representation of this.
toString() - Method in interface dag.DagLevel
Returns a string representation of this.
toString() - Method in class dag.HighCapacityDagLevel
 
toString(int, int) - Method in class dag.ImmutableDag
 
toString() - Method in class dag.ImmutableDag
 
toString(int, int) - Method in class dag.LinkageEquilibriumDag
 
toString() - Method in class dag.LowCapacityDagLevel
 
toString() - Method in class dag.MergeableDag
Returns a string description of this.
toString() - Method in class dag.MergeableDagLevel
Returns a string representation of this.
toString() - Method in class dag.Score
Returns a string representation of this.
toString() - Method in class haplotype.BasicHapPairs
Returns a string representation of this.
toString() - Method in class haplotype.BitHapPair
Returns a string representation of this.
toString() - Method in class haplotype.RevHapPairs
Returns a string representation of this.
toString() - Method in class ibd.Haplotype
Returns a string representation of this.
toString() - Method in class ibd.HapSegment
Returns a string representation of this.
toString() - Method in class ibd.IbdSegment
Returns a string representation of this.
toString() - Method in class main.BasicGenotypeValues
 
toString() - Method in interface main.GeneticMap
Returns a string representation of this genetic map.
toString() - Method in interface main.GenotypeValues
Returns a string representation of this.
toString() - Method in class main.LowMemHapAlleleProbs
Returns a string representation of this.
toString() - Method in class main.NuclearFamilies
Returns a string representation of this.
toString() - Method in class main.PlinkGeneticMap
 
toString() - Method in class main.RevGenotypeValues
 
toString() - Method in class main.SampleGenotypeValues
Returns a string representation of this.
toString() - Method in class sample.DuoBaumLevel
Returns a string description of this.
toString() - Method in class sample.DuoNodes
Returns a string representation of this.
toString() - Method in class sample.HapBaumLevel
Returns a string description of this.
toString() - Method in class sample.HapNodes
Returns a string representation of this.
toString() - Method in class sample.RecombSingleBaumLevel
Returns a string description of this.
toString() - Method in class sample.RecombSingleNodes
Returns a string representation of this.
toString() - Method in class sample.SingleBaumLevel
Returns a string description of this.
toString() - Method in class sample.SingleNodes
Returns a string representation of this.
toString() - Method in interface vcf.AL
Returns a string representation of this.
toString() - Method in class vcf.AllData
Returns a string representation of this.
toString() - Method in class vcf.BasicGL
 
toString() - Method in class vcf.BasicMarker
 
toString() - Method in class vcf.BitSetGT
Returns the data represented by this as a VCF record with a GT format field.
toString() - Method in class vcf.BitSetRefGT
Returns the data represented by this as a VCF record with a GT format field.
toString() - Method in class vcf.BrefIt
 
toString() - Method in class vcf.ByteArrayRefGT
Returns the data represented by this as a VCF record with a GT format field.
toString() - Method in interface vcf.GL
Returns a string representation of this.
toString() - Method in class vcf.GprobsStatistics
Returns a string representation of this.
toString() - Method in class vcf.HbdAL
 
toString() - Method in class vcf.LowMafRefDiallelicGT
Returns the data represented by this as a VCF record with a GT format field.
toString() - Method in class vcf.LowMafRefGT
Returns the data represented by this as a VCF record with a GT format field.
toString() - Method in interface vcf.Marker
Returns a string equal to the first five tab-delimited fields of a VCF record corresponding to this marker.
toString() - Method in class vcf.Markers
Returns a string representation of this.
toString() - Method in class vcf.MaskedEndsGL
 
toString() - Method in class vcf.NoPhaseGL
 
toString() - Method in class vcf.RefGL
 
toString() - Method in class vcf.RefIt
 
toString() - Method in class vcf.RestrictedVcfWindow
Returns a string representation of this.
toString() - Method in class vcf.RevGL
 
toString() - Method in class vcf.SeqCodedRefGT
Returns the data represented by this as a VCF record with a GT format field.
toString() - Method in class vcf.SplicedGL
 
toString() - Method in class vcf.TargetData
Returns a string representation of this.
toString() - Method in class vcf.VcfHeader
Returns the VCF meta-information lines and the VCF header line used to construct this.
toString() - Method in class vcf.VcfIt
 
toString() - Method in class vcf.VcfMetaInfo
Returns the VCF meta-information line represented by this.
toString() - Method in class vcf.VcfRecord
Returns the VCF record.
toString() - Method in class vcf.VcfWindow
Returns a string representation of this.
toVcfRec() - Method in interface vcf.VcfEmission
Returns a VCF record corresponding to this.
trioFather(int) - Method in class main.NuclearFamilies
Returns the sample index of the father of the specified parent-offspring trio.
trioMother(int) - Method in class main.NuclearFamilies
Returns the sample index of the mother of the specified parent-offspring trio.
trioOffspring(int) - Method in class main.NuclearFamilies
Returns the sample index of the offspring of the specified parent-offspring trio.

U

unfilteredSampleIndex(int) - Method in class vcf.VcfHeader
Returns the index of the specified sample in the the list original list of samples before sample exclusions.
unphasedSep - Static variable in class blbutil.Const
The unphased allele separator: '/'
usage() - Static method in class main.Par
Returns a description of the possible Beagle command line arguments.
Utilities - Class in blbutil
Class Utilities contains miscellaneous static utility methods.

V

Validate - Class in blbutil
Class Validate contains static methods for validating command line arguments.
value(int, int, int) - Method in class main.BasicGenotypeValues
 
value(int, int, int) - Method in interface main.GenotypeValues
Returns the specified genotype value.
value(int, int, int) - Method in class main.RevGenotypeValues
 
value(int, int) - Method in class main.SampleGenotypeValues
Returns the specified genotype value.
value(int, int, int) - Method in class sample.DuoNodes
Returns the specified node trio value.
value(int) - Method in class sample.HapNodes
Returns the specified node value.
value(int, int) - Method in class sample.RecombSingleNodes
Returns the value of the specified node pair.
value(int, int) - Method in class sample.SingleNodes
Returns the value of the specified node pair.
value() - Method in class vcf.VcfMetaInfo
Returns the VCF meta-information line value.
valueOf(String) - Static method in enum beagleutil.Phase
Returns the enum constant of this type with the specified name.
values() - Static method in enum beagleutil.Phase
Returns an array containing the constants of this enum type, in the order they are declared.
vcf - package vcf
 
VcfEmission - Interface in vcf
Interface VcfEmission represents genotype emission probabilities for a set of samples at a single marker.
VcfEmissionCompressor - Class in vcf
Class VcfEmissionCompressor compresses a sequence of VcfEmission objects which contain reference genotype data.
VcfEmissionCompressor(Samples, int) - Constructor for class vcf.VcfEmissionCompressor
Constructs a new VcfEmissionCompressor for the specified samples.
VcfHeader - Class in vcf
Class VcfHeader represents the Variant Call Format (VCF) meta-information lines and the Variant Call Format header line that precede the first Variant Call Format record.
VcfHeader(FileIt<String>) - Constructor for class vcf.VcfHeader
Constructs a new VcfHeader object from the VCF meta-information lines and the VCF header line returned by the specified FileIterator<String>.
VcfHeader(FileIt<String>, Filter<String>) - Constructor for class vcf.VcfHeader
Constructs a new VcfHeader object from the VCF meta-information lines and the VCF header line returned by the specified FileIterator<String>.
vcfHeader() - Method in class vcf.VcfRecGTParser
Returns the VCF meta-information lines and header line.
vcfHeader() - Method in class vcf.VcfRecord
Returns the VCF meta-information lines and the VCF header line.
VcfIt<E extends MarkerContainer> - Class in vcf
Class VcfIt represents an iterator whose next() method returns an object storing data from a VCF record.
VcfMetaInfo - Class in vcf
Class VcfMetaInfo represents a VCF meta-information line.
VcfMetaInfo(String) - Constructor for class vcf.VcfMetaInfo
Constructs a VcfMetaInfo instance representing the specified VCF meta-information line.
VcfRecBuilder - Class in vcf
Class VcfRecBuilder contains methods for constructing and printing a VCF record in VCF 4.2 format.
VcfRecBuilder() - Constructor for class vcf.VcfRecBuilder
Constructs a new VcfRecBuilder instance with initial buffer size equal to VcfRecBuilder.DEFAULT_INIT_SIZE.
VcfRecBuilder(int) - Constructor for class vcf.VcfRecBuilder
Constructs a new VcfRecBuilder instance with the specified initial buffer size.
VcfRecGTParser - Class in vcf
Class VcfRecGTParser parses VCF records and extracts the GT format field.
VcfRecGTParser(VcfHeader, String) - Constructor for class vcf.VcfRecGTParser
Constructs a new VcfRecGTParser object from the specified VCF record.
vcfRecord() - Method in class vcf.VcfRecGTParser
Returns the VCF record that is being parsed.
VcfRecord - Class in vcf
Class VcfRecord represents a VCF record.
VcfWindow - Class in vcf
Class VcfWindow represents a sliding window of VCF records.
VcfWindow(SampleFileIt<? extends VcfEmission>) - Constructor for class vcf.VcfWindow
Constructs a new VcfWindow instance.
VcfWriter - Class in vcf
Class VcfWriter contains static methods for writing data in VCF 4.2 format.

W

weight(int) - Method in class sample.ImputationData
Return the specified weight.
Weights - Class in haplotype
Class Weights represents per-haplotype weights.
Weights(NuclearFamilies) - Constructor for class haplotype.Weights
Constructs a new Weights instance with a weight of 1.0f for all samples.
Weights(NuclearFamilies, float) - Constructor for class haplotype.Weights
Constructs a new Weights instance with a weight of 1.0f for reference samples, and a weight of nonRefWt for non-reference samples.
weights() - Method in class main.CurrentData
Returns the per-haplotype weights.
window() - Method in class main.CurrentData
Returns the marker window index.
window() - Method in class main.Par
Returns the window parameter.
window() - Method in class vcf.AllData
 
window() - Method in interface vcf.Data
Returns the current window index.
window() - Method in class vcf.TargetData
 
WindowWriter - Class in main
Class WindowWriter writes VCF and IBD output data.
WindowWriter(Samples, String) - Constructor for class main.WindowWriter
Constructs a new WindowWriter object.
WrappedHapPair - Class in haplotype
Class WrappedHapPair is a HapPair instance that wraps a SampleHapPairs object.
WrappedHapPair(SampleHapPairs, int) - Constructor for class haplotype.WrappedHapPair
Creates a WrappedHapPair instance representing the specified haplotype pair.
WrappedIntArray - Class in blbutil
Class WrappedIntArray represents an immutable int[] array.
WrappedIntArray(int[]) - Constructor for class blbutil.WrappedIntArray
Constructs a new CharCompressedIntArray instance.
write(int) - Method in class blbutil.BGZIPOutputStream
 
write(byte[]) - Method in class blbutil.BGZIPOutputStream
 
write(byte[], int, int) - Method in class blbutil.BGZIPOutputStream
 
writeMetaLines(String[], String, boolean, boolean, boolean, PrintWriter) - Static method in class vcf.VcfWriter
Writes VCF meta-information lines and header line to the specified PrintWriter.
writeMetaLinesGT(String[], String, PrintWriter) - Static method in class vcf.VcfWriter
Writes VCF meta-information lines and header line to the specified PrintWriter.
writeRec(PrintWriter, boolean) - Method in class vcf.VcfRecBuilder
Prints the current VCF record for the current marker to the specified PrintWriter.
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