- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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: '-'
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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 ThreadSafeIndexer
instance 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.
- 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.