- 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(double, double) - Method in class math.Regress
-
Records the specified values of the dependent and independent variables.
- add(float) - Method in class blbutil.FloatList
-
Adds the specified integer to the end of this list.
- add(int) - Method in class ints.IntList
-
Adds the specified integer to the end of this list.
- add(int) - Method in class ints.IntSet
-
Adds the specified element to this set.
- 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(RefGTRec) - Method in class bref.SeqCoder3
-
Attempts to add the specified RefGTRec
object to the list of
compressed RefGTRec
objects, and returns true
if the RefGTRec
object was added.
- addRecords(List<E>, int, int) - Method in class vcf.Window
-
Adds the specified records to he specified list.
- addRestrictedRefHapPairs(List<BitHapPair>) - Method in class main.CurrentData
-
Returns a list with the specified haplotypes following by the
reference haplotype pairs that are restricted to the target data markers.
- 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.
- addSampleData(float[], float[]) - Method in class imp.ImputedRecBuilder
-
Scales the specified probabilities for each allele to each sum to 1.0,
and adds the sample data to the VCF record.
- addToElement(int, float) - Method in class blbutil.FloatList
-
Adds the specified value to the specified element.
- advanceWindow(Markers) - Method in class vcf.RestrictedVcfWindow
-
Advances the sliding marker window, and returns the advanced window
as a GTRec[]
object.
- advanceWindowCm() - Method in class vcf.AllData
-
- advanceWindowCm() - Method in interface vcf.Data
-
Advances the sliding window of VCF records.
- advanceWindowCm() - Method in class vcf.TargetData
-
- allData(Supplier<SampleFileIt<RefGTRec>>, SampleFileIt<GTRec>, Par) - Static method in class vcf.AllData
-
Constructs and returns a new AllData
instance from VCF
recList returned by the specified SampleFileIt
objects.
- AllData - Class in vcf
-
Class AllData
represents a sliding window of
reference and target VCF recList.
- allele(int) - Method in class vcf.BasicMarker
-
- allele(int) - Method in interface vcf.Marker
-
Returns the specified allele.
- allele(int, int) - Method in class haplotype.HapPairPhasedGT
-
- allele(int, int) - Method in class imp.ImpData
-
Returns the specified target marker cluter alleles for the
reference and target haplotypes.
- allele(int, int) - Method in class phase.EstPhase.HapsGT
-
- allele(int, int) - Method in class phase.PhaseData
-
- allele(int, int) - Method in class vcf.BasicGT
-
- allele(int, int) - Method in class vcf.BasicRefGT
-
- allele(int, int) - Method in interface vcf.GT
-
Returns the allele on the specified haplotype for the specified marker
or return -1 if the allele is missing.
- allele(int, int) - Method in class vcf.SplicedGT
-
- allele(int, int) - Method in class vcf.XBasicGT
-
- ALLELE_CODED - Static variable in class bref.AsIsBref3Writer
-
The byte value denoting an allele coded record
- allele1(int) - Method in class haplotype.BitHapPair
-
- allele1(int) - Method in interface haplotype.HapPair
-
Returns the first allele for the specified marker.
- allele1(int) - Method in class haplotype.WrappedHapPair
-
- allele1(int) - Method in class vcf.BitSetGT
-
- allele1(int) - Method in interface vcf.DuplicatesGTRec
-
Returns the first allele for the specified sample or
-1 if the allele is missing.
- allele1(int) - Method in class vcf.LowMafRefDiallelicGT
-
- allele1(int) - Method in class vcf.LowMafRefGT
-
- allele1(int) - Method in class vcf.SeqCodedRefGT
-
- allele1(int) - Method in class vcf.VcfRecord
-
- allele1(int) - Method in class vcf.XBasicGT1
-
- allele1(int) - Method in interface vcf.XGT1
-
Returns the first allele for the specified marker if the observed data
include a non-missing allele, and returns -1 otherwise.
- allele1(int, int) - Method in class haplotype.HapPairPhasedGT
-
- allele1(int, int) - Method in class phase.EstPhase.HapsGT
-
- allele1(int, int) - Method in class vcf.BasicGT
-
- allele1(int, int) - Method in class vcf.BasicRefGT
-
- allele1(int, int) - Method in interface vcf.GT
-
Returns the first allele for the specified marker and sample
or return -1 if the allele is missing.
- allele1(int, int) - Method in class vcf.SplicedGT
-
- allele1(int, int) - Method in class vcf.XBasicGT
-
- allele2(int) - Method in class haplotype.BitHapPair
-
- allele2(int) - Method in interface haplotype.HapPair
-
Returns the second allele for the specified marker.
- allele2(int) - Method in class haplotype.WrappedHapPair
-
- allele2(int) - Method in class vcf.BitSetGT
-
- allele2(int) - Method in interface vcf.DuplicatesGTRec
-
Returns the second allele for the specified sample or
-1 if the allele is missing.
- allele2(int) - Method in class vcf.LowMafRefDiallelicGT
-
- allele2(int) - Method in class vcf.LowMafRefGT
-
- allele2(int) - Method in class vcf.SeqCodedRefGT
-
- allele2(int) - Method in class vcf.VcfRecord
-
- allele2(int) - Method in class vcf.XBasicGT1
-
- allele2(int) - Method in interface vcf.XGT1
-
Returns the second allele for the specified marker if the observed data
include a non-missing allele, and returns -1 otherwise.
- allele2(int, int) - Method in class haplotype.HapPairPhasedGT
-
- allele2(int, int) - Method in class phase.EstPhase.HapsGT
-
- allele2(int, int) - Method in class vcf.BasicGT
-
- allele2(int, int) - Method in class vcf.BasicRefGT
-
- allele2(int, int) - Method in interface vcf.GT
-
Returns the second allele for the specified marker and sample
or return -1 if the allele is missing.
- allele2(int, int) - Method in class vcf.SplicedGT
-
- allele2(int, int) - Method in class vcf.XBasicGT
-
- alleleCodedInstance(Marker, Samples, int[][]) - Static method in interface vcf.RefGTRec
-
Constructs and returns a new allele-coded RefGTRec
instance
from the specified data.
- alleleCodedInstance(RefGTRec) - Static method in interface vcf.RefGTRec
-
Returns an allele-coded RefGTRec
instance for the
specified data.
- alleleCodedInstance(VcfRecGTParser) - Static method in interface vcf.RefGTRec
-
Constructs and returns a new allele-coded RefGTRec
instance
from the specified data.
- alleleCount(int) - Method in class vcf.LowMafRefDiallelicGT
-
- alleleCount(int) - Method in class vcf.LowMafRefGT
-
- alleleCount(int) - Method in interface vcf.RefGTRec
-
Returns the number of haplotypes that carry the specified allele.
- alleleCount(int) - Method in class vcf.SeqCodedRefGT
-
- alleles() - Method in class vcf.BasicMarker
-
- alleles() - Method in class vcf.BitSetGT
-
- alleles() - Method in interface vcf.DuplicatesGTRec
-
Returns an array of length this.size()
whose j
-th
element is equal to this.allele(j
}
- alleles() - Method in class vcf.LowMafRefDiallelicGT
-
- alleles() - Method in class vcf.LowMafRefGT
-
- alleles() - Method in interface vcf.Marker
-
Returns the alleles.
- alleles() - Method in class vcf.SeqCodedRefGT
-
- alleles() - Method in class vcf.VcfRecord
-
- allelesToBits(int[]) - Method in class vcf.Markers
-
Returns a bit array storing the specified haplotype.
- 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
-
- ap() - Method in class main.Par
-
Returns the ap parameter.
- appendRecords(AtomicReferenceArray<StateProbs>, PrintWriter) - Method in class imp.ImputedVcfWriter
-
Writes the VCF records to the specified PrintWriter
.
- appendRecords(GenotypeValues, int, int, PrintWriter) - Static method in class vcf.VcfWriter
-
Writes the specified genotype data as VCF records to the specified
PrintWriter
.
- appendRecords(GT, int, int, boolean, boolean, PrintWriter) - Static method in class vcf.VcfWriter
-
Writes the data in phased genotypes for the specified markers
to the specified PrintWriter
.
- args() - Method in class main.Par
-
Returns the 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.
- AsIsBref3Writer - Class in bref
-
Class AsIsBref3Writer
writes VCF data with phased, non-missing
genotypes to a binary reference format v3 (bref) file.
- AsIsBref3Writer(String, Samples, File) - Constructor for class bref.AsIsBref3Writer
-
Constructs a new AsIsBref4Writer
for the specified data.
- asString(IntArray) - Static method in interface ints.IntArray
-
Returns a string representation of this IntArray
by applying
java.utils.Arrays.toString()
to an equivalent int[]
object.
- asString(LongArray) - Static method in class ints.LongArray
-
Returns a string representation of this LongArray
by applying
java.utils.Arrays.toString()
to an equivalent int[]
object.
- basePos(int, double) - Method in interface vcf.GeneticMap
-
Returns the base position corresponding to the specified genetic map
position.
- basePos(int, double) - Method in class vcf.MarkerMap
-
- basePos(int, double) - Method in class vcf.PlinkGenMap
-
- basePos(int, double) - Method in class vcf.PositionMap
-
- BasicGT - Class in vcf
-
Class BasicGT
represents genotype emission probabilities
for a set of samples.
- BasicGT(Samples, GTRec[]) - Constructor for class vcf.BasicGT
-
Constructs a BasicGT
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 prefix.
- BasicRefGT - Class in vcf
-
Class BasicRefGT
stores a list of samples and a
haplotype pair for each sample.
- BasicRefGT(Markers, Samples, RefGTRec[]) - Constructor for class vcf.BasicRefGT
-
Constructs a new RefHapPairs
instance.
- BasicRefGT(RefGTRec[]) - Constructor for class vcf.BasicRefGT
-
Constructs a new RefHapPairs
instance.
- beagleutil - package beagleutil
-
- beta() - Method in class math.Regress
-
Returns the regression coefficient for the recorded values of the
independent and dependent variables.
- 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.
- binarySearch(int) - Method in class ints.IntList
-
Returns an index associated with the specified value, or
(-insertionPoint - 1)
if the value is not found.
- BitHapPair - Class in haplotype
-
Class BitHapPair
represents a pair of haplotypes for a sample.
- BitHapPair(Markers, 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.
- bitsToAllele(LongArray, int) - Method in class vcf.Markers
-
Returns the specified allele stored in the specified hapBits
array.
- blbutil - package blbutil
-
- 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 - package bref
-
- Bref3 - Class in bref
-
Class Bref3
converts files in VCF format into
bref version 3 format.
- Bref3() - Constructor for class bref.Bref3
-
- Bref3It - Class in bref
-
Class Bref3It
represents an iterator whose next()
which
returns records from a bref version 3 file.
- Bref3It(File) - Constructor for class bref.Bref3It
-
Constructs a new Bref3It
instance.
- Bref3It(File, Filter<Marker>) - Constructor for class bref.Bref3It
-
Constructs a new Bref4It
instance.
- Bref3Reader - Class in bref
-
Class Bref3Reader
contains methods for reading a bref 3
(binary reference format) file.
- Bref3Reader(DataInput, Filter<Marker>) - Constructor for class bref.Bref3Reader
-
Constructs a new Bref3Reader
instance.
- BrefBlock - Class in bref
-
Class BrefBlock
represents starting chromosome coordinates and
file offset for the start of a binary reference format (bref) data block.
- BrefBlock(int, int, long) - Constructor for class bref.BrefBlock
-
Constructs a BrefBlock
for the specified data.
- BrefWriter - Interface in bref
-
Interface BrefWrites
writes phased, non-missing genotypes to a
binary reference format (bref) file.
- bufferedInputStream(File) - Static method in class blbutil.FileUtil
-
Returns an buffered java.io.InputStream
with default buffer
size reading from the specified file.
- bufferedOutputStream(File) - Static method in class blbutil.FileUtil
-
Returns an buffered java.io.OutputStream
with default
buffer size writing to the specified file.
- bufferedOutputStream(File, boolean) - Static method in class blbutil.FileUtil
-
Returns an buffered java.io.OutputStream
with default
buffer size writing to the specified file.
- buildNanos(long) - Method in class main.RunStats
-
Increases the cumulative time to build the DAG models by the
specified number of nanoseconds.
- burnin() - Method in class main.Par
-
Returns the burnin parameter.
- burnin() - Method in class phase.PhaseData
-
Returns true
if the current phasing iteration is a burnin
iteration and returns false
otherwise.
- 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
-
- capacity() - Method in class ints.IntSet
-
Returns the capacity of this set.
- cd() - Method in class imp.ImpData
-
Returns the current data.
- CharArray - Class in ints
-
/**
- CharArray(byte[]) - Constructor for class ints.CharArray
-
Constructs a new CharArray
instance from the specified data.
- CharArray(char[]) - Constructor for class ints.CharArray
-
Constructs a new CharArray
instance from
the specified data.
- CharArray(int[]) - Constructor for class ints.CharArray
-
Constructs a new CharArray
instance from the specified data.
- CharArray(int[], int) - Constructor for class ints.CharArray
-
Constructs a new CharArray
instance from the specified data.
- CharArray(int[], int, int) - Constructor for class ints.CharArray
-
Constructs a new CharArray
instance from the
specified data.
- CharArray(IntList) - Constructor for class ints.CharArray
-
Constructs a new UnsignedByteArray
instance from the specified data.
- CharArray(IntList, int) - Constructor for class ints.CharArray
-
Constructs a new CharArray
instance from the specified data.
- CharArray(IntList, int, int) - Constructor for class ints.CharArray
-
Constructs a new CharArray
instance from the specified data.
- chrom() - Method in class beagleutil.ChromInterval
-
Returns the chromosome identifier.
- chrom() - Method in class vcf.BasicMarker
-
- chrom() - Method in interface vcf.Marker
-
Returns the chromosome.
- chrom() - Method in class vcf.MarkerMap
-
Returns the chromosome corresponding to the list of markers.
- 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 bref.BrefBlock
-
Returns the chromosome index of the first marker in this bref block.
- chromIndex() - Method in class vcf.BasicMarker
-
- chromIndex() - Method in interface vcf.Marker
-
Returns the chromosome index.
- chromIndex() - Method in class vcf.MarkerMap
-
Returns the index of the chromosome corresponding to the list of markers.
- chromIndex() - Method in class vcf.Window
-
Returns the chromosome index of the first maker in the window.
- chromInt() - Method in class main.Par
-
Returns the chromosome interval or null
if no chrom
parameter was specified.
- ChromInterval - Class in beagleutil
-
Class ChromInterval
represents a chromosome interval whose
end points are genome coordinates.
- ChromInterval(String, int, int) - Constructor for class beagleutil.ChromInterval
-
Constructs a new ChromInterval
instance.
- ChromInterval(Marker, Marker) - Constructor for class beagleutil.ChromInterval
-
Constructs a new ChromInterval
instance.
- clear() - Method in class blbutil.FloatList
-
Removes all elements from this list.
- clear() - Method in class ints.IntList
-
Removes all elements from this list.
- clear() - Method in class ints.IntMap
-
Removes all keys from this map.
- clear() - Method in class ints.IntSet
-
Removes all elements from this set.
- clear() - Method in class vcf.R2Estimator
-
Clears all genotype data and sets the number of genotype with
allele dose data to 0.
- 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 bref.AsIsBref3Writer
-
- close() - Method in class bref.Bref3It
-
- close() - Method in interface bref.BrefWriter
-
Flushes any buffered output and releases any system resources that are
held by this BrefWriter
.
- close() - Method in class bref.CompressBref3Writer
-
- close() - Method in class main.WindowWriter
-
- close() - Method in class vcf.AllData
-
- 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.WindowIt
-
Releases any I/O resources controlled by this object.
- closestIndex(int, int) - Method in class vcf.PlinkGenMap
-
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.
- cnt() - Method in class math.Regress
-
Returns the number of recorded values of the independent variable.
- 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
-
- commandLine(String, String[]) - Static method in class blbutil.Utilities
-
Returns a string representation of the command line arguments.
- comparator(Samples) - Static method in interface haplotype.HapPair
-
Returns a Comparator<HapPairInterface>
whose compare(hp1, hp2)
method returns -1, 0, or 1
depending on whether samples.index(hp1.idIndex())
is
less than, equal, or greater than
samples.index(hp2.idIndex())
.
- 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(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.
- COMPRESS_FREQ_THRESHOLD - Static variable in class bref.SeqCoder3
-
The major allele frequency threshold for allele coding.
- CompressBref3Writer - Class in bref
-
Class CompressBref3Writer
writes phased, non-missing genotypes
to a binary reference format v3 (bref) file.
- CompressBref3Writer(String, Samples, int, File) - Constructor for class bref.CompressBref3Writer
-
Constructs a new CompressBref3fWriter
for the specified data.
- confirmEmptyMap(Map<String, String>) - Static method in class blbutil.Validate
-
Checks whether the specified map of key-value pairs is empty.
- Const - Class in blbutil
-
Class Const
provides public static final fields with
string and character constants.
- contains(int) - Method in class ints.IntMap
-
Returns true
if the map contains the specified key,
and returns false
otherwise.
- contains(int) - Method in class ints.IntSet
-
Returns true
if the set contains the specified element,
and returns false
otherwise.
- contains(Marker) - Method in class beagleutil.ChromInterval
-
Returns true
if the specified marker is in this chromosome
interval 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.
- copyOf(int) - Method in class ints.IntList
-
Copies and returns this list of integers, truncating or padding with 0
as necessary so that the copy has the specified length.
- COPYRIGHT - Static variable in class main.Main
-
The copyright string.
- countFields(String) - Static method in class blbutil.StringUtil
-
Returns the number of white-space delimited fields in the specified
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)
.
- create(int[], int) - Static method in interface ints.IntArray
-
Returns a new IntArray
instance that has the same
sequence of integers as the specified array.
- 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>, 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.
- 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>, BiFunction<VcfHeader, String, R>) - Static method in class vcf.VcfIt
-
Create and returns a new VcfIt
instance from the specified
objects.
- create(IntList, int) - Static method in interface ints.IntArray
-
Returns a new IntArray
instance that has the same
sequence of integers as the specified list.
- create(GeneticMap, Markers) - Static method in class vcf.MarkerMap
-
Returns a new MarkerMap
instance that is constructed from the
specified data
- create(Marker[]) - Static method in class vcf.Markers
-
Returns a new Markers
instance that is constructed from
the specified data.
- cumMarkerCnt() - Method in class vcf.RestrictedVcfWindow
-
Returns the number of 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, GT) - Constructor for class main.CurrentData
-
Constructs a new CurrentData
instance from the specified
data.
- Data - Interface in vcf
-
Interface Data
represents a sliding window of target VCF records
or a sliding window of reference and target VCF records.
- decEndComp() - Static method in interface beagleutil.IntInterval
-
Returns a Comparator<IntInterval>
which orders
IntInterval
objects in order of increasing this.start()
value and orders IntInterval
objects with the same
this.start()
value in order of decreasing this.end()
value.
- decrementAndGet(int) - Method in class ints.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_INIT_CAPACITY - Static variable in class beagleutil.ThreadSafeIndexer
-
The default initial capacity, which is 500.
- DEFAULT_INIT_CAPACITY - Static variable in class blbutil.FloatList
-
The default initial capacity of an FloatList
, which is 10.
- DEFAULT_INIT_CAPACITY - Static variable in class ints.IntList
-
The default initial capacity of an IntList
, which is 16.
- DEFAULT_INIT_SIZE - Static variable in class vcf.VcfRecBuilder
-
The default initial size for the string buffer, which is 50
characters.
- defaultMaxNSeq(int) - Static method in class bref.SeqCoder3
-
Returns the default maximum number of sequences for the specified
number of samples.
- DELIMITER - Static variable in class vcf.VcfMetaInfo
-
The VCF meta-information line key-value delimiter: '='
- 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.
- duoOffspring(int) - Method in class main.Pedigree
-
Returns the sample index of the offspring of the specified
parent-offspring duo.
- duoParent(int) - Method in class main.Pedigree
-
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.
- duoPrintNanos(String, long) - Method in class main.RunStats
-
Print the specified message followed by the human
elapsed time as formatted by
blbutil.Utilities.elapsedNanos(nanos)
- DuplicatesGTRec - Interface in vcf
-
Interface DuplicatesGTRec
represents marker alleles for a
list of samples.
- 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 ints.IntSet
-
Returns the specified element.
- 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 class imp.RefHapHash
-
Returns the ending reference marker index (exclusive)
for the reference haplotype allele sequences.
- 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.
- END_OF_DATA - Static variable in class bref.AsIsBref3Writer
-
The end of file code for a bref file.
- END_OF_INDEX - Static variable in class bref.AsIsBref3Writer
-
The integer denoting denoting the end of the index in a bref file
- equals(IntArray, IntArray) - Static method in interface ints.IntArray
-
Returns true
if the specified IntArray
objects
represent the same sequence of integer values, and returns false
otherwise.
- equals(LongArray, LongArray) - Static method in class ints.LongArray
-
Returns true
if the specified LongArray
objects
represent the same sequence of long values, 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.Pair
-
Returns true
if the specified object is a
Pair
instance representing the same
ordered pair of objects as this
, and
returns false
otherwise.
- 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.
- errProb(int) - Method in class imp.ImpData
-
Returns the probability that the allele carried by the specified
target marker cluster matches the allele labeling the latent HMM state.
- EstPhase - Class in phase
-
Class EstPhase
stores haplotype pairs, missing genotypes,
and unphased, nonmissing heteroygote genotypes for a list of samples.
- EstPhase(GT, List<LongArray>) - Constructor for class phase.EstPhase
-
Constructs a new EstPhase
instance from the specified data.
- EstPhase.HapsGT - Class in phase
-
- 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) - Static method in class blbutil.Utilities
-
Prints the specified string to standard error and then terminates the
Java virtual machine.
- exit(String, Throwable) - Static method in class blbutil.Utilities
-
Prints the specified exception, its stack trace, and
the specified string to standard error and then terminates the
Java virtual machine.
- exit(Throwable) - Static method in class blbutil.Utilities
-
Prints the specified exception, its stack trace, and
the specified string to standard error and then terminates the
Java virtual machine.
- father(int) - Method in class main.Pedigree
-
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 bref.Bref3It
-
- 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.WindowIt
-
Returns the file from which VCF recList are read, or returns
null
if the source is standard input.
- FileIt<E> - Interface in blbutil
-
An iterator for data elements in a file.
- FileUtil - Class in blbutil
-
Class FileUtil
contains static methods for working with files.
- filter() - Method in class vcf.VcfRecord
-
Returns the FILTER field.
- Filter<E> - Interface in blbutil
-
A filter for accepting or rejecting objects.
- FilterUtil - Class in vcf
-
Class FilterUtil
contains static methods for constructing
marker filters.
- first() - Method in class blbutil.Pair
-
Returns the first object in the ordered pair of objects.
- flipStrand(String) - Static method in class vcf.BasicMarker
-
Returns the string allele obtained by changing the specified allele
to the opposite chromosome strand
- 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.
- FloatArray - Class in blbutil
-
Class FloatArray
represents an immutable list of float floating
point values.
- FloatArray(float[]) - Constructor for class blbutil.FloatArray
-
Constructs an FloatArray
object with the specified
values.
- FloatList - Class in blbutil
-
Class FloatList
represents a list of floats.
- FloatList() - Constructor for class blbutil.FloatList
-
Constructs an FloatList
object with the default
initial capacity.
- FloatList(int) - Constructor for class blbutil.FloatList
-
Constructs an FloatList
object with the specified
initial capacity.
- 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.
- 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 vcf.PlinkGenMap
-
Constructs and returns a new PlinkGenMap
instance from
the data in the specified file.
- fromPlinkMapFile(File, String) - Static method in class vcf.PlinkGenMap
-
Constructs and returns a new PlinkGenMap
instance from
the data in the specified file.
- fromSignedByteArray(byte[], int) - Static method in class ints.PackedIntArray
-
Constructs and returns a new PackedIntArray
instance from the
specified data.
- fromSignedByteArray(byte[], int, int, int) - Static method in class ints.PackedIntArray
-
Constructs a new PackedIntArray
instance from the
specified data.
- 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.
- fromUnsignedByteArray(byte[], int) - Static method in class ints.PackedIntArray
-
Constructs a new PackedIntArray
instance from the
specified data.
- fromUnsignedByteArray(byte[], int, int, int) - Static method in class ints.PackedIntArray
-
Constructs a new PackedIntArray
instance from the
specified data.
- fromUnsignedTwoByteArray(byte[], int) - Static method in class ints.PackedIntArray
-
Constructs a new PackedIntArray
instance from the
specified data.
- genDist() - Method in class main.CurrentData
-
Return a FloatArray
of size this.nTargMarkers()
whose k
-th element is the genetic distance between the
k
-th target marker and the previous marker, or 0.0
if (k == 0)
.
- genDist() - Method in class phase.PhaseData
-
Return a FloatArray
of size this.nTargMarkers()
whose k
-th element is the genetic distance between the
k
-th target marker and the previous marker, or 0.0
if (k == 0)
.
- geneticMap(File, ChromInterval) - Static method in interface vcf.GeneticMap
-
Constructs and returns a genetic map from the specified data.
- GeneticMap - Interface in vcf
-
Interface GeneticMap
represents a genetic map for one or more
chromosomes.
- genMap() - Method in class vcf.AllData
-
- genMap() - Method in interface vcf.Data
-
Returns the genetic map.
- genMap() - Method in class vcf.TargetData
-
- genMap() - Method in class vcf.WindowIt
-
Returns the genetic map.
- genotype(int, int) - Static method in class vcf.BasicGT
-
Returns the genotype index corresponding to the
specified unordered alleles.
- GenotypeValues - Interface in main
-
Interface GenotypeValues
represents a value for each
possible genotype for each sample at each marker.
- genPos() - Method in class vcf.MarkerMap
-
Returns the array of genetic map positions whose k
-th element
equals this.genPos(k)
.
- genPos(int) - Method in class vcf.MarkerMap
-
Returns the genetic map position of the specified marker.
- genPos(int, int) - Method in interface vcf.GeneticMap
-
Returns the genetic map position of the specified genome coordinate.
- genPos(int, int) - Method in class vcf.MarkerMap
-
- genPos(int, int) - Method in class vcf.PlinkGenMap
-
- genPos(int, int) - Method in class vcf.PositionMap
-
- genPos(Marker) - Method in interface vcf.GeneticMap
-
Returns the genetic map position of the specified marker.
- genPos(Marker) - Method in class vcf.MarkerMap
-
- genPos(Marker) - Method in class vcf.PlinkGenMap
-
- genPos(Marker) - Method in class vcf.PositionMap
-
- genPos(Markers) - Method in interface vcf.GeneticMap
-
Returns the an array of length hapPairs.nMarkers()
whose
whose j
-th element is the genetic map position
of the j
-th marker.
- get(int) - Method in class blbutil.FloatArray
-
Returns the float at the specified position in this list.
- get(int) - Method in class blbutil.FloatList
-
Returns the float at the specified position in this list.
- get(int) - Method in class ints.CharArray
-
- get(int) - Method in class ints.IndexArray
-
- get(int) - Method in interface ints.IntArray
-
Returns the specified array element.
- get(int) - Method in class ints.IntList
-
Returns the element at the specified position in this list.
- get(int) - Method in class ints.IntMap
-
Returns the value for the specified key or null
if the specified key is not present in this map.
- get(int) - Method in class ints.LongArray
-
Returns the specified array element.
- get(int) - Method in class ints.PackedIntArray
-
- get(int) - Method in class ints.UnsignedByteArray
-
- get(int) - Method in class ints.WrappedIntArray
-
- get(int) - Method in class vcf.BasicRefGT
-
- get(int) - Method in class vcf.BitSetGT
-
- get(int) - Method in interface vcf.DuplicatesGTRec
-
Returns the specified allele for the specified haplotype or
-1 if the allele is missing.
- get(int) - Method in class vcf.LowMafRefDiallelicGT
-
- get(int) - Method in class vcf.LowMafRefGT
-
- get(int) - Method in interface vcf.RefGT
-
Returns the RefGTRec
for the specified marker.
- get(int) - Method in class vcf.SeqCodedRefGT
-
- get(int) - Method in class vcf.VcfRecord
-
- getAndDecrement(int) - Method in class ints.IntList
-
Decrements by one the element at the specified position in this list.
- getAndIncrement(int) - Method in class ints.IntList
-
Increments by one the element at the specified position in this list.
- getCompressedList() - Method in class bref.SeqCoder3
-
Returns and clears the stored list of compressed RefGTRec
objects.
- 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, 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, 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.
- getIndices(String[]) - Method in class beagleutil.ChromIds
-
Returns an array of chromosome identifier indices corresponding to the
specified array of chromosome identifiers.
- getIndices(String[]) - Method in class beagleutil.SampleIds
-
Returns an array of sample identifier indices corresponding to the
specified array of sample identifiers.
- getIndices(T[]) - Method in class beagleutil.ThreadSafeIndexer
-
Returns an array of object indices corresponding to the specified
object array.
- getMissing(int) - Method in class phase.EstPhase
-
Returns a list of marker indices in increasing order for which
the specified sample has a missing genotype.
- getMissing(int, boolean[]) - Method in class phase.EstPhase
-
Sets the k
-th entry of the specified isMissing
array
to true
if the specified sample's genotype at the
k
-th marker is missing, and to false
otherwise.
- getUnphasedHets(int) - Method in class phase.EstPhase
-
Returns a list of marker indices in increasing order for which
the specified sample has an unphased, non-missing heterozygote genotype.
- getUnphasedHets(int, boolean[]) - Method in class phase.EstPhase
-
Sets the k
-th entry of the specified isUnphased
array
to true
if the specified sample's genotype at the
k
-th marker is an unphased, nonmissing heterozygote, and
to false
otherwise.
- giga - Static variable in class blbutil.Const
-
The value 1,000,000,000
- gl(int, int, int) - Method in class vcf.BitSetGT
-
- gl(int, int, int) - Method in interface vcf.GTRec
-
Returns the probability of the observed data for the specified 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) - Method in class vcf.SeqCodedRefGT
-
- gl(int, int, int) - Method in class vcf.VcfRecord
-
- gl(int, int, int) - Method in class vcf.XBasicGT1
-
- gl(int, int, int) - Method in interface vcf.XGT1
-
Returns the probability of the observed data for the specified marker
if the specified pair of ordered alleles is the true ordered genotype.
- gl(int, int, int, int) - Method in class vcf.BasicGT
-
- gl(int, int, int, int) - Method in interface vcf.GT
-
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, int) - Method in class vcf.SplicedGT
-
- gl(int, int, int, int) - Method in class vcf.XBasicGT
-
- GL_FORMAT - Static variable in class vcf.VcfRecord
-
The VCF FORMAT code for log-scaled genotype likelihood data: "GL".
- gp() - Method in class main.Par
-
Returns the gp parameter.
- gt() - Method in class main.Par
-
Returns the gt parameter or null
if no gt parameter was
specified.
- GT - Interface in vcf
-
Interface GT
represents genotype data
for a list of markers and a list of samples.
- GT_FORMAT - Static variable in class vcf.BitSetGT
-
The VCF FORMAT code for genotype data: "GT".
- gtIndex(int, int) - Static method in class vcf.VcfRecord
-
Returns the VCF genotype index for the specified pair of alleles.
- GTRec - Interface in vcf
-
Interface GTRec
represents represents genotype data for one
marker.
- gzipPrintWriter(File) - Static method in class blbutil.FileUtil
-
Returns a buffered java.io.PrintWriter
writing to
the specified file.
- gzipPrintWriter(File, boolean) - Static method in class blbutil.FileUtil
-
Returns a buffered java.io.PrintWriter
writing to
the specified file.
- hap(int) - Method in class imp.RefHapHash
-
Return the specified haplotype in the sublist of reference haplotypes.
- hap2Index(int) - Method in class imp.RefHapHash
-
Returns the index of the specified haplotype in the sublist of
reference haplotypes.
- hapIndex(int, int) - Method in class vcf.LowMafRefDiallelicGT
-
- hapIndex(int, int) - Method in class vcf.LowMafRefGT
-
- hapIndex(int, int) - Method in interface vcf.RefGTRec
-
Returns index of the haplotype that carries the specified copy of the
specified allele.
- hapIndex(int, int) - Method in class vcf.SeqCodedRefGT
-
- hapIndices() - Method in class vcf.LowMafRefDiallelicGT
-
- hapIndices() - Method in class vcf.LowMafRefGT
-
- hapIndices() - Method in interface vcf.RefGTRec
-
Returns an array whose j
-th element is null
if j
is the major allele with lowest index, and otherwise is
an array of indices of haplotypes that carry the j
-th allele
sorted in increasing order
- hapIndices() - Method in class vcf.SeqCodedRefGT
-
- haplotype - package haplotype
-
- HaplotypeCoder - Class in imp
-
Class HaplotypeCoder
indexes the observed allele sequences
in phased reference and target genotype data in a chromosome interval.
- HaplotypeCoder(RefGT, GT) - Constructor for class imp.HaplotypeCoder
-
Constructs a new HaplotypeCoder
instance from the specified
data.
- HapPair - Interface in haplotype
-
Interface HapPair
represents a pair of haplotypes for a sample.
- HapPairPhasedGT - Class in haplotype
-
Class HapPairPhasedGT
stores a list of samples and a
haplotype pair for each sample.
- HapPairPhasedGT(Samples, List<BitHapPair>) - Constructor for class haplotype.HapPairPhasedGT
-
Constructs a new BasicPhasedGT
instance from the specified data.
- hapsGT() - Method in class phase.EstPhase
-
- hapToSeq(int) - Method in class imp.ImpData
-
Returns the specified target marker cluster alleles for the
reference and target haplotypes.
- hasFormat(String) - Method in class vcf.VcfRecord
-
Returns true
if the specified FORMAT subfield is
present, and returns false
otherwise.
- hash(int) - Method in class imp.RefHapHash
-
Return a hash code computed from the allele sequence
of the specified haplotype in the sublist of reference haplotypes.
- 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.Pair
-
Returns a hash code value for the 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.
- hasMissingGT(int) - Method in class phase.EstPhase
-
Returns true
if the specified sample has a missing genotype,
and returns false
otherwise.
- hasNext() - Method in class blbutil.InputIt
-
Returns true
if the iteration has more elements.
- hasNext() - Method in class bref.Bref3It
-
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.
- hasNext() - Method in class vcf.WindowIt
-
Returns true
if the sliding window of VCF recList can advance
and returns false
otherwise.
- hasUnphasedHets(int) - Method in class phase.EstPhase
-
Returns true
if the specified sample has an unphased
heterozygote genotype, and returns false
otherwise.
- 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.
- hyphen - Static variable in class blbutil.Const
-
The hyphen character: '-'
- ibsHaps(int, int) - Method in class imp.ImpIbs
-
Returns an array containing reference haplotype indices that
that are IBS with the specified target haplotype in an interval
beginning with the specified step.
- ibsHaps(int, int, int) - Method in class phase.PhaseIbs
-
Returns a set containing the specified number of haplotype
indices that are IBS with haplotype h1
in the specified
step.
- ibsStates(int, int[][]) - Method in class phase.PhaseStates
-
Identifies the HMM state alleles for the specified sample.
- ibsStates(int, int[][], boolean[][]) - Method in class imp.ImpStates
-
Stores the reference haplotype for the j
-th state
at the m
-th marker in hapIndices[m][j]
, and stores
the equality of the allele carried by the reference haplotype for
the j
-th state and the allele carried by the target haplotype
at the m
-th marker in alMatch[m][j]
.
- id() - Method in class vcf.BasicMarker
-
- 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.
- 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(int) - Method in interface vcf.Marker
-
Returns the specified marker identifier.
- IDENTICAL - beagleutil.Phase
-
- 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() - Method in class haplotype.BitHapPair
-
- idIndex() - Method in interface haplotype.HapPair
-
Returns the sample identifier index.
- idIndex() - Method in class haplotype.WrappedHapPair
-
- idIndex() - Method in class vcf.XBasicGT1
-
- idIndex() - Method in interface vcf.XGT1
-
Returns the sample identifier index.
- 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.
- ids(int[]) - Method in class beagleutil.SampleIds
-
Returns a list of sample identifiers with the specified indices.
- idSet(File) - Static method in class blbutil.Utilities
-
Returns a set of identifiers found in a text file that has
one identifier per line.
- imp - package imp
-
- imp_segment() - Method in class main.Par
-
Returns the imp-segment parameter.
- imp_states() - Method in class main.Par
-
Returns the imp-states parameter.
- impData() - Method in class imp.ImpIbs
-
Return the data for genotype imputation in the marker window.
- impData() - Method in class imp.ImpLSBaum
-
Return the input data for genotype imputation
- ImpData - Class in imp
-
Class ImpData
contains the input data for imputation of
ungenotyped markers.
- ImpData(Par, CurrentData, GT, GeneticMap) - Constructor for class imp.ImpData
-
Constructs a new ImpData
instance from the specified data.
- ImpIbs - Class in imp
-
Class ImpIbs
identifies haplotypes that share a long
IBS segment with a specified haplotype.
- ImpIbs(ImpData) - Constructor for class imp.ImpIbs
-
Constructs a new ImpIbs
object from the specified data.
- ImpLS - Class in imp
-
Class ImpLS
computes HMM state probabilities
at genotyped markers in the target haplotypes.
- ImpLSBaum - Class in imp
-
Class ImpLSBaum
implements a Baum hidden Markov model
forward and backward algorithms for computing HMM state probabilities
at genotyped markers using IBS-matched reference haplotypes.
- ImpLSBaum(ImpData, ImpIbs) - Constructor for class imp.ImpLSBaum
-
Creates a LSHapBaum
instance from the specified data.
- ImpStates - Class in imp
-
Class ImpStates
identifies a list of pseudo-reference haplotypes
for a target haplotype.
- ImpStates(ImpIbs) - Constructor for class imp.ImpStates
-
Constructs a new ImpStates
object from the specified data.
- 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.
- impute(int) - Method in class imp.ImpLSBaum
-
Returns HMM state probabilities at genotyped markers for the
specified target haplotype.
- ImputedRecBuilder - Class in imp
-
Class ImputeRecBuilder
contains methods for constructing
and printing a VCF record in VCF 4.3 format.
- ImputedRecBuilder(Marker, int, boolean, boolean) - Constructor for class imp.ImputedRecBuilder
-
Constructs a new ImputedRecBuilder
instance for the specified
number of samples.
- ImputedVcfWriter - Class in imp
-
Class ImputedVcfWriter
writes observed and imputed genotypes
to a VCF output file.
- ImputedVcfWriter(ImpData, int, int, int) - Constructor for class imp.ImputedVcfWriter
-
Constructs a new ImputedVcfWriter
instance from
the specified data.
- incEndComp() - Static method in interface beagleutil.IntInterval
-
Returns a Comparator<IntInterval>
which orders
IntInterval
objects in order of increasing this.start()
value and orders IntInterval
objects with the same
this.start()
value in order of increasing this.end()
value.
- 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.
- INCONSISTENT - beagleutil.Phase
-
- incrementAndGet(int) - Method in class ints.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.
- index2BasePos(int, int) - Method in class vcf.PlinkGenMap
-
Returns the specified base position
- index2GenPos(int, int) - Method in class vcf.PlinkGenMap
-
Returns the specified genetic map position
- IndexArray - Class in ints
-
Class IndexArray
stores an array whose entries
are elements of a bounded set of non-negative integers along with an upper
bound.
- IndexArray(IntArray, int) - Constructor for class ints.IndexArray
-
Constructs a new IndexArray
instance from the specified
data.
- info() - Method in class vcf.VcfRecord
-
Returns the INFO field.
- InitTargHapPairs - Class in sample
-
Class InitTargHapPairs
has a static method for returning
initial target 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() - Method in class ints.IndexArray
-
Returns the wrapped IntArray
object.
- IntArray - Interface in ints
-
Interface IntArray
represents an immutable int[]
array.
- intensity() - Method in class main.CurrentData
-
Returns the intensity used to generate the pRecomb values.
- 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.
- IntList - Class in ints
-
Class IntList
represents a list of integers.
- IntList() - Constructor for class ints.IntList
-
Constructs an IntList
object with the default
initial capacity.
- IntList(int) - Constructor for class ints.IntList
-
Constructs an IntList
object with the specified
initial capacity.
- IntList(int[]) - Constructor for class ints.IntList
-
Constructs an IntList
by cloning the specified array.
- IntList(IntList) - Constructor for class ints.IntList
-
Constructs an IntList
by copying the specified IntList
.
- IntMap<E> - Class in ints
-
Class IntMap
represents a map with integer keys and generic type
values.
- IntMap(int) - Constructor for class ints.IntMap
-
Creates a new IntMap
instance.
- ints - package ints
-
- IntSet - Class in ints
-
Class IntSet
represents an indexed set of integers.
- IntSet(int) - Constructor for class ints.IntSet
-
Creates a new IntSet
instance.
- isAlleleCoded() - Method in class vcf.LowMafRefDiallelicGT
-
- isAlleleCoded() - Method in class vcf.LowMafRefGT
-
- isAlleleCoded() - Method in interface vcf.RefGTRec
-
Returns true
if this instance stores the indices of haplotypes
that carry non-major alleles, and returns false
otherwise.
- isAlleleCoded() - Method in class vcf.SeqCodedRefGT
-
- isCarrier(int, int) - Method in class vcf.LowMafRefDiallelicGT
-
- isCarrier(int, int) - Method in class vcf.LowMafRefGT
-
- isCarrier(int, int) - Method in interface vcf.RefGTRec
-
Returns true
if the specified haplotype carries the specified
allele and return false
otherwise.
- isCarrier(int, int) - Method in class vcf.SeqCodedRefGT
-
- isEmpty() - Method in class blbutil.FloatArray
-
Returns true
if this list has no elements, and returns
false
otherwise.
- isEmpty() - Method in class blbutil.FloatList
-
Returns true
if this list has no elements, and returns
false
otherwise.
- isEmpty() - Method in class ints.IntList
-
Returns true
if this list has no elements, and returns
false
otherwise.
- isGTData() - Method in class vcf.BasicGT
-
- isGTData() - Method in class vcf.BitSetGT
-
- isGTData() - Method in interface vcf.GT
-
Returns true
if the value returned by this.gl()
is
determined by a called or missing genotype, and returns false
otherwise.
- isGTData() - Method in interface vcf.GTRec
-
Returns true
if the value returned by this.gl()
is
determined by a called or missing genotype, and returns false
otherwise.
- isGTData() - Method in class vcf.LowMafRefDiallelicGT
-
- isGTData() - Method in class vcf.LowMafRefGT
-
- isGTData() - Method in class vcf.SeqCodedRefGT
-
- isGTData() - Method in class vcf.SplicedGT
-
- isGTData() - Method in class vcf.VcfRecord
-
- isGTData() - Method in class vcf.XBasicGT
-
- isPhased() - Method in class haplotype.HapPairPhasedGT
-
- isPhased() - Method in class phase.EstPhase.HapsGT
-
- isPhased() - Method in class vcf.BasicGT
-
- isPhased() - Method in class vcf.BasicRefGT
-
- isPhased() - Method in class vcf.BitSetGT
-
- isPhased() - Method in interface vcf.DuplicatesGTRec
-
Returns true
if every genotype for each sample is a phased,
non-missing genotype, and returns false
otherwise.
- isPhased() - Method in interface vcf.GT
-
Returns true
if the genotype for each marker and sample
is a phased, non-missing genotype, and returns false
otherwise.
- isPhased() - Method in class vcf.LowMafRefDiallelicGT
-
Returns true
.
- isPhased() - Method in class vcf.LowMafRefGT
-
Returns true
.
- isPhased() - Method in interface vcf.RefGTRec
-
Returns true
.
- isPhased() - Method in class vcf.SeqCodedRefGT
-
Returns true
.
- isPhased() - Method in class vcf.SplicedGT
-
- isPhased() - Method in class vcf.VcfRecord
-
- isPhased() - Method in class vcf.XBasicGT
-
- isPhased(int) - Method in class haplotype.HapPairPhasedGT
-
- isPhased(int) - Method in class phase.EstPhase.HapsGT
-
- isPhased(int) - Method in class vcf.BasicGT
-
- isPhased(int) - Method in class vcf.BasicRefGT
-
- isPhased(int) - Method in class vcf.BitSetGT
-
- isPhased(int) - Method in interface vcf.DuplicatesGTRec
-
Returns true
if the genotype for the specified sample is
a phased, nonmissing genotype, and returns false
otherwise.
- isPhased(int) - Method in interface vcf.GT
-
Returns true
if the genotype for each marker for the
specified sample is a phased, nonmissing genotype, and returns
false
otherwise.
- isPhased(int) - Method in class vcf.LowMafRefDiallelicGT
-
- isPhased(int) - Method in class vcf.LowMafRefGT
-
- isPhased(int) - Method in interface vcf.RefGTRec
-
Returns true
.
- isPhased(int) - Method in class vcf.SeqCodedRefGT
-
- isPhased(int) - Method in class vcf.SplicedGT
-
- isPhased(int) - Method in class vcf.VcfRecord
-
- isPhased(int) - Method in class vcf.XBasicGT
-
- isPhased(int) - Method in class vcf.XBasicGT1
-
- isPhased(int) - Method in interface vcf.XGT1
-
Returns true
if the observed data for the specified
marker includes a phased genotype, and returns false
otherwise.
- isPhased(int, int) - Method in class haplotype.HapPairPhasedGT
-
- isPhased(int, int) - Method in class phase.EstPhase.HapsGT
-
- isPhased(int, int) - Method in class vcf.BasicGT
-
- isPhased(int, int) - Method in class vcf.BasicRefGT
-
- isPhased(int, int) - Method in interface vcf.GT
-
Returns true
if the genotype for the specified marker
and sample is a phased, nonmissing genotype, and returns false
otherwise.
- isPhased(int, int) - Method in class vcf.SplicedGT
-
- isPhased(int, int) - Method in class vcf.XBasicGT
-
- isRefSample() - Method in class vcf.XBasicGT1
-
- isRefSample() - Method in interface vcf.XGT1
-
Returns true
if the observed data for each marker
includes a phased genotype that has no missing alleles,
and returns false
otherwise.
- item(int) - Method in class beagleutil.ThreadSafeIndexer
-
Returns the object with the specified index.
- items() - Method in class beagleutil.ThreadSafeIndexer
-
Returns an listed of all indexed objects.
- items(int[]) - Method in class beagleutil.ThreadSafeIndexer
-
Returns a list of objects with the specified indices.
- iter() - Method in class phase.PhaseData
-
Returns the iteration index.
- iterationNanos(long) - Method in class main.RunStats
-
Stores the time for updating the haplotype estimates and increases the
cumulative phasing time by the specified number of nanoseconds.
- iterations() - Method in class main.Par
-
Returns the iterations parameter.
- MAGIC_NUMBER_V3 - Static variable in class bref.AsIsBref3Writer
-
The initial integer in a bref version 3 file.
- main - package main
-
- main(String[]) - Static method in class blbutil.BGZIPOutputStream
-
Applies BGZIP compression on the specified files.
- main(String[]) - Static method in class bref.Bref3
-
The main()
method is the entry point to the bref program.
- main(String[]) - Static method in class bref.UnBref3
-
The main()
method is the entry point to the bref program.
- main(String[]) - Static method in class main.Main
-
Entry point to Beagle program.
- main(String[]) - Static method in class math.Regress
-
- Main - Class in main
-
Class Main
is the entry class for the Beagle program.
- MainHelper - Class in main
-
Class MainHelper
is an auxiliary class with methods called by
the main.Main
class.
- majorAllele() - Method in class vcf.LowMafRefDiallelicGT
-
- majorAllele() - Method in class vcf.LowMafRefGT
-
- majorAllele() - Method in interface vcf.RefGTRec
-
Returns the index of the major allele.
- majorAllele() - Method in class vcf.SeqCodedRefGT
-
- map() - Method in class main.CurrentData
-
Returns the genetic map.
- map() - Method in class main.Par
-
Returns the map parameter.
- map(int) - Method in class vcf.LowMafRefDiallelicGT
-
- map(int) - Method in class vcf.LowMafRefGT
-
- map(int) - Method in interface vcf.RefGTRec
-
Returns this.maps()[index]
.
- map(int) - Method in class vcf.SeqCodedRefGT
-
- maps() - Method in class vcf.LowMafRefDiallelicGT
-
- maps() - Method in class vcf.LowMafRefGT
-
- maps() - Method in interface vcf.RefGTRec
-
Returns an array of maps, which when composed map haplotype indices
to values.
- maps() - Method in class vcf.SeqCodedRefGT
-
- marker() - Method in class imp.ImputedRecBuilder
-
Returns the marker in the VCF record.
- marker() - Method in class vcf.BitSetGT
-
- marker() - Method in class vcf.LowMafRefDiallelicGT
-
- marker() - Method in class vcf.LowMafRefGT
-
- marker() - Method in interface vcf.MarkerContainer
-
Returns the marker.
- marker() - Method in class vcf.SeqCodedRefGT
-
- 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
-
- marker(int) - Method in class haplotype.BitHapPair
-
- marker(int) - Method in interface haplotype.HapPair
-
Returns the specified marker.
- marker(int) - Method in class haplotype.HapPairPhasedGT
-
- marker(int) - Method in class haplotype.WrappedHapPair
-
- marker(int) - Method in interface main.GenotypeValues
-
Returns the specified marker.
- marker(int) - Method in class phase.EstPhase.HapsGT
-
- marker(int) - Method in class phase.PhaseData
-
Returns the specified marker.
- marker(int) - Method in class vcf.BasicGT
-
- marker(int) - Method in class vcf.BasicRefGT
-
- marker(int) - Method in interface vcf.GT
-
Returns the specified marker.
- marker(int) - Method in class vcf.MarkerMap
-
Returns the specified marker.
- marker(int) - Method in class vcf.Markers
-
Returns the specified marker.
- marker(int) - Method in class vcf.SplicedGT
-
- marker(int) - Method in class vcf.XBasicGT
-
- marker(int) - Method in class vcf.XBasicGT1
-
- marker(int) - Method in interface vcf.XGT1
-
Returns the specified marker.
- Marker - Interface in vcf
-
Interface Marker
represents a genetic marker.
- 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.nTargMarkers()
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.
- MarkerMap - Class in vcf
-
Class MarkerMap
represents genetic map positions for a
list of markers.
- markers() - Method in class haplotype.BitHapPair
-
- markers() - Method in interface haplotype.HapPair
-
Returns the markers.
- markers() - Method in class haplotype.HapPairPhasedGT
-
- markers() - Method in class haplotype.WrappedHapPair
-
- 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 class phase.EstPhase.HapsGT
-
- markers() - Method in class phase.EstPhase
-
Returns the list of markers.
- markers() - Method in class phase.PhaseData
-
Returns the list of target markers.
- markers() - Method in class vcf.AllData
-
- markers() - Method in class vcf.BasicGT
-
- markers() - Method in class vcf.BasicRefGT
-
- markers() - Method in interface vcf.Data
-
Returns the list of markers in the current window.
- markers() - Method in interface vcf.GT
-
Returns the list of markers.
- markers() - Method in class vcf.MarkerMap
-
Returns the list of markers.
- markers() - Method in class vcf.Markers
-
Returns the list of markers.
- markers() - Method in class vcf.SplicedGT
-
- markers() - Method in class vcf.TargetData
-
- markers() - Method in class vcf.XBasicGT
-
- markers() - Method in class vcf.XBasicGT1
-
- markers() - Method in interface vcf.XGT1
-
Returns the list of markers.
- Markers - Class in vcf
-
Class Markers
represent a list of markers in chromosome order.
- math - package math
-
- max(IntArray) - Static method in interface ints.IntArray
-
Returns the maximum element, or Integer.MIN_VALUE
if
this.size() == 0
.
- MAX_EM_BUFFER_SIZE - Static variable in class vcf.RefIt
-
The default number of GTRec
objects that are
stored in a buffer.
- MAX_EM_BUFFER_SIZE - Static variable in class vcf.VcfIt
-
The default number of VCF records stored in a buffer, which is 1000.
- MAX_NALLELES - Static variable in class bref.SeqCoder3
-
The maximum number of alleles are that permitted in order
for the add()
method to return true
- MAX_SAMPLES - Variable in class bref.AsIsBref3Writer
-
- maxNSeq() - Method in class bref.SeqCoder3
-
Returns the maximum number of distinct allele sequences.
- 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.
- metaInfoLine(int) - Method in class vcf.VcfHeader
-
Returns the specified VCF meta-information line.
- min(IntArray) - Static method in interface ints.IntArray
-
Returns the minimum element, or Integer.MAX_VALUE
if
this.size() == 0
.
- minutesAndSeconds() - Static method in class blbutil.Utilities
-
Returns the current minutes and seconds as a string.
- 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: "."
- mother(int) - Method in class main.Pedigree
-
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 vcf.BasicMarker
-
- nAlleles() - Method in class vcf.BitSetGT
-
- 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 interface vcf.MarkerContainer
-
Returns the number of marker alleles.
- nAlleles() - Method in class vcf.SeqCodedRefGT
-
- nAlleles() - Method in class vcf.VcfRecGTParser
-
Returns this.marker().nAlleles()
.
- 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
-
- nClusters() - Method in class imp.ImpData
-
Return the number of target marker clusters.
- nDuos() - Method in class main.Pedigree
-
Returns the number of parent-offspring duos in the list of samples.
- ne() - Method in class main.Par
-
Returns the ne parameter
- newInstance(Supplier<SampleFileIt<E>>, GeneticMap, float, float) - Static method in class vcf.WindowIt
-
Constructs and returns a new WindowIt
instance for
the specified data.
- next() - Method in class blbutil.InputIt
-
Returns the next element in the iteration.
- next() - Method in class bref.Bref3It
-
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.
- next() - Method in class vcf.WindowIt
-
Advances the sliding window of VCF recList, and returns the advanced
window as a RefGTRec[]
object.
- 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()
the next marker window is from
a different chromosome.
- nextOverlapStart() - Method in class vcf.AllData
-
- nextOverlapStart() - Method in interface vcf.Data
-
Returns the first marker index in the overlap between this
marker window and the next marker window.
- nextOverlapStart() - Method in class vcf.TargetData
-
- 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.nTargMarkers()
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 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.
- nHaps() - Method in class haplotype.HapPairPhasedGT
-
- nHaps() - Method in class imp.ImpData
-
Return the total number of reference and target haplotypes.
- nHaps() - Method in class imp.RefHapHash
-
Returns the size of the sublist of reference haplotypes.
- nHaps() - Method in class main.CurrentData
-
- nHaps() - Method in class phase.EstPhase.HapsGT
-
- nHaps() - Method in class phase.PhaseData
-
Returns the number of reference and target haplotypes.
- nHaps() - Method in class vcf.BasicGT
-
- nHaps() - Method in class vcf.BasicRefGT
-
- nHaps() - Method in interface vcf.GT
-
Returns the number of haplotypes.
- nHaps() - Method in class vcf.SplicedGT
-
- nHaps() - Method in class vcf.XBasicGT
-
- 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.
- nItsRemaining() - Method in class phase.PhaseData
-
Returns the number of iterations remaining.
- nl - Static variable in class blbutil.Const
-
The system-dependent string representing a new line-line:
System.getProperty("line.separator")
- nMapPositions(int) - Method in class vcf.PlinkGenMap
-
Returns the number of mapped loci in this genetic map.
- nMaps() - Method in class vcf.LowMafRefDiallelicGT
-
- nMaps() - Method in class vcf.LowMafRefGT
-
- nMaps() - Method in interface vcf.RefGTRec
-
Returns this.maps().length
- nMaps() - Method in class vcf.SeqCodedRefGT
-
- nMarkers() - Method in class haplotype.BitHapPair
-
- nMarkers() - Method in interface haplotype.HapPair
-
Returns the number of markers.
- nMarkers() - Method in class haplotype.HapPairPhasedGT
-
- nMarkers() - Method in class haplotype.WrappedHapPair
-
- 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 class phase.EstPhase.HapsGT
-
- nMarkers() - Method in class phase.EstPhase
-
Returns the number of markers.
- nMarkers() - Method in class phase.PhaseData
-
Returns the number of target markers
- nMarkers() - Method in class vcf.AllData
-
- nMarkers() - Method in class vcf.BasicGT
-
- nMarkers() - Method in class vcf.BasicRefGT
-
- nMarkers() - Method in interface vcf.Data
-
Returns the number of markers in the current window.
- nMarkers() - Method in interface vcf.GT
-
Returns the number of markers.
- nMarkers() - Method in class vcf.MarkerMap
-
Returns the number of markers.
- nMarkers() - Method in class vcf.Markers
-
Returns the number of markers.
- nMarkers() - Method in class vcf.SplicedGT
-
- nMarkers() - Method in class vcf.TargetData
-
- nMarkers() - Method in class vcf.Window
-
Returns the number of markers in this window.
- nMarkers() - Method in class vcf.XBasicGT
-
- nMarkers() - Method in class vcf.XBasicGT1
-
- nMarkers() - Method in interface vcf.XGT1
-
Returns the number of markers.
- 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.
- nOffspring(int) - Method in class main.Pedigree
-
Returns the number of offspring of the specified sample.
- nonBufferedPrintWriter(File, boolean) - Static method in class blbutil.FileUtil
-
Returns an unbuffered java.io.PrintWriter
writing to
the specified file.
- nonMajRefIndices() - Method in class vcf.VcfRecGTParser
-
Returns an array of length this.nAlleles()
whose
k
-th element is the list of haplotype indices carrying
the k
-th allele if k
is a non-major allele,
and whose k
-th element is null
if k
is
the major allele.
- nRecs() - Method in class bref.SeqCoder3
-
Returns the number of compressed RefGTRec
objects.
- nRefHaps() - Method in class imp.ImpData
-
Return the number of reference haplotypes.
- nRefHaps() - Method in class main.CurrentData
-
Returns the number of reference haplotypes.
- nRefHaps() - Method in class phase.PhaseData
-
Return the number of reference haplotypes.
- 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.HapPairPhasedGT
-
- nSamples() - Method in class imp.ImputedRecBuilder
-
Returns the required number of samples in the VCF record.
- nSamples() - Method in interface main.GenotypeValues
-
Returns the number of samples.
- nSamples() - Method in class main.Pedigree
-
Returns the number of samples.
- nSamples() - Method in class phase.EstPhase.HapsGT
-
- nSamples() - Method in class phase.EstPhase
-
Returns the number of samples.
- nSamples() - Method in class vcf.BasicGT
-
- nSamples() - Method in class vcf.BasicRefGT
-
- nSamples() - Method in class vcf.BitSetGT
-
- nSamples() - Method in interface vcf.DuplicatesGTRec
-
Returns the number of samples.
- nSamples() - Method in interface vcf.GT
-
Returns the number of samples.
- nSamples() - Method in class vcf.LowMafRefDiallelicGT
-
- nSamples() - Method in class vcf.LowMafRefGT
-
- nSamples() - Method in class vcf.RestrictedVcfWindow
-
Returns the number of samples.
- nSamples() - Method in class vcf.SeqCodedRefGT
-
- nSamples() - Method in class vcf.SplicedGT
-
- 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.XBasicGT
-
- nSingles() - Method in class main.Pedigree
-
Returns the number of single individuals in the list of samples.
- nStates() - Method in class imp.ImpIbs
-
Returns the number of HMM states per marker.
- nStates() - Method in class imp.ImpStates
-
Returns the number of HMM states per marker.
- nStates() - Method in class phase.PhaseIbs
-
Returns the number of HMM states per marker.
- nStates() - Method in class phase.PhaseStates
-
Returns the number of HMM states per marker.
- nStates(int) - Method in interface imp.StateProbs
-
Returns the number of stored HMM states at the specified
target marker.
- nsteps() - Method in class main.Par
-
Returns the nsteps parameter.
- nSteps() - Method in class imp.ImpIbs
-
Returns the number of IBS steps in the marker window.
- nSteps() - Method in class phase.PhaseIbs
-
Returns the number of IBS steps in the marker window.
- 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
-
- nTargHaps() - Method in class imp.ImpData
-
Return the number of target haplotypes.
- nTargHaps() - Method in class main.CurrentData
-
Returns the number of target haplotypes.
- nTargHaps() - Method in class phase.PhaseData
-
Return the number of target haplotypes.
- nTargMarkers() - Method in interface imp.StateProbs
-
Returns the number of target markers.
- nTargMarkers() - Method in class imp.StateProbsFactory
-
Returns the number of target marker.
- nTargMarkers() - Method in class main.CurrentData
-
Returns the number of target data markers.
- nTargSamples() - Method in class imp.ImpData
-
Returns the number of target samples.
- nTargSamples() - Method in class phase.PhaseData
-
Returns the number of target samples.
- nthreads() - Method in class main.Par
-
Returns the nthreads parameter.
- nTrios() - Method in class main.Pedigree
-
Returns the number of parent-offspring trios in the list of samples.
- nUnfilteredSamples() - Method in class vcf.VcfHeader
-
Returns the number of samples before sample exclusions.
- nUnphasedHets(int) - Method in class phase.EstPhase
-
Returns the number of unphased, non-missing heterozygote
genotypes.
- PackedIntArray - Class in ints
-
Class PackedIntArray
represents an immutable array of
nonnegative integer values, which are stored in compressed form.
- PackedIntArray(int[], int) - Constructor for class ints.PackedIntArray
-
Constructs a new PackedIntArray
instance from the specified data.
- PackedIntArray(IntList, int) - Constructor for class ints.PackedIntArray
-
Constructs a new PackedIntArray
instance from the specified data.
- Pair<F,S> - Class in blbutil
-
Class Pair
represents a pair of ordered objects.
- Pair(F, S) - Constructor for class blbutil.Pair
-
Constructs a Pair
instance representing the specified
ordered pair of objects.
- par() - Method in class imp.ImpData
-
Returns the command line parameters
- par() - Method in class main.CurrentData
-
Return the analysis parameters.
- par() - Method in class phase.PhaseData
-
Returns the command line parameters
- 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.
- 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.CurrentData
-
Returns the parent-offspring relationships.
- ped() - Method in class main.Par
-
Returns the ped parameter or null
if no ped parameter was specified.
- ped() - Method in class vcf.AllData
-
- ped() - Method in interface vcf.Data
-
Returns the pedigree.
- ped() - Method in class vcf.TargetData
-
- Pedigree - Class in main
-
Class Pedigree
stores parent-offspring relationships
in a list of samples.
- Pedigree(Samples, File) - Constructor for class main.Pedigree
-
Constructs a new NuclearFamilies
instance.
- pErr(int) - Method in class phase.PhaseData
-
Returns the probability that the allele carried by the specified
target marker cluster matches the allele labeling the latent HMM state.
- phase - package phase
-
- phase(EstPhase, int, Regress) - Method in class phase.PhaseBaum1
-
Estimates and returns phased haploytpes for the specified sample
- Phase - Enum in beagleutil
-
Class Phase
represents the equivalence of two phased genotypes
for a marker or for a set of markers.
- phase_segment() - Method in class main.Par
-
Returns the phase-segment parameter.
- phase_states() - Method in class main.Par
-
Returns the phase-states parameter.
- PhaseBaum1 - Class in phase
-
Class PhaseBaum1
implements the forward and backward algorithms
for a haploid Li and Stephens hidden Markov model.
- PhaseBaum1(PhaseData, PhaseIbs) - Constructor for class phase.PhaseBaum1
-
Creates a PhaseLSBaum
instance from the specified data.
- phasedAlleles() - Method in class vcf.VcfRecGTParser
-
Returns the list of phased alleles in the backing VCF record.
- phaseData() - Method in class phase.PhaseIbs
-
Return the data used to phase genotypes in a marker window.
- PhaseData - Class in phase
-
Class PhaseData
contains the input data for phasing
genotypes.
- PhaseData(CurrentData, EstPhase, double, int, long) - Constructor for class phase.PhaseData
-
Constructs a new ImpData
instance from the specified data.
- phasedSep - Static variable in class blbutil.Const
-
The phased allele separator: '|'
- PhaseIbs - Class in phase
-
Class PhaseIbs
identifies haplotypes that share a long
IBS segment with a specified haplotype.
- PhaseIbs(PhaseData) - Constructor for class phase.PhaseIbs
-
Constructs a new PhaseIbs
object from the specified data.
- PhaseLS - Class in phase
-
Class PhaseLS
estimated genotypes phase using
a haploid Li and Stephens hidden Markov model.
- PhaseStates - Class in phase
-
Class PhaseStates
identifies a rolling window of reference
haplotypes for a target sample.
- PhaseStates(PhaseIbs) - Constructor for class phase.PhaseStates
-
Constructs a new PhaseIbs
object from the specified data.
- PL_FORMAT - Static variable in class vcf.VcfRecord
-
The VCF FORMAT code for phred-scaled genotype likelihood data: "PL".
- PlinkGenMap - Class in vcf
-
Class PlinkGenMap
represents a genetic map derived
from a PLINK map file with map positions in cM units for one or more
chromosomes.
- pop() - Method in class ints.IntList
-
Removes and returns the last entry of this list.
- pos() - Method in class bref.BrefBlock
-
Returns the chromosome position of the first marker in this bref block.
- pos() - Method in class imp.ImpData
-
Return an array of size this.nClusters()
containing the
the genetic map positions of the target marker clusters.
- pos() - Method in class phase.PhaseData
-
Returns the array of genetic map positions whose k
-th element
equals this.pos(k)
.
- pos() - Method in class vcf.BasicMarker
-
- pos() - Method in interface vcf.Marker
-
Returns the chromosome position coordinate.
- pos(int) - Method in class imp.ImpData
-
Return the genetic map position of the specified target marker cluster.
- PositionMap - Class in vcf
-
Class PositionMap
represents a genetic map obtained by
multiplying chromosome position by a scale factor.
- PositionMap(double) - Constructor for class vcf.PositionMap
-
Constructs a new PositionMap
instance.
- pRecomb() - Method in class phase.PhaseData
-
Return a FloatArray
of size this.nTargMarkers()
whose k
-th element is the factor multiplied by genetic distance
to obtain the probability of transitioning to a random HMM state
between the k
-th target marker and the previous marker.
- pRecomb(int) - Method in class imp.ImpData
-
Return the probability of recombination between the specified
target marker cluster and the previous target marker cluster.
- pRecomb(Markers, double) - Method in interface vcf.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
.
- PREFIX - Static variable in class vcf.VcfMetaInfo
-
The VCF meta-information line prefix: "##"
- 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(ImpData, AtomicReferenceArray<StateProbs>, int, int) - Method in class main.WindowWriter
-
Prints the data in alProbs
for markers
with index between refStart
(inclusive) and
refEnd
(exclusive) to the output
VCF file: this.outPrefix() + ".vcf.gz"
.
- print(GT, int, int, int) - Method in class main.WindowWriter
-
Writes the data in phased genotypes for the specified markers
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).
- 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.
- printPhasingIterationUpdate(int, boolean, long) - Method in class main.RunStats
-
- printRec(PrintWriter, boolean) - Method in class imp.ImputedRecBuilder
-
Prints the VCF record to the specified PrintWriter
.
- printSampleSummary(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.
- probs(int, int) - Method in interface imp.StateProbs
-
Returns the probability of the specified state at the specified target
marker.
- probsP1(int, int) - Method in interface imp.StateProbs
-
Returns the probability of the specified state at the marker following
the specified target marker.
- PROGRAM - Static variable in class main.Main
-
- put(int, E) - Method in class ints.IntMap
-
Adds the specified key and value to this 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.
- randomAccessFile(File, String) - Static method in class blbutil.FileUtil
-
Returns a java.io.RandomAccessFile
to read from or optionally
to write to the specified file.
- rec(int) - Method in class vcf.Window
-
Returns the specified record.
- recList() - Method in class vcf.Window
-
Returns the list of recList in this window.
- recodeIfLowFreq(RefGTRec) - Static method in class vcf.RefIt
-
- ref() - Method in class main.Par
-
Returns the ref parameter or null
if no ref parameter was
specified.
- refClusterEnd(int) - Method in class imp.ImpData
-
Returns the index of the reference marker corresponding to the end
(exclusive) of the specified target marker cluster.
- refClusterStart(int) - Method in class imp.ImpData
-
Returns the index of the reference marker corresponding to the start
(inclusive) of the specified target marker cluster.
- refGT() - Method in class imp.ImpData
-
Return the reference genotype data
- refGT() - Method in class imp.RefHapHash
-
Returns the phased reference genotypes.
- refGT() - Method in class main.CurrentData
-
Returns the phased, nonmissing reference genotype data
or null
if there are no reference data.
- refGT() - Method in class vcf.AllData
-
- refGT() - Method in interface vcf.Data
-
Returns the phased, nonmissing reference genotype data
for the current window, or null
if there are no reference data
- refGT() - Method in class vcf.TargetData
-
- RefGT - Interface in vcf
-
Interface RefGT
represents phased, compressed, nonmissing
genotype data for a list of markers and a list of reference samples.
- RefGTRec - Interface in vcf
-
Interface RefGTRec
represents represents phased genotype data
for one marker.
- refHap(int, int) - Method in interface imp.StateProbs
-
Returns the specified reference haplotype index.
- RefHapHash - Class in imp
-
Class RefHapHash
stores a hash code for each haplotype
in a sublist of reference haplotypes.
- RefHapHash(AtomicReferenceArray<StateProbs>, int, RefGT, int, int) - Constructor for class imp.RefHapHash
-
Constructs a new RefHapHash
instance for the specified data.
- refHapPairs() - Method in class imp.HaplotypeCoder
-
Returns the phased reference genotypes at the target markers.
- 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
-
- 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.
- 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
-
- Regress - Class in math
-
Class Regress
estimates a regression coefficient.
- Regress() - Constructor for class math.Regress
-
Constructs a new Regress
instance.
- relateds() - Method in class main.Pedigree
-
Returns an array of indices of samples with at least one
parent or child in the list or samples.
- remove() - Method in class blbutil.InputIt
-
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.
- remove(int) - Method in class ints.IntMap
-
Removes the specified key from this map, and returns the value
previously associated with the key or null
if no such
value exists.
- remove(int) - Method in class ints.IntSet
-
Removes the specified element from this set.
- 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 vcf.Markers
-
Returns a Markers
instance that represents
the specified range of marker indices.
- 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
-
- RestrictedVcfWindow - Class in vcf
-
Class RestrictedVcfWindow
represents a sliding window of VCF
records.
- RestrictedVcfWindow(SampleFileIt<? extends GTRec>) - Constructor for class vcf.RestrictedVcfWindow
-
Construct a new RestrictedVcfWindow
instance.
- restrictRefGT() - Method in class main.CurrentData
-
Returns the phased, nonmissing reference genotype data for
the target data markers or null
if there are no reference data.
- restrictRefGT() - Method in class vcf.AllData
-
- restrictRefGT() - Method in interface vcf.Data
-
Returns the phased, nonmissing reference genotype data
for the target data markers in the current window.
- restrictRefGT() - Method in class vcf.TargetData
-
- run(int, int) - Method in class imp.HaplotypeCoder
-
Returns an array mapping haplotype indices to allele sequence indices
in the specified marker interval.
- run(PhaseData, EstPhase, Regress) - Static method in class phase.PhaseLS
-
Estimates and stores phased haplotypes for the target samples.
- run(GT, GT, double, long) - Static method in class sample.InitTargHapPairs
-
Returns initial target haplotype pairs.
- RunStats - Class in main
-
Class RunStats
contains methods for storing and printing
statistics describing a Beagle analysis.
- sample - package sample
-
- sampleCnt() - Method in class imp.ImputedRecBuilder
-
Returns the number of times the this.addSampleData()
method has been invoked.
- sampleData(int) - Method in class vcf.VcfRecord
-
Returns the data for the specified sample.
- sampleData(int, int) - Method in class vcf.VcfRecord
-
Returns the specified data for the specified sample.
- sampleData(int, String) - 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
- sampleIds() - Method in class vcf.VcfHeader
-
Returns this.sample().ids()
.
- SampleIds - Class in beagleutil
-
Class SampleIds
is a singleton class that represents a
list of sample identifiers.
- samples() - Method in interface blbutil.SampleFileIt
-
Returns the list of samples.
- samples() - Method in class bref.AsIsBref3Writer
-
- samples() - Method in class bref.Bref3It
-
- samples() - Method in interface bref.BrefWriter
-
Returns the list of samples.
- samples() - Method in class bref.CompressBref3Writer
-
- samples() - Method in class bref.SeqCoder3
-
Returns the list of samples whose phased genotype data will be compressed.
- samples() - Method in class haplotype.HapPairPhasedGT
-
- samples() - Method in interface main.GenotypeValues
-
Returns the list of samples.
- samples() - Method in class main.Pedigree
-
Returns the list of samples.
- samples() - Method in class main.WindowWriter
-
Returns the samples whose data is written by this
.
- samples() - Method in class phase.EstPhase.HapsGT
-
- samples() - Method in class phase.EstPhase
-
Returns the list of target samples.
- samples() - Method in class vcf.BasicGT
-
- samples() - Method in class vcf.BasicRefGT
-
- samples() - Method in class vcf.BitSetGT
-
- samples() - Method in interface vcf.GT
-
Returns the list of samples.
- samples() - Method in interface vcf.GTRec
-
Returns the list of samples.
- samples() - Method in class vcf.IntervalVcfIt
-
- samples() - Method in class vcf.LowMafRefDiallelicGT
-
- samples() - Method in class vcf.LowMafRefGT
-
- samples() - Method in class vcf.RefIt
-
- samples() - Method in class vcf.RestrictedVcfWindow
-
Returns the list of samples.
- samples() - Method in class vcf.SeqCodedRefGT
-
- samples() - Method in class vcf.SplicedGT
-
- 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.WindowIt
-
Returns the list of samples.
- samples() - Method in class vcf.XBasicGT
-
- 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.
- scaleFactor() - Method in class vcf.PositionMap
-
Returns the scale factor that is multiplied by the chromosome position
to obtain the corresponding genetic map position
- second() - Method in class blbutil.Pair
-
Returns the second object in the ordered pair of objects.
- seed() - Method in class main.Par
-
Returns the seed parameter.
- seed() - Method in class phase.PhaseData
-
Returns the seed for generating random numbers.
- semicolon - Static variable in class blbutil.Const
-
The semicolon character: ';'
- SEQ_CODED - Static variable in class bref.AsIsBref3Writer
-
The byte value denoting a sequence coded record
- 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.
- SeqCoder3 - Class in bref
-
Class SeqCoder3
compresses a sequence of allele-coded
RefGTRec
objects.
- SeqCoder3(Samples) - Constructor for class bref.SeqCoder3
-
Constructs a new SeqCoder3
for the specified samples.
- SeqCoder3(Samples, int) - Constructor for class bref.SeqCoder3
-
Constructs a new SeqCoder3
for the specified samples.
- set(int, float) - Method in class blbutil.FloatList
-
Replaces the element at the specified position in this list with the
specified element.
- set(int, int) - Method in class ints.IntList
-
Replaces the element at the specified position in this list with the
specified element.
- setAlleles(int, int[]) - Method in class imp.RefHapHash
-
Copies the alleles between this.start()
(inclusive) and
this.end()
(exclusive) of the specified haplotype in the sublist
of reference haplotypes to the specified array.
- setCapacity(int) - Method in class ints.IntSet
-
Sets the capacity of this list to the specified value.
- setHapPair(int, int[], int[]) - Method in class phase.EstPhase
-
Sets the haplotype pair for the specified sample to the specified
haplotypes.
- setHapsWithMaskedMissingAlleles(int, int[], int[]) - Method in class phase.EstPhase
-
Sets the k
-th element of the specified hap1
and
hap2
arrays to the specified sample's phased genotype
at the k
-th marker if the genotype is nonmissing, and sets the
k
-th element of hap1
and hap2
to
-1
otherwise.
- setUnphasedHets(int, IntArray) - Method in class phase.EstPhase
-
Sets the array with marker indices of unphased, nonmissing heterozygote
genotypes to the specified array.
- SHORT_HELP - Static variable in class main.Main
-
The program name and a brief help message.
- shuffle(int[], int, Random) - Static method in class blbutil.Utilities
-
Shuffles the specified array so that a random set of ${code nElements}
from the array are the first elements.
- shuffle(int[], Random) - Static method in class blbutil.Utilities
-
Randomly shuffles the elements of the specified array.
- single(int) - Method in class main.Pedigree
-
Returns the sample index of the specified single individual.
- singles() - Method in class main.Pedigree
-
Returns an array of indices of samples with no parents or
children in the list of samples.
- size() - Method in class beagleutil.ChromIds
-
Returns the number of indexed chromosomes identifiers.
- 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.FloatArray
-
Returns the number of elements in this list.
- size() - Method in class blbutil.FloatList
-
Returns the number of elements in this list.
- size() - Method in class ints.CharArray
-
- size() - Method in class ints.IndexArray
-
- size() - Method in interface ints.IntArray
-
Returns the number of elements in this IntArray
.
- size() - Method in class ints.IntList
-
Returns the number of elements in this list.
- size() - Method in class ints.IntMap
-
Returns the number of keys in this map.
- size() - Method in class ints.IntSet
-
Returns the number of elements in this set.
- size() - Method in class ints.LongArray
-
Returns the number of elements in this LongArray
.
- size() - Method in class ints.PackedIntArray
-
- size() - Method in class ints.UnsignedByteArray
-
- size() - Method in class ints.WrappedIntArray
-
- size() - Method in class vcf.BitSetGT
-
- size() - Method in interface vcf.DuplicatesGTRec
-
Returns the number of haplotypes.
- size() - Method in class vcf.LowMafRefDiallelicGT
-
- size() - Method in class vcf.LowMafRefGT
-
- size() - Method in class vcf.SeqCodedRefGT
-
- size() - Method in class vcf.VcfRecord
-
- sort() - Method in class ints.IntList
-
Sorts the elements of this list in increasing order
- SplicedGT - Class in vcf
-
Class SplicedGT
represents genotype emission probabilities
for a set of samples.
- SplicedGT(GT, GT) - Constructor for class vcf.SplicedGT
-
Constructs a new SplicedGL
instance.
- 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 class imp.RefHapHash
-
Returns the starting reference marker index (inclusive)
for the reference haplotype allele sequences.
- stateProbs(int, int, int[][], float[][]) - Method in class imp.StateProbsFactory
-
Stores the reference haplotypes and state probabilities that
will be used to imputed missing state probabilities using linear
interpolation.
- stateProbs(ImpData) - Static method in class imp.ImpLS
-
Returns estimated HMM state probabilities at genotyped markers
for each target haplotype.
- StateProbs - Interface in imp
-
Class StateProbs
stores a subset of Li and Stephens HMM states
and associated probabilities for a target haplotype.
- StateProbsFactory - Class in imp
-
Class StateProbsFactory
stores HMM state probabilities
that that can be used to imputed impute missing HMM state probabilities
using linear interpolation.
- StateProbsFactory(int) - Constructor for class imp.StateProbsFactory
-
Creates an StateProbsFactory
instance from the specified data.
- stdOutPrintWriter() - Static method in class blbutil.FileUtil
-
Returns a java.io.PrintWriter
that writes
to standard out.
- step() - Method in class main.Par
-
Returns the step parameter.
- stepStart(int) - Method in class imp.ImpIbs
-
Returns the index of the first marker in the specified step.
- stepStart(int) - Method in class phase.PhaseIbs
-
Returns the first marker index in the specified step.
- storeAlleles(BitSet, BitSet, BitSet, BitSet, BitSet) - Method in class vcf.VcfRecGTParser
-
Stores the genotypes genotypes in the specified BitSets.
- stream() - Method in class ints.IntList
-
Returns an IntStream
containing the sequence of elements in this
list.
- 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() - Method in class vcf.Markers
-
Returns this.sumAlleles(this.nMarkers())
.
- 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.
- sumGenotypes() - Method in class vcf.Markers
-
Returns this.sumGenotypes(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.
- sumHaplotypeBits() - Method in class vcf.Markers
-
Returns this.sumHaplotypeBits(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.
- tab - Static variable in class blbutil.Const
-
The tab character: '\t'
- targClusterEnd(int) - Method in class imp.ImpData
-
Returns the target marker index corresponding to the end (exclusive) of
the specified marker cluster.
- targClusterStart(int) - Method in class imp.ImpData
-
Returns the target marker index corresponding to the start (inclusive)
of the specified marker cluster.
- targetData(Par, Supplier<SampleFileIt<GTRec>>) - Static method in class vcf.TargetData
-
Constructs and returns a new TargetData
instance from
VcfRecords returned by the specified SampleFileIt
objects.
- TargetData - Class in vcf
-
Class TargetData
represents a sliding window of
target VCF records.
- 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
-
- 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 vcf.AllData
-
- targetSamples() - Method in interface vcf.Data
-
Returns the list of target samples.
- targetSamples() - Method in class vcf.TargetData
-
- targGT() - Method in class imp.ImpData
-
Return the phased target genotype data.
- targGT() - Method in class main.CurrentData
-
Returns the genotype likelihoods for the
target samples at the target data markers.
- targGT() - Method in class vcf.AllData
-
- targGT() - Method in interface vcf.Data
-
Returns the genotype likelihoods for the target samples
restricted to the target data markers in the current window.
- targGT() - Method in class vcf.TargetData
-
- targHap() - Method in interface imp.StateProbs
-
Returns the target haplotype index.
- targHapPairs() - Method in class imp.HaplotypeCoder
-
Returns the phased target genotypes.
- targMarker() - Method in class imp.RefHapHash
-
Returns the target marker.
- targMarkerIndex(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.
- targMarkerIndices() - 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.
- targMarkers() - Method in class main.CurrentData
-
Returns the list of target data markers.
- targSamples() - Method in class imp.ImpData
-
Returns the list of target samples.
- targSamples() - Method in class main.CurrentData
-
Returns the list of target samples.
- tempFile(String) - Static method in class blbutil.FileUtil
-
Returns a temporary File
that will be deleted when
the Java virtual machine exits.
- tempFile(String, File) - Static method in class blbutil.FileUtil
-
Creates and returns a new empty temporary file in the specified
directory.
- 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 blbutil.FloatArray
-
Returns an integer array containing the sequence of elements in this
list.
- toArray() - Method in class blbutil.FloatList
-
Returns an integer array containing the sequence of elements in this
list.
- toArray() - Method in class ints.IntList
-
Returns an integer array containing the sequence of elements in this
list.
- toArray() - Method in class ints.IntSet
-
Returns an array containing the elements in this set.
- toArray(IntArray) - Static method in interface ints.IntArray
-
Returns a copy of the specified array.
- toArray(LongArray) - Static method in class ints.LongArray
-
Returns a copy of the specified array.
- toBitSetGT - Static variable in class vcf.VcfIt
-
A function mapping a string VCF record with GT format fields
to a GTRec
object.
- 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.
- toList(AtomicReferenceArray<E>) - Static method in class main.MainHelper
-
- 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 interface blbutil.FileIt
-
Returns a string representation of this
.
- toString() - Method in class blbutil.FloatArray
-
Returns a string representation of this list that is
obtained by calling java.util.Arrays.toString(this.toArray())
.
- toString() - Method in class blbutil.FloatList
-
Returns a string representation of this list.
- toString() - Method in class blbutil.InputIt
-
Returns a string representation of this iterator.
- toString() - Method in class blbutil.Pair
-
Returns a string representation of this
.
- toString() - Method in class bref.Bref3It
-
- toString() - Method in class bref.Bref3Reader
-
- toString() - Method in class bref.BrefBlock
-
Returns a string description of this
.
- toString() - Method in class haplotype.BitHapPair
-
Returns a string representation of this
.
- toString() - Method in class ints.IntList
-
Returns java.util.Arrays.toString(this.toArray())
- toString() - Method in class ints.IntMap
-
Returns java.util.Arrays.toString(this.keys())
.
- toString() - Method in class ints.IntSet
-
Returns java.util.Arrays.toString(this.toArray())
.
- toString() - Method in class ints.UnsignedByteArray
-
- toString() - Method in class ints.WrappedIntArray
-
- toString() - Method in interface main.GenotypeValues
-
Returns a string representation of this
.
- toString() - Method in class main.Pedigree
-
Returns a string representation of this
.
- toString() - Method in class vcf.AllData
-
Returns a string representation of this
.
- toString() - Method in class vcf.BasicGT
-
- 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 interface vcf.GeneticMap
-
Returns a string representation of this genetic map.
- 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.PlinkGenMap
-
- toString() - Method in class vcf.RefIt
-
- toString() - Method in class vcf.RestrictedVcfWindow
-
Returns a string representation of this
.
- 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.SplicedGT
-
- 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.WindowIt
-
Returns a string representation of this
.
- toString() - Method in class vcf.XBasicGT
-
- toString() - Method in class vcf.XBasicGT1
-
- toString() - Method in interface vcf.XGT1
-
Returns a string representation of this
.
- toVcfRec(GTRec) - Static method in interface vcf.GTRec
-
Returns a VCF record corresponding to the specified GTRec
object.
- toVcfRecord - Static variable in class vcf.VcfIt
-
A function mapping a string VCF record with GT or GL format fields
to a VcfRecord
object.
- trioFather(int) - Method in class main.Pedigree
-
Returns the sample index of the father of the specified
parent-offspring trio.
- trioMother(int) - Method in class main.Pedigree
-
Returns the sample index of the mother of the specified
parent-offspring trio.
- trioOffspring(int) - Method in class main.Pedigree
-
Returns the sample index of the offspring of the specified
parent-offspring trio.
- truncate(int) - Method in class ints.IntList
-
Truncates this list of integer by removing all elements whose
index is greater than or equal to the specified size.
- truth() - Method in class main.Par
-
Returns the truth parameter
- Validate - Class in blbutil
-
Class Validate contains static methods for validating command line
arguments.
- value() - Method in class vcf.VcfMetaInfo
-
Returns the VCF meta-information line value.
- value(int, int, int) - Method in interface main.GenotypeValues
-
Returns the specified genotype 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.
- values() - Method in class ints.IntMap
-
Returns a list containing the values in this map.
- valueSize() - Method in class ints.IndexArray
-
Returns the value size that was specified at construction.
- valueSize(int[]) - Static method in class ints.IndexArray
-
Returns the minimum integer that is greater than all elements in the
specified array of non-negative values.
- valueSize(IntArray) - Static method in class ints.IndexArray
-
Returns the minimum integer that is greater than all elements in the
specified list of non-negative values.
- vcf - package vcf
-
- vcfHeader() - Method in class vcf.VcfRecGTParser
-
Returns the VCF meta-information lines and header line for the backing
VCF record
- vcfHeader() - Method in class vcf.VcfRecord
-
Returns the VCF meta-information lines and the VCF header line.
- 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>
.
- 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 backing VCF record.
- VcfRecord - Class in vcf
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Class VcfRecord
represents a VCF record.
- VcfWriter - Class in vcf
-
Class VcfWriter
contains static methods for writing data in
VCF 4.2 format.
- VERSION - Static variable in class main.Main
-
The program name and version.