A B C D E F G H I K L M N O P Q R S T U V W X Z
All Classes All Packages
All Classes All Packages
All Classes All Packages
A
- accept(E) - Method in interface blbutil.Filter
-
Returns
true
if the specified object is accepted and returnsfalse
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(Regress) - Method in class math.Regress
-
Records the specified values of the dependent and independent variables.
- add(RefGTRec) - Method in class bref.SeqCoder3
-
Attempts to add the specified
RefGTRec
object to the list of compressedRefGTRec
objects, and returnstrue
if theRefGTRec
object was added. - addIbsHaps(int, int, PhaseStates) - Method in class phase.LowFreqPhaseIbs
- addIbsHaps(int, int, PhaseStates) - Method in class phase.PbwtPhaseIbs
- addIbsHaps(int, int, PhaseStates) - Method in interface phase.PhaseIbs
-
Adds haplotypes that are IBS with the specified haplotype to the HMM state space.
- addRecords(List<E>, int, int) - Method in class vcf.Window
-
Adds the specified records to he specified list.
- 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.
- addSampleData(int, int) - Method in class vcf.VcfRecBuilder
-
Adds the FORMAT field for a sample to the VCF record for the current marker.
- 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 specifiedSampleFileIt
objects. - AllData - Class in vcf
-
Class
AllData
represents a sliding window of reference and target VCF records. - allele(int) - Method in class vcf.BasicMarker
- allele(int) - Method in interface vcf.Marker
-
Returns the specified allele.
- 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.PhaseData
-
Returns the allele carried by the specified high-frequency marker and haplotype.
- allele(int, int) - Method in class vcf.BasicGT
- 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.HapsGT
- allele(int, int) - Method in class vcf.RefGT
- allele(int, int) - Method in class vcf.RestrictedGT
- 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 vcf.BitSetGTRec
- 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.LowMafRefDiallelicGTRec
- allele1(int) - Method in class vcf.LowMafRefGTRec
- allele1(int) - Method in class vcf.SeqCodedRefGTRec
- allele1(int) - Method in class vcf.VcfRec
- 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 vcf.BasicGT
- 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.HapsGT
- allele1(int, int) - Method in class vcf.RefGT
- allele1(int, int) - Method in class vcf.RestrictedGT
- allele1(int, int) - Method in class vcf.SplicedGT
- allele1(int, int) - Method in class vcf.XBasicGT
- allele2(int) - Method in class vcf.BitSetGTRec
- 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.LowMafRefDiallelicGTRec
- allele2(int) - Method in class vcf.LowMafRefGTRec
- allele2(int) - Method in class vcf.SeqCodedRefGTRec
- allele2(int) - Method in class vcf.VcfRec
- 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 vcf.BasicGT
- 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.HapsGT
- allele2(int, int) - Method in class vcf.RefGT
- allele2(int, int) - Method in class vcf.RestrictedGT
- 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.LowMafRefDiallelicGTRec
- alleleCount(int) - Method in class vcf.LowMafRefGTRec
- alleleCount(int) - Method in interface vcf.RefGTRec
-
Returns the number of haplotypes that carry the specified allele.
- alleleCount(int) - Method in class vcf.SeqCodedRefGTRec
- alleleCounts(GTRec) - Static method in interface vcf.GTRec
-
Returns the allele counts.
- alleleFreq(GTRec) - Static method in interface vcf.GTRec
-
Returns the allele frequencies.
- AlleleImputer - Class in phase
-
Class
AlleleImputer
imputes alleles from marker allele frequencies. - AlleleImputer(GT, GT, long) - Constructor for class phase.AlleleImputer
-
Constructs a new
AlleleImputer
instance from the specified data. - alleles() - Method in class vcf.BasicMarker
- alleles() - Method in class vcf.BitSetGTRec
- alleles() - Method in interface vcf.DuplicatesGTRec
-
Returns an array of length
this.size()
whosej
-th element is equal tothis.allele(j
} - alleles() - Method in class vcf.LowMafRefDiallelicGTRec
- alleles() - Method in class vcf.LowMafRefGTRec
- alleles() - Method in interface vcf.Marker
-
Returns the alleles.
- alleles() - Method in class vcf.SeqCodedRefGTRec
- alleles() - Method in class vcf.VcfRec
- allelesToBits(int[]) - Method in class vcf.Markers
-
Returns a bit array storing the specified haplotype.
- 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(GT, int, int, PrintWriter) - Static method in class vcf.VcfWriter
-
Writes the data in phased genotypes for the specified markers to the specified
PrintWriter
. - areIbs2(int, int, int) - Method in class phase.Ibs2
-
Returns
true
if the specified samples are estimated to be IBS2 at the specified marker, and the IBS2 interval is at leastthis.minCmIbs2()
cM in length, and returnsfalse
otherwise. - 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 applyingjava.utils.Arrays.toString()
to an equivalentint[]
object. - asString(LongArray) - Static method in class ints.LongArray
-
Returns a string representation of this
LongArray
by applyingjava.utils.Arrays.toString()
to an equivalentint[]
object.
B
- 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.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. - beagleutil - package beagleutil
- BestMatch - Class in phase
-
Class
BestMatch
has methods for finding a haplotype that shares a long IBS sequence containing a specified genomic interval with a target haplotype and that originates from a sample which carries a rare variant in the specified genomic interval that is also carried by the target sample. - BestMatch(PhaseData) - Constructor for class phase.BestMatch
-
Constructs a new
BestMatch
instance from the specified data - 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. - BitSetGTRec - Class in vcf
-
Class
BitSetGT
represents genotype emission probabilities for a list of samples at a single marker. - BitSetGTRec(VcfHeader, String) - Constructor for class vcf.BitSetGTRec
-
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. - bitsToAlleles(LongArray) - 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 whosenext()
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. - buffer() - Method in class main.Par
-
Return the buffer parameter.
- 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.
- bwdMatch(int) - Method in class phase.BestMatch
-
Returns an array mapping each target haplotype to a matching haplotype.
- bwdUpdate(float[], float, byte[], int) - Method in class phase.HmmUpdater
-
Updates the backward values.
- bwdUpdate(IntArray, int, int, int[], int[]) - Method in class beagleutil.PbwtUpdater
-
Update the specified prefix and divergence arrays using the backward Positional Burrows-Wheeler Transform.
C
- canAdvanceWindow() - Method in class vcf.AllData
- canAdvanceWindow() - Method in interface vcf.Data
-
Returns
true
if the sliding window of VCF records can advance and returnsfalse
otherwise. - canAdvanceWindow() - Method in class vcf.TargetData
- carriers(int) - Method in class vcf.AllData
- carriers(int) - Method in interface vcf.Data
-
Returns the indices of the reference and target carriers for each low-frequency allele at the target data markers.
- carriers(int) - Method in class vcf.TargetData
- carriers(int, int) - Method in class phase.FixedPhaseData
-
Returns the indices of the reference and target samples for the specified low-frequency allele.
- 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.
- 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.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.IntIntMap
-
Removes all keys from this map.
- clear() - Method in class ints.IntList
-
Removes all elements from this list.
- 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.
- codedSteps() - Method in class imp.ImpIbs
-
Returns the coded steps.
- codedSteps() - Method in class phase.BestMatch
-
Returns the coded steps.
- codedSteps() - Method in class phase.PhaseData
-
Returns the coded steps.
- CodedSteps - Class in imp
-
Class
CodedSteps
divides phased genotype data into non-overlapping intervals (the steps), indexes the unique allele sequences in each interval, and stores a map of haplotype index to allele sequence index for each interval. - CodedSteps - Class in phase
-
Class
CodedSteps
divides phased genotype data into non-overlapping intervals (the steps), indexes the unique allele sequences in each interval, and stores a map of haplotype index to allele sequence index for each interval. - CodedSteps(ImpData) - Constructor for class imp.CodedSteps
-
Constructs a new
CodedSteps
instance from the specified data. - CodedSteps(GT, GT, MarkerMap, double, float, long) - Constructor for class phase.CodedSteps
-
Constructs a new
CodedSteps
instance from the specified data. - 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.
- compareTo(ChromInterval) - Method in class beagleutil.ChromInterval
-
Compares this
ChromInteval
with the specifiedChromInterval
instance for order, and returns -1, 0, or 1 depending on whetherthis
is less than, equal or greater than the specified instance. - compareTo(CompHapSegment) - Method in class main.CompHapSegment
-
Compares the specified segment to
this
for order. - compareTo(SampleSeg) - Method in class phase.SampleSeg
-
Compares this object with the specified object for order.
- compareTo(Marker) - Method in class vcf.BasicMarker
- compareTo(Marker) - Method in interface vcf.Marker
-
Compares this marker with the specified marker for order, and returns a negative integer, 0, or a positive integer depending on whether this marker is less than, equal to, or greater than the specified marker.
- compHapIndex() - Method in class main.CompHapSegment
-
Returns the composite haplotype index.
- CompHapSegment - Class in main
-
Class
CompHapSegment
represents a copied haplotype segment in a composite reference haplotype. - CompHapSegment(int, int, int) - Constructor for class main.CompHapSegment
-
Constructs a new
CompHapSegment
from the specified data. - 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.IntIntMap
-
Returns
true
if the map contains the specified key, and returnsfalse
otherwise. - contains(Marker) - Method in class beagleutil.ChromInterval
-
Returns
true
if the specified marker is in this chromosome interval and returnsfalse
otherwise. - contains(Marker) - Method in class vcf.Markers
-
Returns
true
if the specified marker is notnull
and is an element in the list of markers represented bythis
, and returnsfalse
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.
- copyOfRange(int, int) - Method in class ints.IntList
-
Returns the specified range of elements adding 0 values to the end of the copied values if necessary so that the returned array has length
end - start
. - 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 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.
D
- 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 ordersIntInterval
objects in order of increasingthis.start()
value and ordersIntInterval
objects with the samethis.start()
value in order of decreasingthis.inclEnd()
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: '='
- 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.
- DoubleArray - Class in blbutil
-
Class
DoubleArray
represents an immutable list of double floating point values. - DoubleArray(double[]) - Constructor for class blbutil.DoubleArray
-
Constructs an
DoubleArray
object with the specified values. - 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.
E
- 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".
- 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 specifiedIntArray
objects represent the same sequence of integer values, and returnsfalse
otherwise. - equals(LongArray, LongArray) - Static method in class ints.LongArray
-
Returns
true
if the specifiedLongArray
objects represent the same sequence of long values, and returnsfalse
otherwise. - equals(Object) - Method in class beagleutil.ChromInterval
-
Returns
true
if the specified object is aChromInterval
instance representing the same interval of genome coordinates asthis
, and returnsfalse
otherwise. - equals(Object) - Method in class beagleutil.Samples
-
Returns
true
if the specified object is aSamples
object which represents the same ordered list of samples asthis
, and returnsfalse
otherwise. - equals(Object) - Method in class blbutil.Pair
-
Returns
true
if the specified object is aPair
instance representing the same ordered pair of objects asthis
, and returnsfalse
otherwise. - equals(Object) - Method in class phase.SampleSeg
-
Compares the specified object with this
SampleSeg
for equality. - equals(Object) - Method in class vcf.BasicMarker
- equals(Object) - Method in interface vcf.Marker
-
Returns
true
if the specified object is aMarker
with the same chromosome, position, allele lists, and INFO END field, and returnsfalse
otherwise. - equals(Object) - Method in class vcf.Markers
-
Returns
true
if the specified object is aMarkers
instance which represents the same list of markers asthis
, and returnsfalse
otherwise. - err() - Method in class phase.FixedPhaseData
-
Return the allele mismatch emission probability.
- err() - Method in class phase.PhaseData
-
Return the allele mismatch probability.
- err(int) - Method in class main.Par
-
Returns the allele mismatch parameter for the specified number of samples.
- 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() - Method in class phase.PhaseData
-
Returns the estimated phase.
- EstPhase - Class in phase
-
Class
EstPhase
stores original input genotype data. - EstPhase(GT, RefGT, int, long) - Constructor for class phase.EstPhase
-
Constructs a new
EstPhase
instance from the specified data. - 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.
F
- 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.VcfRec
-
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.
- FixedPhaseData - Class in phase
-
Class
FixedPhaseData
stores immutable data for a marker window. - FixedPhaseData(Par, GeneticMap, Data, GT) - Constructor for class phase.FixedPhaseData
-
Constructs a new
FixedPhaseData
instance from the specified data. - 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(double[]) - Constructor for class blbutil.FloatArray
-
Constructs an
FloatArray
object with the specified 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.VcfRec
-
Returns the FORMAT field.
- formatData(String) - Method in class vcf.VcfRec
-
Returns an array of length
this.nSamples()
containing the specified FORMAT subfield data for each sample. - formatIndex(String) - Method in class vcf.VcfRec
-
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.VcfRec
-
Returns the specified FORMAT subfield.
- fpd() - Method in class phase.PhaseData
-
Returns the input data for phasing that is the same in each iteration.
- fromGL(VcfHeader, String, float) - Static method in class vcf.VcfRec
-
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.VcfRec
-
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.VcfRec
-
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. - FwdBwd - Class in phase
-
Class
FwdBwd
implements computes HMM reference haplotypes and state probabilities. - FwdBwd(PhaseIbs) - Constructor for class phase.FwdBwd
-
Creates a
FwdBwd
instance from the specified data. - fwdMatch(int) - Method in class phase.BestMatch
-
Returns an array mapping each target haplotype to a matching haplotype.
- fwdUpdate(float[], float, float, byte[], int) - Method in class phase.HmmUpdater
-
Updates the forward values and returns the sum of the updated forward values.
- fwdUpdate(IntArray, int, int, int[], int[]) - Method in class beagleutil.PbwtUpdater
-
Update the specified prefix and divergence arrays using the forward Positional Burrows-Wheeler Transform.
G
- genDist() - Method in class vcf.MarkerMap
-
Return a
FloatArray
of sizethis.markers().nMarkers()
whosek
-th element is the genetic distance between thek
-th target marker and the previous marker, or0.0
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.
- genPos() - Method in class vcf.MarkerMap
-
Returns a
DoubleArray
of sizethis.markers().nMarkers()
whosek
-th element is the genetic map position of thek
-th 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.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.PlinkGenMap
- genPos(Marker) - Method in class vcf.PositionMap
- genPos(Markers) - Method in interface vcf.GeneticMap
-
Returns the an array of length
hapPairs.nMarkers()
whose whosej
-th element is the genetic map position of thej
-th marker. - get(int) - Method in class blbutil.DoubleArray
-
Returns the double at the specified position in this list.
- 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 imp.CodedSteps
-
Returns a map from haplotype index to allele sequence index for the specified step
- 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.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 phase.CodedSteps
-
Returns a map from haplotype index to allele sequence index for the specified step
- get(int) - Method in class vcf.BitSetGTRec
- 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.LowMafRefDiallelicGTRec
- get(int) - Method in class vcf.LowMafRefGTRec
- get(int) - Method in class vcf.RefGT
-
Returns the
RefGTRec
for the specified marker. - get(int) - Method in class vcf.SeqCodedRefGTRec
- get(int) - Method in class vcf.VcfRec
- get(int, int) - Method in class ints.IntIntMap
-
Returns the value for the specified key or the specified sentinel value if the specified key is not present in this map.
- 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 ornull
iffilename == null
- getHaps(int, int[], int[]) - Method in class phase.EstPhase
-
Sets the
k
-th element of the specifiedhap1
andhap2
arrays to the specified sample's phased genotype at thek
-th marker. - 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.
- giga - Static variable in class blbutil.Const
-
The value 1,000,000,000
- gl(int, int, int) - Method in class vcf.BitSetGTRec
- 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.LowMafRefDiallelicGTRec
- gl(int, int, int) - Method in class vcf.LowMafRefGTRec
- gl(int, int, int) - Method in class vcf.SeqCodedRefGTRec
- gl(int, int, int) - Method in class vcf.VcfRec
- 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(GT, int, int, int, int) - Static method in interface vcf.GT
-
Returns the probability of the observed data for the specified marker and sample if the specified pair of unordered alleles is the true genotype.
- GL_FORMAT - Static variable in class vcf.VcfRec
-
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. - gtIndex(int, int) - Static method in class vcf.VcfRec
-
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.
H
- hap() - Method in class main.CompHapSegment
-
Returns the copied haplotype.
- 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.
- HapImputer - Class in phase
-
Class
ImputableHaps
performs imputation to estimate missing alleles and missing haplotype phase. - HapImputer(Markers, Samples) - Constructor for class phase.HapImputer
-
Constructs a new
ImputedHaps
instance from the specified data. - hapIndex(int, int) - Method in class vcf.LowMafRefDiallelicGTRec
- hapIndex(int, int) - Method in class vcf.LowMafRefGTRec
- 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.SeqCodedRefGTRec
- hapIndices() - Method in class vcf.LowMafRefDiallelicGTRec
- hapIndices() - Method in class vcf.LowMafRefGTRec
- hapIndices() - Method in interface vcf.RefGTRec
-
Returns an array whose
j
-th element isnull
ifj
is the major allele with lowest index, and otherwise is an array of indices of haplotypes that carry thej
-th allele sorted in increasing order - hapIndices() - Method in class vcf.SeqCodedRefGTRec
- 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. - hapsGT() - Method in class phase.EstPhase
-
Returns the current estimated phased genotypes for the target samples.
- HapsGT - Class in vcf
-
Class
HapsGT
implements thevcf.GT
interface by storing the haplotypes as bit arrays. - HapsGT(Markers, Samples, LongArray[]) - Constructor for class vcf.HapsGT
-
Constructs a new
HapsGT
instance from the specified data. - HapsGT(Markers, Samples, AtomicReferenceArray<LongArray>) - Constructor for class vcf.HapsGT
-
Constructs a new
HapsGT
instance from the specified data. - 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.VcfRec
-
Returns
true
if the specified FORMAT subfield is present, and returnsfalse
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 phase.SampleSeg
-
Returns the hash code value for this object.
- hashCode() - Method in class vcf.BasicMarker
- hashCode() - Method in interface vcf.Marker
-
Returns the hash code value for this object.
- hashCode() - Method in class vcf.Markers
-
Returns a hash code value for the object.
- hasNext() - Method in class blbutil.InputIt
-
Returns
true
if the iteration has more elements. - hasNext() - Method in class bref.Bref3It
-
Returns
true
if the iteration has more elements, and returnsfalse
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 returnsfalse
otherwise. - hasNext() - Method in class vcf.VcfIt
-
Returns
true
if the iteration has more elements, and returnsfalse
otherwise. - hasNext() - Method in class vcf.WindowIt
-
Returns
true
if the sliding window of VCF recList can advance and returnsfalse
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.
- hiFreqIbs2() - Method in class phase.FixedPhaseData
-
Returns the IBS2 data for the high-frequency markers.
- hiFreqIndices() - Method in class phase.FixedPhaseData
-
Returns the indices of the high-frequency markers.
- hiFreqMap() - Method in class phase.FixedPhaseData
-
Returns the genetic map for the high-frequency markers.
- hiFreqOverlap() - Method in class phase.FixedPhaseData
-
Returns the number of initial high-frequency markers that have phased target genotypes due to overlap with the previous window.
- hiFreqRefGT() - Method in class phase.FixedPhaseData
-
Returns the phased, nonmissing reference genotypes for the high-frequency markers or
null
if there are no reference samples. - hiFreqTargGT() - Method in class phase.FixedPhaseData
-
Returns the input target genotypes at the high-frequency markers.
- HIGH_FREQ_ARRAY - Static variable in interface vcf.Data
- HmmUpdater - Class in phase
-
Instances of class
HmmUpdater
have methods for one-step updates of forward or backward HMM values. - HmmUpdater(float) - Constructor for class phase.HmmUpdater
-
Constructs a new
HmmUpdater
instance from the specified data. - hyphen - Static variable in class blbutil.Const
-
The hyphen character:
'-'
I
- ibs2() - Method in class phase.PhaseData
-
Returns the ibs2 status at each high-frequency marker.
- Ibs2 - Class in phase
-
Class
Ibs2
stores IBS2 segments that any target sample shares with another target or reference sample. - Ibs2(GT, RefGT, MarkerMap, double) - Constructor for class phase.Ibs2
-
Constructs a new
Ibs2
instance from the specified data. - 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.
- ibsStates(int, int[][], boolean[][]) - Method in class imp.ImpStates
-
Stores the reference haplotype for the
j
-th state at them
-th marker inhapIndices[m][j]
, and stores the equality of the allele carried by the reference haplotype for thej
-th state and the allele carried by the target haplotype at them
-th marker inalMatch[m][j]
. - ibsStates(int, int[][], byte[][]) - Method in class phase.PhaseStates
-
Stores the Li and Stephens HMM for the specified target haplotype in the specified arrays.
- ibsStates(int, int[], int[], List<int[]>, byte[][], byte[][]) - Method in class phase.PhaseStates
-
Stores the Li and Stephens HMM for the specified target sample in the specified arrays.
- 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
- identity(int) - Static method in interface ints.IntArray
-
Returns an
IntArray
instance of the specified size whosek
-th element isk
. - 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 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_nsteps() - Method in class main.Par
-
Returns the imp-nsteps parameter.
- imp_segment() - Method in class main.Par
-
Returns the imp-segment parameter.
- imp_states() - Method in class main.Par
-
Returns the imp-states parameter.
- imp_step() - Method in class main.Par
-
Returns the imp-step parameter.
- impData() - Method in class imp.CodedSteps
-
Return the input data for genotype imputation used to construct
this
. - 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, Data, 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.
- imputeAllele(int, Random) - Method in class phase.AlleleImputer
-
Returns an imputed allele for the specified marker.
- ImputeBaum - Class in phase
-
Class
ImputeBaum
applies the forward and backward algorithms for a haploid Li and Stephens hidden Markov model at high-frequency markers, and imputes missing genotypes and heterozygote phase at low-frequency markers. - ImputeBaum(PhaseIbs, HapImputer) - Constructor for class phase.ImputeBaum
-
Creates a
ImputeBaum
instance from the specified data. - imputedHaps() - Method in class phase.HapImputer
-
Returns the imputed haplotypes.
- 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 ordersIntInterval
objects in order of increasingthis.start()
value and ordersIntInterval
objects with the samethis.start()
value in order of increasingthis.inclEnd()
value. - inclEnd() - Method in class beagleutil.ChromInterval
-
Returns the last genome coordinate in this chromosome interval.
- inclEnd() - Method in interface beagleutil.IntInterval
-
Returns the end of the interval (inclusive).
- inclEnd() - Method in class phase.SampleSeg
-
Returns the end of the segment (inclusive).
- 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.VcfRec
-
Returns the INFO field.
- InputIt - Class in blbutil
-
Class
InputIt
is a buffered iterator whosenext()
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.
- inTarg(GTRec[]) - Static method in class vcf.AllData
- intArray() - Method in class ints.IndexArray
-
Returns the wrapped
IntArray
object. - IntArray - Interface in ints
-
Interface
IntArray
represents an immutableint[]
array. - IntervalVcfIt<E extends MarkerContainer> - Class in vcf
-
Class
IntervalVcfIterator
is a sample file iterator whosenext()
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. - IntIntMap - Class in ints
-
Class
IntIntMap
represents a map with integer keys and integer values. - IntIntMap(int) - Constructor for class ints.IntIntMap
-
Creates a new
IntMap
instance. - 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 specifiedIntList
. - ints - package ints
- isAlleleCoded() - Method in class vcf.LowMafRefDiallelicGTRec
- isAlleleCoded() - Method in class vcf.LowMafRefGTRec
- isAlleleCoded() - Method in interface vcf.RefGTRec
-
Returns
true
if this instance stores the indices of haplotypes that carry non-major alleles, and returnsfalse
otherwise. - isAlleleCoded() - Method in class vcf.SeqCodedRefGTRec
- isCarrier(int, int) - Method in class vcf.LowMafRefDiallelicGTRec
- isCarrier(int, int) - Method in class vcf.LowMafRefGTRec
- isCarrier(int, int) - Method in interface vcf.RefGTRec
-
Returns
true
if the specified haplotype carries the specified allele and returnfalse
otherwise. - isCarrier(int, int) - Method in class vcf.SeqCodedRefGTRec
- isEmpty() - Method in class blbutil.DoubleArray
-
Returns
true
if this list has no elements, and returnsfalse
otherwise. - isEmpty() - Method in class blbutil.FloatArray
-
Returns
true
if this list has no elements, and returnsfalse
otherwise. - isEmpty() - Method in class blbutil.FloatList
-
Returns
true
if this list has no elements, and returnsfalse
otherwise. - isEmpty() - Method in class ints.IntList
-
Returns
true
if this list has no elements, and returnsfalse
otherwise. - isGTData() - Method in class vcf.BitSetGTRec
- isGTData() - Method in interface vcf.GTRec
-
Returns
true
if the value returned bythis.gl()
is determined by a called or missing genotype, and returnsfalse
otherwise. - isGTData() - Method in class vcf.LowMafRefDiallelicGTRec
- isGTData() - Method in class vcf.LowMafRefGTRec
- isGTData() - Method in class vcf.SeqCodedRefGTRec
- isGTData() - Method in class vcf.VcfRec
- isLowFreq(int, int) - Method in class phase.FixedPhaseData
-
Returns
true
if the specified allele is a low-frequency allele, and returnsfalse
otherwise. - isPhased() - Method in class vcf.BasicGT
- isPhased() - Method in class vcf.BitSetGTRec
- isPhased() - Method in interface vcf.DuplicatesGTRec
-
Returns
true
if every genotype for each sample is a phased, non-missing genotype, and returnsfalse
otherwise. - isPhased() - Method in interface vcf.GT
-
Returns
true
if the genotype for each marker and sample is a phased, non-missing genotype, and returnsfalse
otherwise. - isPhased() - Method in class vcf.HapsGT
- isPhased() - Method in class vcf.LowMafRefDiallelicGTRec
-
Returns
true
. - isPhased() - Method in class vcf.LowMafRefGTRec
-
Returns
true
. - isPhased() - Method in class vcf.RefGT
- isPhased() - Method in interface vcf.RefGTRec
-
Returns
true
. - isPhased() - Method in class vcf.RestrictedGT
- isPhased() - Method in class vcf.SeqCodedRefGTRec
-
Returns
true
. - isPhased() - Method in class vcf.SplicedGT
- isPhased() - Method in class vcf.VcfRec
- isPhased() - Method in class vcf.XBasicGT
- isPhased(int) - Method in class vcf.BitSetGTRec
- isPhased(int) - Method in interface vcf.DuplicatesGTRec
-
Returns
true
if the genotype for the specified sample is a phased, nonmissing genotype, and returnsfalse
otherwise. - isPhased(int) - Method in class vcf.LowMafRefDiallelicGTRec
- isPhased(int) - Method in class vcf.LowMafRefGTRec
- isPhased(int) - Method in interface vcf.RefGTRec
-
Returns
true
. - isPhased(int) - Method in class vcf.SeqCodedRefGTRec
- isPhased(int) - Method in class vcf.VcfRec
- it() - Method in class phase.PhaseData
-
Returns the current iteration (0 based).
- 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.
- 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.
K
- key() - Method in class vcf.VcfMetaInfo
-
Returns the VCF meta-information line key.
- key(int) - Method in class ints.IntIntMap
-
Returns the specified key.
- keys() - Method in class ints.IntIntMap
-
Returns an array containing the keys in this map.
L
- lastWindow() - Method in class vcf.Window
-
Returns
true
if the sliding window of genotype records is the last window and returnsfalse
otherwise. - lastWindowOnChrom() - Method in class vcf.AllData
- lastWindowOnChrom() - Method in interface vcf.Data
-
Returns
true
if the current window of VCF records is the last window for the chromosome and returnsfalse
otherwise. - lastWindowOnChrom() - Method in class vcf.TargetData
- lastWindowOnChrom() - Method in class vcf.Window
-
Returns
true
if the sliding window of genotype records is the last window for its chromosome and returnsfalse
otherwise. - leaveUnphasedProp(int) - Method in class phase.PhaseData
-
Returns the proportion of unphased heterozygotes that should be left unphased at the end of iteration
this.it()
for the specified sample. - longArg(String, Map<String, String>, boolean, long, long, long) - Static method in class blbutil.Validate
-
Removes the specified key from the specified map, and returns the long value corresponding to the specified key.
- LongArray - Class in ints
-
Interface
LongArray
represents an immutablelong[]
array. - LongArray(long[]) - Constructor for class ints.LongArray
-
Constructs a
LongArray
instance from the specified values. - LowFreqPhaseIbs - Class in phase
-
Class
LowFreqPhaseIbs
identifies haplotypes that share a long IBS segment or a low frequency variant with a specified haplotype in a specified genomic interval. - LowFreqPhaseIbs(PhaseData) - Constructor for class phase.LowFreqPhaseIbs
-
Constructs a new
LowFreqPhaseIbs
object from the specified data. - LowMafRefDiallelicGTRec - Class in vcf
-
Class
LowMafRefDiallelicGT
represent represents phased, non-missing genotypes for a list of reference samples at a single diallelic marker. - LowMafRefDiallelicGTRec(Marker, Samples, int[][]) - Constructor for class vcf.LowMafRefDiallelicGTRec
-
Constructs a new
LowMafRefDiallelicGT
instance from the specified data. - LowMafRefDiallelicGTRec(RefGTRec) - Constructor for class vcf.LowMafRefDiallelicGTRec
-
Constructs a new
LowMafRefDiallelicGT
instance with phased non-missing genotypes from the specified data. - LowMafRefDiallelicGTRec(VcfRecGTParser) - Constructor for class vcf.LowMafRefDiallelicGTRec
-
Constructs a new
LowMafRefDiallelicGT
instance with phased non-missing genotypes from the specified data. - LowMafRefGTRec - Class in vcf
-
Class
LowMafRefGT
represent represents phased, non-missing genotypes for a list of reference samples at a single marker. - LowMafRefGTRec(Marker, Samples, int[][]) - Constructor for class vcf.LowMafRefGTRec
-
Constructs a new
LowMafRefGT
instance from the specified data. - LowMafRefGTRec(RefGTRec) - Constructor for class vcf.LowMafRefGTRec
-
Constructs a new
LowMafRefGT
instance with phased non-missing genotypes from the specified data. - LowMafRefGTRec(VcfRecGTParser) - Constructor for class vcf.LowMafRefGTRec
-
Constructs a new
LowMafRefGT
instance with phased non-missing genotypes from the specifiedVcfRecGTParser
object.
M
- 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 - 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 themain.Main
class. - MainHelper(Par, RunStats, long) - Constructor for class main.MainHelper
-
Constructs a new
MainHelper
instance. - majorAllele() - Method in class vcf.LowMafRefDiallelicGTRec
- majorAllele() - Method in class vcf.LowMafRefGTRec
- majorAllele() - Method in interface vcf.RefGTRec
-
Returns the index of the major allele.
- majorAllele() - Method in class vcf.SeqCodedRefGTRec
- map() - Method in class main.Par
-
Returns the map parameter.
- map() - Method in class phase.FixedPhaseData
-
Returns the genetic map for the markers.
- map() - Method in class phase.PhaseData
-
Return the marker map that stores genetic positions of each high-frequency marker.
- map(int) - Method in class vcf.LowMafRefDiallelicGTRec
- map(int) - Method in class vcf.LowMafRefGTRec
- map(int) - Method in interface vcf.RefGTRec
-
Returns
this.maps()[index]
. - map(int) - Method in class vcf.SeqCodedRefGTRec
- maps() - Method in class vcf.LowMafRefDiallelicGTRec
- maps() - Method in class vcf.LowMafRefGTRec
- maps() - Method in interface vcf.RefGTRec
-
Returns an array of maps, which when composed map haplotype indices to values.
- maps() - Method in class vcf.SeqCodedRefGTRec
- marker() - Method in class imp.ImputedRecBuilder
-
Returns the marker in the VCF record.
- marker() - Method in class vcf.BitSetGTRec
- marker() - Method in class vcf.LowMafRefDiallelicGTRec
- marker() - Method in class vcf.LowMafRefGTRec
- marker() - Method in interface vcf.MarkerContainer
-
Returns the marker.
- marker() - Method in class vcf.SeqCodedRefGTRec
- marker() - Method in class vcf.VcfRec
- marker() - Method in class vcf.VcfRecBuilder
-
Returns the current marker.
- marker() - Method in class vcf.VcfRecGTParser
-
Returns the marker.
- marker(int) - Method in class vcf.BasicGT
- marker(int) - Method in interface vcf.GT
-
Returns the specified marker.
- marker(int) - Method in class vcf.HapsGT
- marker(int) - Method in class vcf.Markers
-
Returns the specified marker.
- marker(int) - Method in class vcf.RefGT
- marker(int) - Method in class vcf.RestrictedGT
- 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 uniquevcf.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 theexcludeMarkersFile
parameter isnull
. - markerIndices() - Method in class imp.ImpData
- markerIndices() - Method in class vcf.AllData
- markerIndices() - Method in interface vcf.Data
-
Return a
MarkerIndices
instance which stores the overlap with the current marker window and adjacent marker windows and the mappings between marker indices and target marker indices. - markerIndices() - Method in class vcf.TargetData
- MarkerIndices - Class in vcf
-
Class
MarkerIndices
stores the overlap with adjacent marker windows and the mappings between marker indices and the target marker indices. - MarkerIndices(boolean[], int, int) - Constructor for class vcf.MarkerIndices
-
Constructs a
MarkerIndices
instance from the specified data. - MarkerIndices(int, int, int) - Constructor for class vcf.MarkerIndices
-
Constructs a
MarkerIndices
instance from the specified data - 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 returnsfalse
otherwise. - MarkerMap - Class in vcf
-
Class
MarkerRecombMap
represents genetic map positions and inter-marker haplotype switch probabilities for a sequence of genomic loci. - markers() - Method in class phase.HapImputer
-
Returns the list of markers.
- markers() - Method in class vcf.BasicGT
- markers() - Method in interface vcf.GT
-
Returns the list of markers.
- markers() - Method in class vcf.HapsGT
- markers() - Method in class vcf.Markers
-
Returns the list of markers.
- markers() - Method in class vcf.RefGT
- markers() - Method in class vcf.RestrictedGT
- markers() - Method in class vcf.SplicedGT
- 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. - markerToTargMarker() - Method in class vcf.MarkerIndices
-
Returns an array of length
this.nMarkers()
whosek
-th element is the index of thek
-th marker in the list of target markers or is -1 if the marker is not present in the target data. - markerToTargMarker(int) - Method in class vcf.MarkerIndices
-
Returns the index of the specified marker in the target data, or returns -1 if the marker is not present in the target data.
- math - package math
- max(IntArray) - Static method in interface ints.IntArray
-
Returns the maximum element, or
Integer.MIN_VALUE
ifthis.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 returntrue
- MAX_SAMPLES - Variable in class bref.AsIsBref3Writer
- maxNSeq() - Method in class bref.SeqCoder3
-
Returns the maximum number of distinct allele sequences.
- maxStates() - Method in class imp.ImpStates
-
Returns the maximum number of HMM states at a marker.
- maxStates() - Method in class phase.FwdBwd
-
Returns the maximum number of HMM states.
- maxStates() - Method in class phase.PhaseStates
-
Returns the maximum number of HMM states at a marker.
- 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
ifthis.size() == 0
. - minCmIbs2() - Method in class phase.Ibs2
-
Returns the minimum cM length of a stored IBS2 segment.
- minutesAndSeconds() - Static method in class blbutil.Utilities
-
Returns the current minutes and seconds as a string.
- missing(int) - Method in class phase.EstPhase
-
Returns a list of marker indices in increasing order for which the specified sample has a missing genotype.
- 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.
N
- nAlleles() - Method in class vcf.BasicMarker
- nAlleles() - Method in class vcf.BitSetGTRec
- nAlleles() - Method in class vcf.LowMafRefDiallelicGTRec
- nAlleles() - Method in class vcf.LowMafRefGTRec
- 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.SeqCodedRefGTRec
- nAlleles() - Method in class vcf.VcfRec
- nAlleles() - Method in class vcf.VcfRecGTParser
-
Returns
this.marker().nAlleles()
. - 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. - nextOverlap() - Method in class vcf.MarkerIndices
-
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. - nextOverlap() - Method in class vcf.Window
-
Returns the index of the first marker in the overlap with the next marker window.
- nextSplice() - Method in class vcf.MarkerIndices
-
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. - nextTargOverlap() - Method in class vcf.MarkerIndices
-
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. - nextTargSplice() - Method in class vcf.MarkerIndices
-
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.VcfRec
-
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
. - nHaps() - Method in class beagleutil.PbwtUpdater
-
Returns the number of haplotypes.
- 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 phase.CodedSteps
-
Returns the number of target and reference haplotypes.
- nHaps() - Method in class phase.FixedPhaseData
-
Return the sum of the number of reference and target haplotypes.
- nHaps() - Method in class phase.PhaseData
-
Return the total number of target and reference haplotypes.
- nHaps() - Method in class vcf.BasicGT
- nHaps() - Method in interface vcf.GT
-
Returns the number of haplotypes.
- nHaps() - Method in class vcf.HapsGT
- nHaps() - Method in class vcf.RefGT
- nHaps() - Method in class vcf.RestrictedGT
- 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.
- 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.LowMafRefDiallelicGTRec
- nMaps() - Method in class vcf.LowMafRefGTRec
- nMaps() - Method in interface vcf.RefGTRec
-
Returns
this.maps().length
- nMaps() - Method in class vcf.SeqCodedRefGTRec
- nMarkers() - Method in class phase.AlleleImputer
-
Returns the number of markers.
- nMarkers() - Method in class phase.CodedSteps
-
Returns the number of markers
- nMarkers() - Method in class vcf.AllData
- nMarkers() - Method in class vcf.BasicGT
- 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.HapsGT
- nMarkers() - Method in class vcf.Markers
-
Returns the number of markers.
- nMarkers() - Method in class vcf.RefGT
- nMarkers() - Method in class vcf.RestrictedGT
- 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()
whosek
-th element is the list of haplotype indices carrying thek
-th allele ifk
is a non-major allele, and whosek
-th element isnull
ifk
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.
- nSamples() - Method in class beagleutil.Samples
-
Returns the number of samples in this list.
- nSamples() - Method in class imp.ImputedRecBuilder
-
Returns the required number of samples in the VCF record.
- nSamples() - Method in class main.Pedigree
-
Returns the number of samples.
- nSamples() - Method in class phase.Ibs2
-
Returns the total number of target and reference samples.
- nSamples() - Method in class vcf.BasicGT
- nSamples() - Method in class vcf.BitSetGTRec
- 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.HapsGT
- nSamples() - Method in class vcf.LowMafRefDiallelicGTRec
- nSamples() - Method in class vcf.LowMafRefGTRec
- nSamples() - Method in class vcf.RefGT
- nSamples() - Method in class vcf.RestrictedGT
- nSamples() - Method in class vcf.RestrictedVcfWindow
-
Returns the number of samples.
- nSamples() - Method in class vcf.SeqCodedRefGTRec
- 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.VcfRec
- nSamples() - Method in class vcf.VcfRecGTParser
-
Returns the number of samples.
- nSamples() - Method in class vcf.XBasicGT
- nSingles() - Method in class main.Pedigree
-
Returns the number of single individuals in the list of samples.
- nStates(int) - Method in interface imp.StateProbs
-
Returns the number of stored HMM states at the specified target marker.
- nSteps() - Method in class imp.CodedSteps
-
Returns the number of steps.
- nSteps() - Method in class phase.CodedSteps
-
Returns the number of steps.
- nTargHaps() - Method in class imp.ImpData
-
Return the number of target haplotypes.
- nTargHaps() - Method in class phase.CodedSteps
-
Returns 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.
- nTargMarkersSoFar() - Method in class vcf.AllData
- nTargMarkersSoFar() - Method in interface vcf.Data
-
Returns the number of target VCF records in the union of the current window and all previous windows.
- nTargMarkersSoFar() - Method in class vcf.TargetData
- nTargSamples() - Method in class imp.ImpData
-
Returns the number of target samples.
- nTargSamples() - Method in class phase.ImputeBaum
-
Returns the number of target samples.
- nTargSamples() - Method in class phase.PhaseBaum1
-
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.
O
- offset() - Method in class bref.BrefBlock
-
Returns the file offset of the first marker in this bref block.
- offspring(int, int) - Method in class main.Pedigree
-
Returns the sample index of the offspring of the specified sample.
- OPPOSITE - beagleutil.Phase
- out() - Method in class main.Par
-
Returns the out parameter.
- outPrefix() - Method in class main.WindowWriter
-
Returns the output file prefix.
- overlap() - Method in class main.Par
-
Return the overlap parameter.
- overlap() - Method in class phase.FixedPhaseData
-
Returns the number of initial markers that have phased target genotypes due to overlap with the previous marker window.
- overlap() - Method in class vcf.RestrictedVcfWindow
-
Returns the number of VCF records in the overlap between the current window and the previous window.
- overlap(ChromInterval, ChromInterval) - Static method in class beagleutil.ChromInterval
-
Returns
true
if the specified chromosome intervals have non-empty intersection and returnsfalse
otherwise.
P
- 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 phase.FixedPhaseData
-
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 returnsnull
if the specified string does not represent a valid chromosome interval or if the specified string isnull
. - PbwtPhaseIbs - Class in phase
-
Class
PbwtPhaseIBS
uses the Positional Burrows-Wheeler Transform (PBWT) to find long IBS haplotypes for each sample that contain a specified small genomic interval. - PbwtPhaseIbs(PhaseData, boolean) - Constructor for class phase.PbwtPhaseIbs
-
Constructs a new
PbwtPhaseIBS
instance from the specified data. - PbwtUpdater - Class in beagleutil
-
Class
PbwtUpdater
updates prefix and divergence arrays using the positional Burrows-Wheeler transform (PBWT). - PbwtUpdater(int) - Constructor for class beagleutil.PbwtUpdater
-
Constructs a new
PbwtUpdater
instance for the specified data. - ped() - Method in class main.Par
-
Returns the ped parameter or
null
if no ped parameter was specified. - ped() - Method in class phase.FixedPhaseData
-
Returns the parent-offspring relationships.
- 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. - phase - package phase
- phase(int) - Method in class phase.ImputeBaum
-
Estimates phased haplotypes for the specified sample.
- phase(int) - Method in class phase.PhaseBaum1
-
Estimates and stores the phased haplotypes for the specified sample
- phase(FixedPhaseData) - Method in class main.MainHelper
-
Phases the current window of genotype data.
- Phase - Enum in beagleutil
-
Class
Phase
represents the equivalence of two phased genotypes for a marker or for a set of markers. - phase_states() - Method in class main.Par
-
Returns the phase-states parameter.
- phase_step() - Method in class main.Par
-
Returns the phase-step parameter.
- PhaseBaum1 - Class in phase
-
Class
PhaseBaum1
implements the forward and backward algorithms for a haploid Li and Stephens hidden Markov model. - PhaseBaum1(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.LowFreqPhaseIbs
- phaseData() - Method in class phase.PbwtPhaseIbs
- phaseData() - Method in interface phase.PhaseIbs
-
Returns the input data for the next phase update.
- phaseData() - Method in class phase.RecombRegress
-
Returns the current input data for genotype phasing.
- PhaseData - Class in phase
-
Class
PhaseData
contains the current input data for updating genotype phase. - PhaseData(FixedPhaseData, EstPhase, float, int, long) - Constructor for class phase.PhaseData
-
Constructs a new
PhaseData
instance from the specified data. - phasedSep - Static variable in class blbutil.Const
-
The phased allele separator:
'|'
- phasedTarg() - Method in class phase.PhaseData
-
Returns the estimated phased target haplotypes at the high-frequency markers.
- phaseIbs() - Method in class phase.FwdBwd
-
Return the haplotype IBS
- PhaseIbs - Interface in phase
-
Instances of interface
PhaseIbs
identify haplotypes that are identical by state with a specified haplotype in a specified genomic interval. - PhaseLS - Class in phase
-
Class
PhaseLS
estimated genotypes phase using a haploid Li and Stephens hidden Markov model. - PhaseStates - Class in phase
-
Class
PhaseStates
has methods for constructing a Li and Stephens HMM for a target haplotype or target sample. - PhaseStates(PhaseIbs, int) - Constructor for class phase.PhaseStates
-
Constructs a new
PhaseStates
object from the specified data. - PL_FORMAT - Static variable in class vcf.VcfRec
-
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 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 sizethis.targGT().nMarkers()
whosek
-th element is the probability of transitioning to a random HMM state between thek
-th high-frequency target marker and the previous high-frequency marker. - pRecomb(float) - Method in class vcf.MarkerMap
-
Returns a map of marker index to the probability of recombination in the interval between the marker and the preceding 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 whosej
-th element forj > 0
is the probability of recombination between markerj - 1
and markerj
. - PREFIX - Static variable in class vcf.VcfMetaInfo
-
The VCF meta-information line prefix: "##"
- prevHiFreqMarker(int) - Method in class phase.FixedPhaseData
-
Returns the index of the closest high-frequency marker with position less than or equal to the position of the specified marker, or 0 if no such high-frequency marker exists.
- prevOverlap() - Method in class vcf.Window
-
Returns the index of the first marker after the overlap with the preceding marker window.
- prevSplice() - Method in class vcf.MarkerIndices
-
Returns the first marker index after the splice point with the previous marker window.
- prevTargSplice() - Method in class vcf.MarkerIndices
-
Returns the first target marker index after the splice point with the previous marker window.
- prevWt(int) - Method in class phase.FixedPhaseData
-
Returns the linear interpolation weight for the high-frequency marker with index
this.prevHiFreqMarker(marker)
. - printFixedFieldsGT(Marker, PrintWriter) - Static method in class vcf.VcfWriter
-
Prints the first 9 VCF record fields for the specified marker to the specified
PrintWriter
. - printImputationUpdate() - Method in class main.RunStats
-
Prints run time for most recent imputation to a log file and to standard output.
- printImputed(ImpData, int, int, AtomicReferenceArray<StateProbs>) - Method in class main.WindowWriter
-
Prints the data in
alProbs
for markers with index betweenrefStart
(inclusive) andrefEnd
(exclusive) to the output VCF file:this.outPrefix() + ".vcf.gz"
. - 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.
- printPhased(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"
. - printPhasingItUpdate(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, int) - Method in class ints.IntIntMap
-
Adds the specified key and value to this map.
Q
R
- 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. - rare() - Method in class main.Par
-
Returns the rare parameter
- 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
- recombFactor() - Method in class phase.PhaseData
-
Returns the factor multiplied by genetic distance to obtain the probability of transitioning to a random HMM state.
- RecombRegress - Class in phase
-
Class
RecombRegress
uses linear regression to estimate the recombination factor for a haploid Li and Stephens hidden Markov model. - RecombRegress(PhaseIbs, Regress) - Constructor for class phase.RecombRegress
-
Creates a
RecombRegress
instance for the specified data. - 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 phase.FixedPhaseData
-
Returns the input phased, nonmissing reference genotypes or
null
if there are no reference samples. - refGT() - Method in class phase.Ibs2
-
Returns the genotype data for the reference samples.
- refGT() - Method in class phase.PhaseData
-
Returns the phased, nonmissing reference genotypes at the high-frequency markeres, or
null
if there are no reference samples. - 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 - Class in vcf
-
Class
BasicRefGT
stores a list of samples and a haplotype pair for each sample. - RefGT(Markers, Samples, RefGTRec[]) - Constructor for class vcf.RefGT
-
Constructs a new
RefHapPairs
instance. - RefGT(RefGTRec[]) - Constructor for class vcf.RefGT
-
Constructs a new
RefHapPairs
instance. - 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.
- RefIt - Class in vcf
-
Class
RefIt
represents an iterator whosenext()
method returns an object storing data from a VCF record with phased, non-missing genotypes. - 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.IntIntMap
-
Removes the specified key from this map.
- reset() - Method in class math.Regress
-
Deletes all recorded values from
this
. - restrict(int[]) - Method in class vcf.MarkerMap
-
Return a marker map restricted to the specified markers
- restrict(int[]) - Method in class vcf.Markers
-
Returns a
Markers
instance that represents the specified markers. - restrict(int, int) - Method in class vcf.Markers
-
Returns a
Markers
instance that represents the specified range of marker indices. - restrict(Markers, int[]) - Method in class vcf.BasicGT
- restrict(Markers, int[]) - Method in interface vcf.GT
-
Returns a
GT
instance restricted to genotype data for the specified markers. - restrict(Markers, int[]) - Method in class vcf.HapsGT
- restrict(Markers, int[]) - Method in class vcf.RefGT
- restrict(Markers, int[]) - Method in class vcf.RestrictedGT
- restrict(Markers, int[]) - Method in class vcf.SplicedGT
- restrict(Markers, int[]) - Method in class vcf.XBasicGT
- RestrictedGT - Class in vcf
-
Class
RestrictedGT
is a wrapper for aGT
instance that restricts the data to a subset of the VCF records. - RestrictedGT(GT, Markers, int[]) - Constructor for class vcf.RestrictedGT
-
Constructs a new
NoPhaseGTWrapper
instance from the specified data - 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 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(int, int[][], float[][]) - Method in class phase.FwdBwd
-
Stores the HMM reference haplotypes and states probabilities for the specified target haplotype, and returns the number of HMM states per marker.
- runStage1(PhaseData, boolean) - Static method in class phase.PhaseLS
-
Estimates phased haplotypes at high-frequency markers in the target samples.
- runStage2(PhaseData) - Static method in class phase.PhaseLS
-
Returns phased genotypes at all markers.
- RunStats - Class in main
-
Class
RunStats
contains methods for storing and printing statistics describing a Beagle analysis.
S
- sample() - Method in class phase.SampleSeg
-
Returns the sample index.
- sampleCnt() - Method in class imp.ImputedRecBuilder
-
Returns the number of times the
this.addSampleData()
method has been invoked. - sampleComp() - Static method in class phase.SampleSeg
-
Returns a comparator that orders first by
this.sample()
, then bythis.start()
, and finally bythis.end()
. - sampleData(int) - Method in class vcf.VcfRec
-
Returns the data for the specified sample.
- sampleData(int, int) - Method in class vcf.VcfRec
-
Returns the specified data for the specified sample.
- sampleData(int, String) - Method in class vcf.VcfRec
-
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 theexcludeSamplesFile
parameter isnull
- 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 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 vcf.BasicGT
- samples() - Method in class vcf.BitSetGTRec
- 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.HapsGT
- samples() - Method in class vcf.IntervalVcfIt
- samples() - Method in class vcf.LowMafRefDiallelicGTRec
- samples() - Method in class vcf.LowMafRefGTRec
- samples() - Method in class vcf.RefGT
- samples() - Method in class vcf.RefIt
- samples() - Method in class vcf.RestrictedGT
- samples() - Method in class vcf.RestrictedVcfWindow
-
Returns the list of samples.
- samples() - Method in class vcf.SeqCodedRefGTRec
- 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.VcfRec
- samples() - Method in class vcf.VcfRecGTParser
-
Returns the list of samples.
- 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. - SampleSeg - Class in phase
-
Class
SampleSeg
represents a haplotype shared with a sample. - SampleSeg(int, int, int) - Constructor for class phase.SampleSeg
-
Constructs a new
SampleSeg
instance from the specified data. - scaleFactor() - Method in class main.Par
-
Return the ratio of the phase-states parameter and the default phase-states parameter
- 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
- SeqCodedRefGTRec - Class in vcf
-
Class
SeqCodedRefGT
represents phased, non-missing genotypes for a list of reference samples at a single marker. - SeqCodedRefGTRec(Marker, Samples, IntArray, IntArray) - Constructor for class vcf.SeqCodedRefGTRec
-
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-codedRefGTRec
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) andthis.end()
(exclusive) of the specified haplotype in the sublist of reference haplotypes to the specified array. - setHap(int, int[]) - Method in class phase.HapImputer
-
Stores the specified haplotype.
- setHapPair(int, int[], int[]) - Method in class phase.EstPhase
-
Sets the haplotype pair for the specified sample to the specified haplotypes.
- setPartlyImputedAllele(int, int, float[], IntList, FloatList) - Method in class phase.HapImputer
-
Stores a partially-imputed allele.
- setRecombFactor(float) - Method in class phase.PhaseData
-
Sets the recombination factor to the specified value.
- setUnphased(int, IntArray) - Method in class phase.EstPhase
-
Sets the list of remaining marker indices with unphased heterozygote genotypes for the specified sample to the specified list
- 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.DoubleArray
-
Returns the number of elements in this list.
- 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.IntIntMap
-
Returns the number of keys in this map.
- size() - Method in class ints.IntList
-
Returns the number of elements in this list.
- 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.BitSetGTRec
- size() - Method in interface vcf.DuplicatesGTRec
-
Returns the number of haplotypes.
- size() - Method in class vcf.LowMafRefDiallelicGTRec
- size() - Method in class vcf.LowMafRefGTRec
- size() - Method in class vcf.SeqCodedRefGTRec
- size() - Method in class vcf.VcfRec
- sort() - Method in class ints.IntList
-
Sorts the elements of this list in increasing order
- SplicedGT - Class in vcf
-
Class
SplicedGT
represents genotypes for a set of samples that are obtained by replacing the initial markers of oneGT
instance with phased genotypes from anotherGT
instance. - 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.
- start() - Method in class phase.SampleSeg
-
Returns the start of the segment (inclusive).
- 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.CompHapSegment
-
Returns the last recorded step for
this.hap()
. - stepEnd(int) - Method in class phase.CodedSteps
-
Returns the last marker index (exclusive) in the specified step.
- stepStart(int) - Method in class imp.CodedSteps
-
Returns the first marker index in the specified step.
- stepStart(int) - Method in class phase.CodedSteps
-
Returns the first marker index in the specified step.
- storeAlleles(long[], long[], long[], long[], long[]) - Method in class vcf.VcfRecGTParser
-
Stores the genotypes genotypes in the specified long arrays.
- 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.
- sumX() - Method in class math.Regress
-
Returns the sum of recorded values of the independent variable.
- sumXX() - Method in class math.Regress
-
Returns the sum of the squared recorded values of the independent variable.
- sumXY() - Method in class math.Regress
-
Returns the sum of the products of the recorded values of the independent and dependent variables.
- sumY() - Method in class math.Regress
-
Returns the sum of recorded values of the dependent variable.
- sumY() - Method in class phase.RecombRegress
-
Returns the sum of the probabilities of switching reference haplotypes between consecutive markers stored by
this.update()
.
T
- 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 specifiedSampleFileIt
objects. - TargetData - Class in vcf
-
Class
TargetData
represents a sliding window of target VCF records. - targGT() - Method in class imp.ImpData
-
Return the phased target genotype data.
- targGT() - Method in class phase.EstPhase
-
Returns the input target genotype data.
- targGT() - Method in class phase.FixedPhaseData
-
Returns the input target genotypes.
- targGT() - Method in class phase.Ibs2
-
Returns the genotype data for the target samples.
- targGT() - Method in class phase.PhaseData
-
Returns the input genotypes for the target samples at the high-frequency 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.
- targMarkerToMarker() - Method in class vcf.MarkerIndices
-
Returns an array of length
this.nTargMarkers()
which maps thek
-th marker in the list of target data markers to the index of the marker in the list of reference data markers. - targMarkerToMarker(int) - Method in class vcf.MarkerIndices
-
Returns the index of the specified marker in the reference data markers.
- targSamples() - Method in class imp.ImpData
-
Returns the list of target samples.
- targSamples() - Method in class phase.HapImputer
-
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.DoubleArray
-
Returns an integer array containing the sequence of elements in this list.
- 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(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. - toString() - Method in class beagleutil.ChromIds
-
Returns
java.util.Arrays.toString(this.ids())
. - toString() - Method in class beagleutil.ChromInterval
-
Returns the string:
this.chrom() + ":" + this.start() + "-" + this.end()
- toString() - Method in class beagleutil.SampleIds
-
Returns
java.util.Arrays.toString(this.ids())
. - toString() - Method in class beagleutil.Samples
-
Returns
java.util.Arrays.toString(this.ids())
. - toString() - Method in class beagleutil.ThreadSafeIndexer
-
Returns
this.items().toString()
. - toString() - Method in class blbutil.DoubleArray
-
Returns a string representation of this list that is obtained by calling
java.util.Arrays.toString(this.toArray())
. - 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 ints.IntIntMap
-
Returns
java.util.Arrays.toString(this.keys())
. - toString() - Method in class ints.IntList
-
Returns
java.util.Arrays.toString(this.toArray())
- toString() - Method in class ints.UnsignedByteArray
- toString() - Method in class ints.WrappedIntArray
- toString() - Method in class main.Pedigree
-
Returns a string representation of
this
. - toString() - Method in class phase.SampleSeg
-
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.BitSetGTRec
-
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.LowMafRefDiallelicGTRec
-
Returns the data represented by
this
as a VCF record with a GT format field. - toString() - Method in class vcf.LowMafRefGTRec
-
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.RestrictedGT
- toString() - Method in class vcf.RestrictedVcfWindow
-
Returns a string representation of
this
. - toString() - Method in class vcf.SeqCodedRefGTRec
-
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.VcfRec
-
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
U
- UnBref3 - Class in bref
-
Class
UnBref3
converts files in bref version 3 format into VCF format. - UnBref3() - Constructor for class bref.UnBref3
- unfilteredSampleIndex(int) - Method in class vcf.VcfHeader
-
Returns the index of the specified sample in the the list original list of samples before sample exclusions.
- UNKNOWN - beagleutil.Phase
- unphased(int) - Method in class phase.EstPhase
-
Returns a list of remaining marker indices in increasing order for which the specified sample has an unphased heterozygote genotype.
- unphasedSep - Static variable in class blbutil.Const
-
The unphased allele separator:
'/'
- UnsignedByteArray - Class in ints
-
Class
ShiftedByteIndexArray
represents an immutable array of integer values between 0 and 255 inclusive that is stored as abyte[]
array whose values have been translated by -128. - UnsignedByteArray(byte[]) - Constructor for class ints.UnsignedByteArray
-
Constructs a new
UnsignedByteArray
instance from the specified data. - UnsignedByteArray(byte[], int, int) - Constructor for class ints.UnsignedByteArray
-
Constructs a new
UnsignedByteArray
instance from the specified data. - UnsignedByteArray(int[]) - Constructor for class ints.UnsignedByteArray
-
Constructs a new
UnsignedByteArray
instance from the specified data. - UnsignedByteArray(int[], int) - Constructor for class ints.UnsignedByteArray
-
Constructs a new
UnsignedByteArray
instance from the specified data. - UnsignedByteArray(int[], int, int) - Constructor for class ints.UnsignedByteArray
-
Constructs a new
UnsignedByteArray
instance from the specified data. - UnsignedByteArray(IntList) - Constructor for class ints.UnsignedByteArray
-
Constructs a new
UnsignedByteArray
instance from the specified data. - UnsignedByteArray(IntList, int) - Constructor for class ints.UnsignedByteArray
-
Constructs a new
UnsignedByteArray
instance from the specified data. - UnsignedByteArray(IntList, int, int) - Constructor for class ints.UnsignedByteArray
-
Constructs a new
UnsignedByteArray
instance from the specified data. - update(int) - Method in class phase.RecombRegress
-
Stores regression data for regressing the probability of switching reference haplotypes between consecutive markers on genetic distance for the specified sample.
- updateFields(int, int) - Method in class phase.PhaseStates
-
Add the specified segment of the specified reference haplotype to the HMM state space.
- updateHap(int) - Method in class main.CompHapSegment
-
Update the copied haplotype to the specified haplotype
- updateStep(int) - Method in class main.CompHapSegment
-
Updates the step to the specified value
- usage() - Static method in class main.Par
-
Returns a description of the Beagle command line arguments.
- Utilities - Class in blbutil
-
Class
Utilities
contains miscellaneous static utility methods.
V
- Validate - Class in blbutil
-
Class Validate contains static methods for validating command line arguments.
- value() - Method in class vcf.VcfMetaInfo
-
Returns the VCF meta-information line value.
- valueOf(String) - Static method in enum beagleutil.Phase
-
Returns the enum constant of this type with the specified name.
- values() - Static method in enum beagleutil.Phase
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Method in class ints.IntIntMap
-
Returns an array 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.VcfRec
-
Returns the VCF meta-information lines and the VCF header line.
- vcfHeader() - Method in class vcf.VcfRecGTParser
-
Returns the VCF meta-information lines and header line for the backing VCF record
- 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 specifiedFileIterator<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 specifiedFileIterator<String>
. - VcfIt<E extends MarkerContainer> - Class in vcf
-
Class
VcfIt
represents an iterator whosenext()
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. - VcfRec - Class in vcf
-
Class
VcfRecord
represents a VCF record. - VcfRecBuilder - Class in vcf
-
Class
VcfRecBuilder
contains methods for constructing and printing a VCF record in VCF 4.2 format. - VcfRecBuilder(Marker, int) - Constructor for class vcf.VcfRecBuilder
-
Constructs a new
VcfRecBuilder
instance with an initial capacity for the specified number of samples. - 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.
- 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.
W
- weight(int) - Method in class imp.ImpData
-
Return the weight for the HMM state probability at the preceding target marker cluster when estimating the HMM state probability at the specified reference marker via linear interpolation of HMM state probabilities at the preceding and succeeding target marker clusters.
- window() - Method in class main.Par
-
Returns the window parameter.
- window() - Method in class phase.FixedPhaseData
-
Returns the index of the marker window.
- Window<E extends GTRec> - Class in vcf
-
Class
Window
represents a window of VCF records. - Window(List<E>, int, int, boolean, boolean) - Constructor for class vcf.Window
-
Constructs a new
Window
instance from the specified data. - windowIndex() - Method in class vcf.AllData
- windowIndex() - Method in interface vcf.Data
-
Returns the current window index.
- windowIndex() - Method in class vcf.TargetData
- WindowIt<E extends GTRec> - Class in vcf
-
Class
WindowIt
represents a sliding window of VCF recList. - WindowWriter - Class in main
-
Class
WindowWriter
writes VCF and IBD output data. - WindowWriter(Samples, String) - Constructor for class main.WindowWriter
-
Constructs a new
WindowWriter
object. - WrappedIntArray - Class in ints
-
Class
WrappedIntArray
represents an immutableint[]
array. - WrappedIntArray(int[]) - Constructor for class ints.WrappedIntArray
-
Constructs a new
WrappedIntArray
instance. - WrappedIntArray(int[], int) - Constructor for class ints.WrappedIntArray
-
Constructs a new
WrappedIntArray
instance. - WrappedIntArray(IntList) - Constructor for class ints.WrappedIntArray
-
Constructs a new
WrappedIntArray
instance. - WrappedIntArray(IntList, int) - Constructor for class ints.WrappedIntArray
-
Constructs a new
WrappedIntArray
instance. - write(byte[]) - Method in class blbutil.BGZIPOutputStream
- write(byte[], int, int) - Method in class blbutil.BGZIPOutputStream
- write(int) - Method in class blbutil.BGZIPOutputStream
- write(RefGTRec) - Method in class bref.AsIsBref3Writer
- write(RefGTRec) - Method in interface bref.BrefWriter
-
Writes the specified phased genotype data in binary reference format.
- write(RefGTRec) - Method in class bref.CompressBref3Writer
- writeMetaLines(String[], String, boolean, boolean, boolean, boolean, PrintWriter) - Static method in class vcf.VcfWriter
-
Writes VCF meta-information lines and header line to the specified
PrintWriter
. - writeMetaLinesGT(String[], String, PrintWriter) - Static method in class vcf.VcfWriter
-
Writes VCF meta-information lines and header line to the specified
PrintWriter
. - writeRec(PrintWriter) - Method in class vcf.VcfRecBuilder
-
Prints the current VCF record for the current marker to the specified
PrintWriter
.
X
- XBasicGT - Class in vcf
-
Class
XBasicGT
represents genotype and genotype emission probabilities for a set of samples optimized by sample. - XBasicGT(GT, Pedigree) - Constructor for class vcf.XBasicGT
-
Constructs a
XBasicGT
instance from the specified data. - XBasicGT1 - Class in vcf
-
Class
XBasicGT1
represents genotype likelihoods for one sample. - XBasicGT1(GT, int) - Constructor for class vcf.XBasicGT1
-
Constructs a
XBasicGL1
instance from the specified data. - XBasicGT1(GT, int, int, int) - Constructor for class vcf.XBasicGT1
-
Constructs a
XBasicGL1
instance from the specified data. - XGT1 - Interface in vcf
-
Interface
XGT1
(Genotype Likelihoods) represents genotype likelihoods for one sample.
Z
- ZERO_FREQ_ARRAY - Static variable in interface vcf.Data
All Classes All Packages