Index

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

A

accept(E) - Method in interface blbutil.Filter: Returns true if the specified object is accepted and returns false if the specified object is rejected.
acceptAllFilter() - Static method in interface blbutil.Filter: Returns a filter that accepts all non-null objects.
add(float) - Method in class blbutil.FloatList: Adds the specified integer to the end of this list.
add(int) - Method in class ints.IntList: Adds the specified integer to the end of this list.
add(int) - Method in class ints.SynchedIntList: Adds the specified integer to the end of this list.
add(RefGTRec) - Method in class bref.SeqCoder3: Attempts to add the specified RefGTRec object to the list of compressed RefGTRec objects, and returns true if the RefGTRec object was added.
addEstimationData(ParamEstimates) - Method in class phase.HmmParamData: Adds the generated data for estimating allele mismatch and recombination intensity parameters to the specified object.
addMismatchData(int, double) - Method in class phase.ParamEstimates: Records the specified allele mismatch data if markerCnt and pMismatchSum are finite positive values.
addSampleData(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(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) - Method in class vcf.VcfRecBuilder: Adds the specified haploid phased genotype to the VCF record for the current marker.
addSampleData(int, int) - Method in class vcf.VcfRecBuilder: Adds the specified diploid phased genotype to the VCF record for the current marker.
addSwitchData(double, double) - Method in class phase.ParamEstimates: Records the specified genetic distance and switch probability if genDistances and switchProbs are finite positive values.
addToElement(int, float) - Method in class blbutil.FloatList: Adds the specified value to the specified element.
addToQ(BlockingQueue<E>, E) - Static method in interface vcf.SlidingWindow: Adds the specified element to the specified queue.
advanceToFirstPhasingIt() - Method in class phase.PhaseData: Sets the iteration equal to the maximum of this.it() and this.fpd().par().burnin().
advanceWindow(Markers) - Method in class vcf.RestrictedVcfWindow: Advances the sliding marker window, and returns the advanced window as a GTRec[] object.
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.FwdPbwtPhaser: Returns the specified allele
allele(int, int) - Method in class phase.RevPbwtPhaser: Returns the specified allele
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.RefGT
allele(int, int) - Method in class vcf.RestrictedGT
allele(int, int) - Method in class vcf.SplicedGT
allele(int, int) - Method in class vcf.XRefGT
allele(BitArray, int) - Method in class vcf.Markers: Returns the specified allele
ALLELE_CODED - Static variable in class bref.AsIsBref3Writer: The byte value denoting an allele coded record
allele1(int) - Method in class phase.SamplePhase: Returns the allele on the first haplotype for the specified marker.
allele1(int) - Method in class vcf.BasicGTRec
allele1(int) - Method in class vcf.BitArrayGTRec
allele1(int) - Method in class vcf.BitArrayRefGTRec
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.LowMafDiallelicGTRec
allele1(int) - Method in class vcf.LowMafGTRec
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, 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.RefGT
allele1(int, int) - Method in class vcf.RestrictedGT
allele1(int, int) - Method in class vcf.SplicedGT
allele1(int, int) - Method in class vcf.XRefGT
allele2(int) - Method in class phase.SamplePhase: Returns the allele on the second haplotype for the specified marker.
allele2(int) - Method in class vcf.BasicGTRec
allele2(int) - Method in class vcf.BitArrayGTRec
allele2(int) - Method in class vcf.BitArrayRefGTRec
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.LowMafDiallelicGTRec
allele2(int) - Method in class vcf.LowMafGTRec
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, 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.RefGT
allele2(int, int) - Method in class vcf.RestrictedGT
allele2(int, int) - Method in class vcf.SplicedGT
allele2(int, int) - Method in class vcf.XRefGT
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.LowMafDiallelicGTRec: Returns the number of copies of the specified allele.
alleleCount(int) - Method in class vcf.LowMafGTRec: Returns the number of copies of the specified allele.
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 non-major allele.
alleleCount(int) - Method in class vcf.SeqCodedRefGTRec
alleleCounts() - Method in class vcf.LowMafRefDiallelicGTRec
alleleCounts() - Method in class vcf.LowMafRefGTRec
alleleCounts() - Method in interface vcf.RefGTRec: Returns an array of length this.nAlleles() whose j-th element is the allele count of the j-th allele.
alleleCounts() - 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.
alleles() - Method in class vcf.BasicGTRec
alleles() - Method in class vcf.BasicMarker
alleles() - Method in class vcf.BitArrayGTRec
alleles() - Method in class vcf.BitArrayRefGTRec
alleles() - Method in interface vcf.DuplicatesGTRec: Returns an array of length this.size() whose j-th element is equal to this.allele(j}
alleles() - Method in class vcf.LowMafDiallelicGTRec
alleles() - Method in class vcf.LowMafGTRec
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[], BitArray) - Method in class vcf.Markers: Stores the specified alleles in the specified bitList
allHaps() - Method in class phase.CodedSteps: Return the phased target and reference genotype data that was used to construct this CodedSteps instance.
allHaps() - Method in class phase.LowFreqPbwtPhaseIbs: Returns the estimated phased genotypes for the target and reference samples.
allHaps() - Method in class phase.LowFreqPhaseIbs: Returns the estimated phased genotypes for the target and reference samples.
allHaps() - Method in class phase.PbwtPhaseIbs: Returns the estimated phased genotypes for the target and reference samples.
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.
appendRecords(Samples, GTRec[], 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 (otherSample < this.nTargSamples() and the specified samples are estimated to be IBS2 at the specified marker, and returns false otherwise.
areIbs2(int, int, int, int) - Method in class phase.Ibs2: Returns true if (0 <= otherSample && otherSample < this.nTargSamples()) and the specified samples are estimated to be IBS2 within the specified interval and returns false 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 applying java.utils.Arrays.toString() to an equivalent int[] object.
await(CountDownLatch) - Static method in class blbutil.MultiThreadUtils: Blocks the current thread until the specified CountDownLatch has counted down to 0.

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 genotypes for a list of markers and samples.
BasicGT(GTRec[]) - Constructor for class vcf.BasicGT: Constructs a BasicGT instance from the specified data
BasicGT(Markers, Samples, GTRec[]) - Constructor for class vcf.BasicGT: Constructs a BasicGT instance from the specified data.
BasicGT(Samples, GTRec[]) - Constructor for class vcf.BasicGT: Constructs a BasicGT instance from the specified data
BasicGTRec - Class in vcf: Class BasicGTRec stores genotypes for a list of samples at a single marker.
BasicGTRec(VcfRecGTParser) - Constructor for class vcf.BasicGTRec: Constructs a new BasicGTRec instance representing the specified VCF record's GT format field data.
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.
BasicPhaseStates - Class in phase: Class BasicPhaseStates has methods for constructing a Li and Stephens HMM for a target haplotype or target sample.
BasicPhaseStates(PbwtPhaseIbs, int) - Constructor for class phase.BasicPhaseStates: Constructs a new BasicPhaseStates object from the specified data.
beagleutil - package beagleutil
BGZIPOutputStream - Class in blbutil: Class BGZIPOutputStream is an output stream filter that performs BGZIP compression.
BGZIPOutputStream(OutputStream, boolean) - Constructor for class blbutil.BGZIPOutputStream: Creates a new BGZIPOutputStream instance that writes to the specified output stream.
bgzipPrintWriter(File) - Static method in class blbutil.FileUtil: Returns a buffered java.io.PrintWriter that compresses data using the BGZIP algorithm and writes the compressed data to the specified file.
bgzipPrintWriter(File, boolean) - Static method in class blbutil.FileUtil: Returns a buffered java.io.PrintWriter that compresses data using the BGZIP algorithm and writes the compressed data to the specified file.
binarySearch(double) - Method in class blbutil.DoubleArray: Searches this for the specified value using the binary search algorithm.
binarySearch(float) - Method in class blbutil.FloatArray: Searches this for the specified value using the binary search algorithm.
binarySearch(int) - Method in class ints.IntList: Returns an index associated with the specified value, or (-insertionPoint - 1) if the value is not found.
binarySearch(int) - Method in class ints.WrappedIntArray: Searches this for the specified value using the binary search algorithm.
binarySearch(int, int, double) - Method in class blbutil.DoubleArray: Searches the specified range of this for the specified value using the binary search algorithm.
binarySearch(int, int, float) - Method in class blbutil.FloatArray: Searches the specified range of this for the specified value using the binary search algorithm.
binarySearch(int, int, int) - Method in class ints.WrappedIntArray: Searches the specified range of this for the specified value using the binary search algorithm.
BitArray - Class in blbutil: Interface BitArray represents a mutable sequence of bits with a fixed length.
BitArray(int) - Constructor for class blbutil.BitArray: Constructs a BitArray instance with the specified size and having all bits set to 0 (unset).
BitArray(long[], int) - Constructor for class blbutil.BitArray: Constructs a BitArray instance from the specified values.
BitArray(BitArray) - Constructor for class blbutil.BitArray: Constructs a new BitArray instance with the same sequence of bits and the same size as the specified BitArray.
BitArrayGTRec - Class in vcf: Class BitArrayGT represents genotypes for a list of samples at a single marker.
BitArrayGTRec(VcfRecGTParser) - Constructor for class vcf.BitArrayGTRec: Constructs a new BitArrayGT instance representing the specified VCF record's GT format field data.
BitArrayGTRec(VcfRecGTParser.HapListRep) - Constructor for class vcf.BitArrayGTRec: Constructs a new BitArrayGT instance representing the specified VCF record's GT format field data.
BitArrayRefGTRec - Class in vcf: Class BitArrayRefGTRec represents phased, nonmissing, genotypes for a list of samples at a single marker.
bitSets(int, int) - Static method in class phase.PbwtRecPhaser: Returns an array of bit sets.
bitsPerAllele() - Method in class vcf.BasicMarker
bitsPerAllele() - Method in interface vcf.Marker: Returns the minimum number of bits required to store a non-missing allele.
bitsPerAllele(int) - Method in class phase.RevPbwtPhaser: Returns the minimum number of bits required to store a non-missing allele for the specified marker
bitsToAlleles(BitArray) - Method in class vcf.Markers: Returns the specified allele stored in the specified hapBits array.
blbutil - package blbutil
BlockLineReader - Class in blbutil: Class BlockLineReader is a blbutil.FileIt that reads blocks of lines from a file.
booleanArg(String, Map<String, String>, boolean, boolean) - Static method in class blbutil.Validate: Removes the specified key from the specified map, and returns the boolean value corresponding to the specified key.
bref - package bref
Bref3 - Class in bref: Class Bref3 converts files in VCF format into bref version 3 format.
Bref3() - Constructor for class bref.Bref3
Bref3It - Class in bref: Class Bref3It represents an iterator whose next() which returns records from a bref version 3 file.
Bref3It(File) - Constructor for class bref.Bref3It: Constructs a new Bref3It instance.
Bref3It(File, Filter<Marker>) - Constructor for class bref.Bref3It: Constructs a new Bref4It instance.
Bref3Reader - Class in bref: Class Bref3Reader contains methods for reading a bref 3 (binary reference format) file.
Bref3Reader(DataInput, Filter<Marker>) - Constructor for class bref.Bref3Reader: Constructs a new Bref3Reader instance.
BrefBlock - Class in bref: Class BrefBlock represents starting chromosome coordinates and file offset for the start of a binary reference format (bref) data block.
BrefBlock(int, int, long) - Constructor for class bref.BrefBlock: Constructs a BrefBlock for the specified data.
BrefWriter - Interface in bref: Interface BrefWrites writes phased, non-missing genotypes to a binary reference format (bref) file.
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.
burnin() - Method in class main.Par: Returns the burnin parameter.
bwdIbsHap(int, int) - Method in class phase.LowFreqPhaseIbs: Returns the IBS haplotype index for the specified haplotype in the specified genomic interval, when the PBWT is performed in order of decreasing marker index.
bwdUpdate(float[], float, float[], byte[], int) - Static method in class phase.HmmUpdater: Updates the backward values.
bwdUpdate(IntArray, int, int, int[], int[]) - Method in class beagleutil.PbwtDivUpdater: Update the specified prefix and divergence arrays using the backward Positional Burrows-Wheeler Transform.

C

carriers(int) - Method in class vcf.Window: Returns the indices of the reference and target carriers for each low-frequency allele at the target data markers.
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 for the markers in this 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.BitArray: Clears all bits.
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.
clear() - Method in class ints.SynchedIntList: Removes all elements from this list.
clear() - Method in class phase.ParamEstimates: Clears all data that has been added via the this.addMismatchData and this.addSwitchData() methods.
clear(int) - Method in class blbutil.BitArray: Clears the specified bit.
close() - Method in class blbutil.BGZIPOutputStream
close() - Method in class blbutil.BlockLineReader
close() - Method in interface blbutil.FileIt: Stops reading data elements 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.IntervalVcfIt
close() - Method in class vcf.RefIt
close() - Method in class vcf.RefTargSlidingWindow
close() - Method in class vcf.RestrictedVcfWindow: Releases any I/O resources controlled by this object.
close() - Method in interface vcf.SlidingWindow: Releases any I/O resources controlled by this object.
close() - Method in class vcf.TargSlidingWindow
close() - Method in class vcf.VcfIt
closestIndex(int, int) - Method in class vcf.PlinkGenMap: Returns the index of the genetic map position that is closest to the specified base position.
clustEnds() - Method in class phase.SamplePhase: Returns the (exclusive) end marker indices of each marker cluster.
cluster() - Method in class main.Par: Returns the cluster parameter.
clusterEnd(int) - Method in class phase.MarkerCluster: Returns the exclusive end marker for the cluster.
clusterStart(int) - Method in class phase.MarkerCluster: Returns the inclusive start marker for the cluster.
clustHasMissingGT(int) - Method in class phase.MarkerCluster: Returns true if the cluster has at least one missing genotype, and returns false otherwise.
codedSteps() - Method in class imp.ImpIbs: Returns the coded steps.
codedSteps() - Method in class phase.PbwtIbsData: Returns the coded steps.
codedSteps() - Method in class phase.PhaseData: Constructs and 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(EstPhase) - Constructor for class phase.CodedSteps: Constructs a new CodedSteps instance from the specified data.
colon - Static variable in class blbutil.Const: The colon character: ':'
combine(Samples, Samples) - Static method in class vcf.Samples: Returns a new samples instance by combining the two list of samples in the specified order
combine(XRefGT, XRefGT) - Static method in class vcf.XRefGT: Returns a new XRefGT instance from the specified data.
comma - Static variable in class blbutil.Const: The comma character: ','
COMMAND - Static variable in class main.Main: The command to invoke the program.
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 specified ChromInterval instance for order, and returns -1, 0, or 1 depending on whether this is less than, equal or greater than the specified instance.
compareTo(CompHapSegment) - Method in class beagleutil.CompHapSegment: Compares the specified segment to this for order.
compareTo(SampleSeg) - Method in class phase.SampleSeg: Compares this SampleSeg with the specified SampleSeg 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 beagleutil.CompHapSegment: Returns the composite haplotype index.
CompHapSegment - Class in beagleutil: Class CompHapSegment represents a copied haplotype segment in a composite reference haplotype.
CompHapSegment(int, int, int, int) - Constructor for class beagleutil.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 returns false otherwise.
contains(Marker) - Method in class beagleutil.ChromInterval: Returns true if the specified marker is in this chromosome interval and returns false otherwise.
contains(Marker) - Method in class vcf.Markers: Returns true if the specified marker is not null and is an element in the list of markers represented by this, and returns false otherwise.
copyFrom(BitArray, int, int) - Method in class blbutil.BitArray: Replaced the specified bits in this Bitlist with the corresponding bits in the specified BitArray.
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.
copyTo(int, int, int, BitArray) - Method in class vcf.XRefGT: Copies the specified bit sequence to the specified bitList
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 of non-negative integers.
create(FileIt<String>) - Static method in class vcf.RefIt: Create and returns a new RefIt instance from the specified iterator.
create(FileIt<String>, int, int) - Static method in class blbutil.BlockLineReader: Constructs and returns a new BlockLineReader for the specified data.
create(FileIt<String>, Filter<String>, Filter<Marker>) - Static method in class vcf.RefIt: Create and returns a new RefIt instance from the specified objects.
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>, 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 of non-negative integers.
create(GeneticMap, double, Markers) - Static method in class vcf.MarkerMap: Returns a new MarkerMap instance constructed from the specified data.
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.
cumMarkers() - Method in class vcf.RefTargSlidingWindow
cumMarkers() - Method in interface vcf.SlidingWindow: Returns the number of distinct markers returned in preceding this.nextWindow() method calls.
cumMarkers() - Method in class vcf.TargSlidingWindow
cumTargMarkers() - Method in class vcf.RefTargSlidingWindow
cumTargMarkers() - Method in interface vcf.SlidingWindow: Returns the number of distinct target markers returned in preceding this.nextWindow() method calls.
cumTargMarkers() - Method in class vcf.TargSlidingWindow

D

decEndComp() - Static method in interface beagleutil.IntInterval: Returns a Comparator<IntInterval> which orders IntInterval objects in order of increasing this.start() value and orders IntInterval objects with the same this.start() value in order of decreasing this.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 vcf.VcfIt: The default number of VCF records stored in a buffer.
DEFAULT_INIT_CAPACITY - Static variable in class beagleutil.ThreadSafeIndexer: The default initial capacity, which is 500.
DEFAULT_INIT_CAPACITY - Static variable in class blbutil.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_CAPACITY - Static variable in class ints.SynchedIntList: The default initial capacity of an SynchedIntList, 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.
DoubleArray(DoubleStream) - 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".
em() - Method in class main.Par: Returns the em parameter.
end() - Method in class imp.RefHapHash: Returns the ending reference marker index (exclusive) for the reference haplotype allele sequences.
end() - Method in class phase.FwdPbwtPhaser: Return the exclusive end marker index.
end() - Method in class phase.RevPbwtPhaser: Return the exclusive end marker index.
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(int) - Method in class vcf.Steps: Returns the index of the last marker (exclusive) in the specified step.
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
equal(BitArray, int, int) - Method in class blbutil.BitArray: Returns true if this Bitlist and the specified BitArray have identical sequences of bits for the specified indices, and returns false otherwise.
equals(BitArray, BitArray) - Static method in class blbutil.BitArray: Returns true if the specified BitArray objects represent identical bit sequences having the same size, and returns false otherwise.
equals(IntArray, IntArray) - Static method in interface ints.IntArray: Returns true if the specified IntArray objects represent the same sequence of integer values, and returns false otherwise.
equals(Object) - Method in class beagleutil.ChromInterval: Returns true if the specified object is a ChromInterval instance representing the same interval of genome coordinates as this, and returns false otherwise.
equals(Object) - Method in class 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 a Marker with the same chromosome, position, allele lists, and INFO END field, and returns false otherwise.
equals(Object) - Method in class vcf.Markers: Returns true if the specified object is a Markers instance which represents the same list of markers as this, and returns false otherwise.
equals(Object) - Method in class vcf.Samples: Returns true if the specified object is a Samples object which represents the same ordered list of samples as this, and returns false otherwise.
err(int) - Method in class main.Par: Returns the default allele mismatch parameter for the specified number of haplotypes.
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 phased genotypes.
EstPhase - Class in phase: Class EstPhase stores input genotype data and the current estimated phased genotypes for each target sample.
EstPhase(FixedPhaseData, 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() - Static method in class blbutil.Utilities: Prints "Terminating program." to standard error and terminates the Java virtual machine.
exit(String) - Static method in class blbutil.Utilities: Prints 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 then terminates the Java virtual machine.
exit(Throwable, String) - 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 class blbutil.BlockLineReader
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 if the data source is unknown.
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.VcfIt
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.
FixedPhaseData - Class in phase: Class FixedPhaseData stores immutable data for a marker window.
FixedPhaseData(Par, Pedigree, Window, 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.size() 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.EstPhase: Returns the input data for phasing that is the same in each iteration.
fpd() - Method in class phase.PhaseData: Returns the input data for phasing that is the same in each iteration.
fpd() - Method in class phase.Stage2Haps: Returns the input data for phasing that is the same in each iteration.
from(Markers, Samples, BitArray[]) - Static method in class vcf.XRefGT: Returns a new XRefGT instance from the specified data.
from(Samples, AtomicReferenceArray<SamplePhase>) - Static method in class vcf.XRefGT: Returns a new XRefGT instance from the specified data.
fromGL(VcfHeader, String, float) - Static method in class vcf.VcfRec: Constructs and returns a new VcfRec 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 VcfRec 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 VcfRec 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[], boolean[]) - Static method in class vcf.Samples: Constructs and returns a Samples instance corresponding to the specified list of sample identifiers.
fromIntBits(int[]) - Static method in class blbutil.FloatArray: Constructs and returns a FloatArray from the specified list of bit representations.
fromPhasedGT(GT, int) - Static method in class vcf.XRefGT: Returns a new XRefGT instance from the specified data.
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.
fwdIbsHap(int, int) - Method in class phase.LowFreqPhaseIbs: Returns the IBS haplotype index for the specified haplotype in the specified genomic interval, when the PBWT is performed in order of increasing marker index.An index of -1 is stored in an entry if no IBS haplotype is available.
FwdPbwtPhaser - Class in phase: Class FwdPbwtPhaser phases input genotype data and imputes missing alleles using the Positional Burrows-Wheeler Transform (PBWT).
FwdPbwtPhaser(FixedPhaseData, int, int, long) - Constructor for class phase.FwdPbwtPhaser: Creates a new FwdPbwtPhaser for the specified data.
fwdUpdate(float[], float, float, float[], byte[], int) - Static 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.PbwtDivUpdater: 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 size this.markers().nMarkers() whose k-th element is the genetic distance between the k-th target marker and the previous marker, or 0.0 if (k == 0).
geneticMap(File, ChromInterval) - Static method in interface vcf.GeneticMap: Constructs and returns a genetic map from the specified data.
GeneticMap - Interface in vcf: Interface GeneticMap represents a genetic map for one or more chromosomes.
genMap() - Method in class vcf.RefTargSlidingWindow
genMap() - Method in interface vcf.SlidingWindow: Returns the genetic map.
genMap() - Method in class vcf.TargSlidingWindow
genMap() - Method in class vcf.Window: 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 size this.markers().nMarkers() whose k-th element is the genetic map position of the k-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(GeneticMap, double, Markers) - Static method in interface vcf.GeneticMap: Returns the an array of length markers.nMarkers() whose whose j-th element is the genetic map position of the j-th marker.
genPos(GeneticMap, Markers) - Static method in interface vcf.GeneticMap: Returns the an array of length markers.nMarkers() whose whose j-th element is the genetic map position of the j-th marker.
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
get(int) - Method in class blbutil.BitArray: Returns the specified bit as a boolean value.
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.PackedIntArray
get(int) - Method in class ints.SynchedIntList: Returns the element at the specified position in this list.
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 phase.EstPhase: Return the estimated phase for the specified sample.
get(int) - Method in class vcf.BasicGTRec
get(int) - Method in class vcf.BitArrayGTRec
get(int) - Method in class vcf.BitArrayRefGTRec
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.LowMafDiallelicGTRec
get(int) - Method in class vcf.LowMafGTRec
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.
getAndResetSwapRate() - Static method in class phase.PhaseBaum1: Returns the proportion of unphased heterozygotes whose phase relative to the previous heterozygote has been changed.
getAsInt(int) - Method in class blbutil.BitArray: Returns the specified bit as a int value.
getCompressedList() - Method in class bref.SeqCoder3: Returns and clears the stored list of compressed RefGTRec objects.
getFields(String) - Static method in class blbutil.StringUtil: Returns an array obtained by trimming white-space from the beginning and end of the specified string, and splitting the resulting string around white space.
getFields(String, char) - Static method in class blbutil.StringUtil: Returns an array obtained by splitting the specified string around the specified delimiter.
getFields(String, char, int) - Static method in class blbutil.StringUtil: Returns an array obtained by splitting the specified string around the first (limit - 1) occurrences of the specified delimiter.
getFields(String, int) - Static method in class blbutil.StringUtil: Returns an array obtained by trimming white-space from the beginning and end of the specified string, and splitting the resulting string around the first (limit-1) white-space delimiters.
getFile(String) - Static method in class blbutil.Validate: Returns a File object corresponding to the specified filename or null if filename == null
getHaps(BitArray, BitArray) - Method in class phase.SamplePhase: Copies the stored haplotypes to the specified BitList objects
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.VcfRec: Returns the probability of the observed data for the specified sample 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 beagleutil.CompHapSegment: Returns the haplotype.
hap(int) - Method in class imp.RefHapHash: Return the specified haplotype in the sublist of reference haplotypes.
hap1() - Method in class phase.SamplePhase: Returns the first haplotype.
hap2() - Method in class phase.SamplePhase: Returns the second haplotype.
hap2Index(int) - Method in class imp.RefHapHash: Returns the index of the specified haplotype in the sublist of reference haplotypes.
hapCnt() - Method in class imp.ImputedRecBuilder: Returns the number of imputed alleles added by the addSampleData() methods.
hapCodedInstance(Marker, Samples, int[][]) - Static method in interface vcf.RefGTRec: Constructs and returns a new allele-coded RefGTRec 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 is null if j is the major allele with lowest index, and otherwise is an array of indices of haplotypes that carry the j-th allele sorted in increasing order
hapIndices() - Method in class vcf.SeqCodedRefGTRec
hapListRep() - Method in class vcf.VcfRecGTParser
hapLists(boolean) - Method in class vcf.VcfRecGTParser.HapListRep: Returns an array of length this.marker().nAlleles() that contains lists of haplotypes carrying each allele.
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.
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 returns false otherwise.
hash(int) - Method in class imp.RefHapHash: Return a hash code computed from the allele sequence of the specified haplotype in the sublist of reference haplotypes.
hash(int, int) - Method in class blbutil.BitArray: Returns a hash code for the specified bits in this Bitlist
hash(int, int, int) - Method in class vcf.XRefGT: Returns a hash code for the specified alleles.
hashCode() - Method in class beagleutil.ChromInterval: 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.
hashCode() - Method in class vcf.Samples: Returns a hash code value for the object.
hasNext() - Method in class blbutil.BlockLineReader: Returns the next element in the iteration.
hasNext() - Method in class blbutil.InputIt: Returns true if the iteration has more elements.
hasNext() - Method in class bref.Bref3It: Returns true if the iteration has more elements, and returns false otherwise.
hasNext() - Method in class vcf.IntervalVcfIt: Returns true if the iteration has more elements.
hasNext() - Method in class vcf.RefIt: Returns true if the iteration has more elements, and returns false otherwise.
hasNext() - Method in class vcf.VcfIt: Returns true if the iteration has more elements, and returns false otherwise.
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.
HIGH_FREQ_ARRAY - Static variable in class vcf.Window: An array that replaces an array of allele counts for a marker with high minor allele frequency.
HmmParamData - Class in phase: Class HmmParamData generates data for estimating allele mismatch and recombination intensity parameters for a haploid Li and Stephens hidden Markov model.
HmmParamData(PbwtPhaseIbs) - Constructor for class phase.HmmParamData: Creates a HmmParamData instance for the specified data.
HmmStateProbs - Class in phase: Class HmmStateProbs has a method that returns the reference haplotype and probability associated with each HMM state.
HmmStateProbs(LowFreqPhaseIbs) - Constructor for class phase.HmmStateProbs: Creates a HmmStateProbs instance from the specified data.
HmmUpdater - Class in phase: Class HmmUpdater has static methods for next marker updates of forward and backward HMM values.
hyphen - Static variable in class blbutil.Const: The hyphen character: '-'

I

Ibs2 - Class in phase: Class Ibs2 stores IBS2 segments that any target sample shares with another target sample.
Ibs2(GT, MarkerMap, FloatArray) - Constructor for class phase.Ibs2: Constructs a new Ibs2 instance from the specified data.
Ibs2Markers - Class in phase: Class Ibs2Markers stores the markers and intervals that are used to detect IBS2 segments.
Ibs2Markers(GT, MarkerMap, FloatArray) - Constructor for class phase.Ibs2Markers: Constructs a new Ibs2Markers instance from the specified data.
Ibs2Sets - Class in phase: Class Ibs2Sets partitions markers into steps, and stores the sets of samples whose genotypes are consistent with IBS2 in each step.
Ibs2Sets(GT, Ibs2Markers) - Constructor for class phase.Ibs2Sets: Constructs a new Ibs2Sets instance from the specified data.
ibsHap(int, int) - Method in class phase.LowFreqPbwtPhaseIbs: Returns the index of a haplotype that is identical by state with the specified target haplotype in the specified genomic interval, or -1 if there is no identical-by-state haplotype.
ibsHap(int, int) - Method in class phase.PbwtPhaseIbs: Returns the index of a haplotype that is identical by state with the specified target haplotype in the specified genomic interval, or -1 if there is no identical-by-state haplotype.
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, byte[][][]) - Method in class phase.BasicPhaseStates: Stores the Li and Stephens HMM for the specified target sample in the specified arrays.
ibsStates(int, int[][], boolean[][]) - Method in class imp.ImpStates: Stores the reference haplotype for the j-th state at the m-th marker in hapIndices[m][j], and stores the equality of the allele carried by the reference haplotype for the j-th state and the allele carried by the target haplotype at the m-th marker in alMatch[m][j].
ibsStates(int, int[][], byte[][]) - Method in class phase.LowFreqPhaseStates: Stores the Li and Stephens HMM for the specified target haplotype in the specified arrays.
ibsStates(int, MarkerCluster, List<int[]>, byte[][][]) - Method in class phase.BasicPhaseStates: Stores the Li and Stephens HMM for the specified target sample in the specified arrays.
ibsStep() - Method in class beagleutil.CompHapSegment: Returns the last recorded IBS ibsStep for this.hap().
ibsStep() - Method in class phase.FixedPhaseData: Returns the minimum cM step length for composite reference haplotype construction.
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 vcf.BasicMarker
id(int) - Method in interface vcf.Marker: Returns the specified marker identifier.
id(int) - Method in class vcf.Samples: Returns the identifier for the sample with the specified index in this list of samples.
idFilter(Collection<String>) - Static method in class vcf.FilterUtil: Returns a filter that accepts all markers which do not have an identifier or chromomsome position present in the specified collection.
idIndex(int) - Method in class vcf.Samples: Returns the sample identifier index corresponding to the sample with the specified index in this list of samples.
idIndexToIndex() - Method in class vcf.Samples: Returns an array mapping sample identifier indices to sample indices.
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 vcf.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, Window, GT, GeneticMap) - Constructor for class imp.ImpData: Constructs a new ImpData instance from the specified data.
ImpIbs - Class in imp: Class ImpIbs identifies haplotypes that share a long IBS segment with a specified haplotype.
ImpIbs(ImpData) - Constructor for class imp.ImpIbs: Constructs a new ImpIbs object from the specified data.
ImpLS - Class in imp: Class ImpLS computes HMM state probabilities at genotyped markers in the target haplotypes.
ImpLSBaum - Class in imp: Class ImpLSBaum implements a Baum hidden Markov model forward and backward algorithms for computing HMM state probabilities at genotyped markers using IBS-matched reference haplotypes.
ImpLSBaum(ImpData, ImpIbs) - Constructor for class imp.ImpLSBaum: Creates a LSHapBaum instance from the specified data.
ImpStates - Class in imp: Class ImpStates identifies a list of pseudo-reference haplotypes for a target haplotype.
ImpStates(ImpIbs) - Constructor for class imp.ImpStates: Constructs a new ImpStates object from the specified data.
imputationNanos(long) - Method in class main.RunStats: Stores the time for imputing ungenotyped marker and increases the cumulative imputation time by the specified number of nanoseconds.
impute() - Method in class main.Par: Returns the impute parameter.
impute(int) - Method in class imp.ImpLSBaum: Returns HMM state probabilities at genotyped markers for the specified target haplotype.
ImputedRecBuilder - Class in imp: Class ImputeRecBuilder contains methods for constructing and printing a VCF record in VCF 4.3 format.
ImputedRecBuilder(Marker, int, boolean, boolean) - Constructor for class imp.ImputedRecBuilder: Constructs a new ImputedRecBuilder instance for the specified number of samples.
ImputedVcfWriter - Class in imp: Class ImputedVcfWriter writes observed and imputed genotypes to a VCF output file.
ImputedVcfWriter(ImpData, int, int, int) - Constructor for class imp.ImputedVcfWriter: Constructs a new ImputedVcfWriter instance from the specified data.
incEndComp() - Static method in interface beagleutil.IntInterval: Returns a Comparator<IntInterval> which orders IntInterval objects in order of increasing this.start() value and orders IntInterval objects with the same this.start() value in order of increasing this.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 marker index (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.
incrementAndGet(int) - Method in class ints.IntList: Increments by one the element at the specified position in this list.
incrementIt() - Method in class phase.PhaseData: Increments the iteration by one.
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(int[], int) - Constructor for class ints.IndexArray: Constructs a new IndexArray instance from the specified data.
IndexArray(IntArray, int) - Constructor for class ints.IndexArray: Constructs a new IndexArray instance from the specified data.
indices() - Method in class vcf.Window: Return a MarkerIndices instance which stores the overlap and splice points between this window and the preceding and next windows, and the map between reference and target marker indices.
info() - Method in class vcf.VcfRec: Returns the INFO field.
initPhase(FixedPhaseData, long) - Static method in class phase.PbwtPhaser: Returns an initial phasing for first-stage markers in the target samples.
InputIt - Class in blbutil: Class InputIt is a buffered iterator whose next() method returns lines of a text input stream.
instance() - Static method in class beagleutil.ChromIds: Returns the singleton ChromIds instance.
instance() - Static method in class beagleutil.SampleIds: Returns the singleton SampleIds instance.
instance(Par) - Static method in class vcf.RefTargSlidingWindow: Constructs and returns a new RefTargSlidingWindow instance for the specified reference and target data.
instance(Par) - Static method in class vcf.TargSlidingWindow: Constructs and returns a new TargSlidingWindow instance for the specified target data.
intArg(String, Map<String, String>, boolean, int, int, int) - Static method in class blbutil.Validate: Removes the specified key from the specified map, and returns the integer value corresponding to the specified key.
intArray() - Method in class ints.IndexArray: Returns the wrapped IntArray object.
IntArray - Interface in ints: Interface IntArray represents an immutable int[] array.
IntervalVcfIt<E extends MarkerContainer> - Class in vcf: Class IntervalVcfIterator is a sample file iterator whose next() method returns a marker container.
IntervalVcfIt(SampleFileIt<E>, ChromInterval) - Constructor for class vcf.IntervalVcfIt: Constructs a new IntervalVcfIterator instance.
IntInterval - Interface in beagleutil: Interface IntInterval represents an interval of consecutive integers.
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 specified IntList.
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 returns false 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 return false otherwise.
isCarrier(int, int) - Method in class vcf.SeqCodedRefGTRec
isDiploid(int) - Method in class vcf.Samples: Returns true if the specified sample has two alleles per genotype, and returns false if the sample has one allele per genotype.
isEmpty() - Method in class blbutil.DoubleArray: Returns true if this list has no elements, and returns false otherwise.
isEmpty() - Method in class blbutil.FloatArray: Returns true if this list has no elements, and returns false otherwise.
isEmpty() - Method in class blbutil.FloatList: Returns true if this list has no elements, and returns false otherwise.
isEmpty() - Method in class ints.IntList: Returns true if this list has no elements, and returns false otherwise.
isLowFreq(int, int) - Method in class phase.FixedPhaseData: Returns true if the specified allele is a low-frequency allele, and returns false otherwise.
isPhased() - Method in class vcf.BasicGT
isPhased() - Method in class vcf.BasicGTRec
isPhased() - Method in class vcf.BitArrayGTRec
isPhased() - Method in class vcf.BitArrayRefGTRec
isPhased() - Method in interface vcf.DuplicatesGTRec: Returns true if every genotype for each sample is a phased, non-missing genotype, and returns false otherwise.
isPhased() - Method in interface vcf.GT: Returns true if the genotype for each marker and sample has non-missing alleles and is either haploid or diploid with a phased allele separator, and returns false otherwise.
isPhased() - Method in class vcf.LowMafDiallelicGTRec
isPhased() - Method in class vcf.LowMafGTRec
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.VcfRecGTParser.HapListRep: Returns true if all genotypes are phased and there are no missing alleles, and returns false otherwise.
isPhased() - Method in class vcf.XRefGT
isPhased(int) - Method in class vcf.BasicGTRec
isPhased(int) - Method in class vcf.BitArrayGTRec
isPhased(int) - Method in class vcf.BitArrayRefGTRec
isPhased(int) - Method in interface vcf.DuplicatesGTRec: Returns true if the genotype for the specified sample has non-missing alleles and is either haploid or diploid with a phased allele separator, and returns false otherwise.
isPhased(int) - Method in class vcf.LowMafDiallelicGTRec
isPhased(int) - Method in class vcf.LowMafGTRec
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
isReversed() - Method in class vcf.BasicGT
isReversed() - Method in interface vcf.GT: Returns true if the markers are ordered by decreasing chromosome base position, and returns false otherwise.
isReversed() - Method in class vcf.RefGT
isReversed() - Method in class vcf.RestrictedGT
isReversed() - Method in class vcf.SplicedGT
isReversed() - Method in class vcf.XRefGT
it() - Method in class phase.PhaseData: Returns the current iteration.
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.
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 this window is the last window in the analysis, and returns false otherwise.
leaveUnphasedProp(int) - Method in class phase.PhaseData: Returns the proportion of unphased heterozygotes at the start of a phasing iteration that will be left unphased at the end of a phasing iteration.
liStephensPMismatch(int) - Static method in class main.Par: Return an approximation to the allele mismatch probability suggested by Li and Stephens.
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.
LowFreqPbwtPhaseIbs - Class in phase: Class AltPbwtPhaseIBS uses the Positional Burrows-Wheeler Transform (PBWT) and rare variants to select IBS haplotypes for each sample for each specified genomic interval.
LowFreqPbwtPhaseIbs(PhaseData, CodedSteps, boolean) - Constructor for class phase.LowFreqPbwtPhaseIbs: Constructs a new PbwtPhaseIBS instance from the specified data.
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.
LowFreqPhaseStates - Class in phase: Class LowFreqPhaseStates has methods for constructing a Li and Stephens HMM for a target haplotype.
LowFreqPhaseStates(LowFreqPhaseIbs, int) - Constructor for class phase.LowFreqPhaseStates: Constructs a new LowFreqPhaseStates object from the specified data.
LowMafDiallelicGTRec - Class in vcf: Class LowMafDiallelicGTRc stores genotypes for a list of samples at a diallelic marker.
LowMafDiallelicGTRec(VcfRecGTParser.HapListRep) - Constructor for class vcf.LowMafDiallelicGTRec: Constructs a new LowMafDiallelicGTRec representing the specified VCF record's GT format field data.
LowMafGTRec - Class in vcf: Class LowMafGTRc stores genotypes for a list of samples at a marker.
LowMafGTRec(VcfRecGTParser.HapListRep) - Constructor for class vcf.LowMafGTRec: Constructs a new LowMafGTRec representing the specified VCF record's GT format field data.
LowMafRefDiallelicGTRec - Class in vcf: Class LowMafRefDiallelicGTRec 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 LowMafRefDiallelicGTRec instance from the specified data.
LowMafRefDiallelicGTRec(RefGTRec) - Constructor for class vcf.LowMafRefDiallelicGTRec: Constructs a new LowMafRefDiallelicGTRec instance from the specified data.
LowMafRefDiallelicGTRec(VcfRecGTParser) - Constructor for class vcf.LowMafRefDiallelicGTRec: Constructs a new LowMafRefDiallelicGTRec instance from the specified data.
LowMafRefGTRec - Class in vcf: Class LowMafRefGTRec 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 LowMafRefGTRec instance from the specified data.
LowMafRefGTRec(RefGTRec) - Constructor for class vcf.LowMafRefGTRec: Constructs a new LowMafRefGTRec instance from the specified data.
LowMafRefGTRec(VcfRecGTParser) - Constructor for class vcf.LowMafRefGTRec: Constructs a new LowMafRefGTRc instance from the specified data.

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.
majorAllele() - Method in class vcf.LowMafDiallelicGTRec: Returns the major allele.
majorAllele() - Method in class vcf.LowMafGTRec: Returns the major allele.
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
majorAllele() - Method in class vcf.VcfRecGTParser.HapListRep: Returns the major allele.
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 vcf.Steps: Return the marker map.
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 alleles.
maps() - Method in class vcf.SeqCodedRefGTRec
marker() - Method in class imp.ImputedRecBuilder: Returns the marker in the VCF record.
marker() - Method in class vcf.BasicGTRec
marker() - Method in class vcf.BitArrayGTRec
marker() - Method in class vcf.BitArrayRefGTRec
marker() - Method in class vcf.LowMafDiallelicGTRec
marker() - Method in class vcf.LowMafGTRec
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.HapListRep: Returns the 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.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.XRefGT
Marker - Interface in vcf: Interface Marker represents a genetic marker.
MarkerCluster - Class in phase: Class MarkerCluster represents a partition of markers into contiguous marker clusters.
MarkerCluster(PhaseData, int) - Constructor for class phase.MarkerCluster: Constructs a new MarkerCluster instance from the specified data.
MarkerContainer - Interface in vcf: Interface MarkerContainer represents an object that stores a unique vcf.Marker instance.
markerFilter(File) - Static method in class vcf.FilterUtil: Returns a filter that excludes markers that have an identifier or genome coordinates that matches a line of the specified file, or returns null if the excludeMarkersFile parameter is null.
markerIndices() - Method in class imp.ImpData
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 returns false otherwise.
MarkerMap - Class in vcf: Class MarkerRecombMap represents genetic map positions and inter-marker genetic distances for a sequence of genomic loci.
markers() - Method in class phase.SamplePhase: Returns the list of markers.
markers() - Method in class vcf.BasicGT
markers() - Method in interface vcf.GT: Returns the list of markers in order of increasing chromosome position.
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.XRefGT
markers(int, int) - Method in class phase.Ibs2Markers: Returns an increasing list of marker indices that are used to detect IBS2 segments in the specified interval
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() whose k-th element is the index of the k-th marker in the list of target markers or is -1 if the marker is not present in the target data.
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.
max(IntArray) - Static method in interface ints.IntArray: Returns the maximum element, or Integer.MIN_VALUE if this.size() == 0.
MAX_NALLELES - Static variable in class bref.SeqCoder3: The maximum number of alleles are that permitted in order for the add() method to return true
MAX_SAMPLES - Variable in class bref.AsIsBref3Writer
maxBackoffSteps() - Method in class phase.PbwtIbsData: Returns the number of backoff steps
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.BasicPhaseStates: Returns the maximum number of HMM states at a marker.
maxStates() - Method in class phase.HmmStateProbs: Returns the maximum number of HMM states.
maxStates() - Method in class phase.LowFreqPhaseStates: Returns the maximum number of HMM states at a marker.
meanSingleBaseGenDist(GeneticMap, Markers) - Static method in class vcf.MarkerMap: Returns the mean genetic distance between two consecutive base positions.
mega - Static variable in class blbutil.Const: The value 1,000,000
merge(ChromInterval, ChromInterval) - Static method in class beagleutil.ChromInterval: Returns the union of the specified overlapping chromosome intervals.
metaInfoLine(int) - Method in class vcf.VcfHeader: Returns the specified VCF meta-information line.
min(IntArray) - Static method in interface ints.IntArray: Returns the minimum element, or Integer.MAX_VALUE if this.size() == 0.
minutesAndSeconds() - Static method in class blbutil.Utilities: Returns the current minutes and seconds as a string.
missing() - Method in class phase.SamplePhase: Returns a list of marker indices in increasing order for which the genotype is missing.
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: "."
missingSamples() - Method in class vcf.VcfRecGTParser.HapListRep: Returns a list of samples with missing indices
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.
MultiThreadUtils - Class in blbutil: Class Utilities contains miscellaneous static utility methods for multi-threaded programming.

N

nAlleles() - Method in class vcf.BasicMarker
nAlleles() - Method in interface vcf.Marker: Returns the number of alleles for the marker, including the REF allele.
nAlleles() - Method in class vcf.VcfRecGTParser: Returns this.marker().nAlleles().
nBatches() - Method in class phase.PbwtIbsData: Returns the number of batches.
nCandidates() - Method in class phase.PbwtIbsData: Returns the number of candidate haplotypes
nClusters() - Method in class imp.ImpData: Return the number of target marker clusters.
nClusters() - Method in class phase.MarkerCluster: Returns the number of 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
ne() - Method in class phase.PhaseData: Returns the effective population size.
next() - Method in class blbutil.BlockLineReader: Returns true if the iteration has more elements, and returns false otherwise.
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.
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.
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
nextWindow() - Method in class vcf.RefTargSlidingWindow
nextWindow() - Method in interface vcf.SlidingWindow: Returns the next sliding window of VCF records.
nextWindow() - Method in class vcf.TargSlidingWindow
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.PbwtDivUpdater: Returns the number of haplotypes.
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.FixedPhaseData: Return the sum of the number of reference and target haplotypes.
nHaps() - Method in class phase.PbwtIbsData: Returns the total number of target and reference haplotypes.
nHaps() - Method in class phase.PbwtRecPhaser: Returns 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.RefGT
nHaps() - Method in class vcf.RestrictedGT
nHaps() - Method in class vcf.SplicedGT
nHaps() - Method in class vcf.XRefGT
nHeaderFields() - Method in class vcf.VcfHeader: Returns the number of fields in the VCF header line before sample exclusions.
nIbs2Segments(int) - Method in class phase.Ibs2: Returns the number of IBS2 segments for the specified target sample
nIds() - Method in class vcf.BasicMarker
nIds() - Method in interface vcf.Marker: Returns the number of marker identifiers.
nInputTargHaps() - Method in class imp.ImpData: Return the number of input target haplotypes.
nInputTargHaps() - Method in class imp.ImputedRecBuilder: Returns the number of input target haplotypes for haploid and diploid samples.
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.BasicPhaseStates: Returns the number of markers.
nMarkers() - Method in class phase.HmmStateProbs: Returns the number of markers
nMarkers() - Method in class phase.Ibs2: Returns the number of markers.
nMarkers() - Method in class phase.Ibs2Markers: Returns the number of markers.
nMarkers() - Method in class phase.LowFreqPhaseStates: Returns the number of markers.
nMarkers() - Method in class vcf.BasicGT
nMarkers() - Method in interface vcf.GT: Returns the number of markers.
nMarkers() - Method in class vcf.MarkerIndices: 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.XRefGT
nMetaInfoLines() - Method in class vcf.VcfHeader: Returns the number of VCF meta-information lines.
nMissingGTClusters() - Method in class phase.MarkerCluster: Returns the number of clusters containing at least one missing genotype.
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.
nonmajorAlleleCnt() - Method in class vcf.VcfRecGTParser.HapListRep: Returns the non-major allele count.
nonMajRefIndices() - Method in class vcf.VcfRecGTParser: Returns an array of length this.nAlleles() whose k-th element is the list of haplotype indices carrying the k-th allele if k is a non-major allele, and whose k-th element is null if k is the major allele.
noNThreads() - Method in class main.Par: Returns true if the command line does not include an nthreads parameter and returns false otherwise.
nOverlapSteps() - Method in class phase.PbwtIbsData: Returns the number of overlap steps
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 main.Pedigree: Returns the number of samples.
nSamples() - Method in class vcf.BasicGT
nSamples() - Method in interface vcf.GT: Returns the number of samples.
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.SplicedGT
nSamples() - Method in class vcf.VcfHeader: Returns the number of samples after sample exclusions.
nSamples() - Method in class vcf.VcfRecGTParser: Returns the number of samples.
nSamples() - Method in class vcf.XRefGT
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.
nTargHaps() - Method in class imp.ImpData: Return the number of target haplotypes.
nTargHaps() - Method in class phase.HmmStateProbs: Returns the number of target haplotypes.
nTargHaps() - Method in class phase.LowFreqPhaseStates: Returns the number of target haplotypes.
nTargHaps() - Method in class phase.PbwtIbsData: 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.
nTargMarkers() - Method in class vcf.MarkerIndices: Returns the number of target markers
nTargSamples() - Method in class imp.ImpData: Returns the number of target samples.
nTargSamples() - Method in class phase.BasicPhaseStates: Returns the number of target samples.
nTargSamples() - Method in class phase.HmmParamData: Returns the number of target samples.
nTargSamples() - Method in class phase.Ibs2: Returns the number of target samples.
nTargSamples() - Method in class phase.Ibs2Sets: Returns the number of target samples.
nTargSamples() - Method in class phase.PhaseBaum1: Returns the number of target samples.
nTargSamples() - Method in class phase.Stage2Baum: 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.
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 returns false otherwise.
overlapEnd() - Method in class vcf.MarkerIndices: Returns the end marker index (exclusive) of the overlap with the previous window.
overlapStart() - Method in class vcf.MarkerIndices: Returns the first marker index in the overlap between this marker window and the next marker window.

P

packedCreate(int[], int) - Static method in interface ints.IntArray: Returns a new IntArray instance that has the same sequence of integers as the specified array of non-negative integers.
packedCreate(IntList, int) - Static method in interface ints.IntArray: Returns a new IntArray instance that has the same sequence of integers as the specified list of non-negative integers.
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.
par() - Method in class imp.ImpData: Returns the command line parameters
par() - Method in class main.RunStats: Returns the analysis parameters.
par() - Method in class phase.FixedPhaseData: Return the analysis 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.
ParamEstimates - Class in phase: Class ParamEstimates estimates the allele mismatch probability and the recombination intensity for a haploid Li and Stephens hidden Markov model.
ParamEstimates() - Constructor for class phase.ParamEstimates: Constructs a new ParamEstimates instance for the specified data.
parse(String) - Static method in class beagleutil.ChromInterval: Returns a ChromInterval instance corresponding to the specified string, or returns null if the specified string does not represent a valid chromosome interval or if the specified string is null.
PbwtDivUpdater - Class in beagleutil: Class PbwtDivUpdater updates prefix and divergence arrays using the positional Burrows-Wheeler transform (PBWT).
PbwtDivUpdater(int) - Constructor for class beagleutil.PbwtDivUpdater: Constructs a new PbwtUpdater instance for the specified data.
PbwtIbsData - Class in phase: Class PbwtIbsData contains parameters and data for finding haplotypes that share an IBS segment with a target haplotype.
PbwtIbsData(PhaseData, CodedSteps) - Constructor for class phase.PbwtIbsData: Constructs a new PbwtIbsData instance from the specified data.
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, CodedSteps, boolean) - Constructor for class phase.PbwtPhaseIbs: Constructs a new PbwtPhaseIBS instance from the specified data.
PbwtPhaser - Class in phase: Class PbwtPhaser phases input genotype data and imputes missing alleles using the Positional Burrows-Wheeler Transform (PBWT)
PbwtRecPhaser - Class in phase: Class PbwtRecPhaser partially phases and imputes genotypes using the Positional Burrows-Wheeler transform.
PbwtRecPhaser(FixedPhaseData) - Constructor for class phase.PbwtRecPhaser: Creates a new PbwtPhaser for the specified data.
PbwtUpdater - Class in beagleutil: Class PbwtDivUpdater updates prefix 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.RefTargSlidingWindow
ped() - Method in interface vcf.SlidingWindow: Returns the target sample pedigree data.
ped() - Method in class vcf.TargSlidingWindow
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.PhaseBaum1: Estimates and stores the phased haplotypes for the specified sample
phase(int) - Method in class phase.Stage2Baum: Estimates and stores the phased haplotypes for the specified sample.
phase(int, int[], int, boolean[], boolean[]) - Method in class phase.PbwtRecPhaser: Copies input target and reference alleles for the marker nextMkr to the alleles array and partially phases and imputes the alleles.
phase_states() - Method in class main.Par: Returns the phase-states parameter.
PhaseBaum1 - Class in phase: Class PhaseBaum1 implements the forward and backward algorithms for a haploid Li and Stephens hidden Markov model.
PhaseBaum1(PbwtPhaseIbs) - Constructor for class phase.PhaseBaum1: Creates a PhaseLSBaum instance from the specified data.
phaseData() - Method in class phase.LowFreqPbwtPhaseIbs: Returns the current genotype phase estimates and parameter values.
phaseData() - Method in class phase.LowFreqPhaseIbs: Returns the input data for the next phase update.
phaseData() - Method in class phase.PbwtPhaseIbs: Returns the current genotype phase estimates and parameter values.
PhaseData - Class in phase: Class PhaseData stores the current genotype phase estimates and parameter values.
PhaseData(FixedPhaseData, long) - Constructor for class phase.PhaseData: Constructs a new PhaseData instance from the specified data.
phasedHaps() - Method in class phase.EstPhase: Returns the current estimated phased genotypes for the target samples.
phasedSep - Static variable in class blbutil.Const: The phased allele separator: '|'
PhaseLS - Class in phase: Class PhaseLS contains static methods for estimated genotypes phase using a haploid Li and Stephens hidden Markov model.
phaseNanos(long) - Method in class main.RunStats: Increases the cumulative phasing time by the specified number of nanoseconds.
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.
pMismatch() - Method in class phase.ParamEstimates: Returns the estimated allele mismatch rate.
pMismatch() - Method in class phase.PhaseData: Returns the allele mismatch probability.
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.MarkerCluster: Return a FloatArray of size this.nClusters() whose k-th element is the probability of transitioning to a random HMM state between the k-th cluster and the previous cluster.
pRecomb() - Method in class phase.PhaseData: Return a FloatArray of size this.fpd().stage1TargXGT().nMarkers() whose k-th element is the probability of transitioning to a random HMM state between the (k-1)-st and k-th markers.
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.
PREFIX - Static variable in class vcf.VcfMetaInfo: The VCF meta-information line prefix: "##"
prevSplice() - Method in class vcf.MarkerIndices: Returns the first marker index after the splice point with the previous marker window.
prevStage1Marker(int) - Method in class phase.FixedPhaseData: Returns the index of the closest stage1 marker (in the list of stage1 markers) with position less than or equal to the position of the specified marker, or 0 if no such stage1 marker exists.
prevStage1Wt(int) - Method in class phase.FixedPhaseData: Returns the linear interpolation weight associated with the preceding stage1 marker (see this.prevStage1Marker(marker)).
prevTargSplice() - Method in class vcf.MarkerIndices: Returns the first target marker index after the splice point with the previous marker window.
printEstimatedParameters(long, float) - Method in class main.RunStats: Prints the specified estimated effective population size.
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 between refStart (inclusive) and refEnd (exclusive) to the output VCF file: this.outPrefix() + ".vcf.gz".
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(Stage2Haps, int, int) - Method in class main.WindowWriter
printPhased(GT, int, int) - Method in class main.WindowWriter: Appends the data in phased genotypes for the specified markers to the output VCF file: this.outPrefix() + ".vcf.gz".
printRec(PrintWriter, boolean) - Method in class imp.ImputedRecBuilder: Prints the VCF record to the specified PrintWriter.
printSampleSummary(Pedigree, Window) - Method in class main.RunStats: Prints information about the samples to a log file and to standard output.
printStage1Info(PhaseData, long) - Method in class main.RunStats: Prints information about the specified iteration, and adds the specified elapsed nanoseconds to the total phasing time.
printStage2Info(long) - Method in class main.RunStats: Prints the specified elapsed nanoseconds for stage 2 phasing.
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(Window) - 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: The program name and commit version.
put(int, int) - Method in class ints.IntIntMap: Adds the specified key and value to this map.
putInBlockingQ(BlockingQueue<E>, E) - Static method in class blbutil.MultiThreadUtils: Inserts the specified element at the tail of the specified blocking queue, waiting for space to become available if the queue is full.
putInBlockingQ(BlockingQueue<E>, E, long, TimeUnit) - Static method in class blbutil.MultiThreadUtils: Inserts the specified element at the tail of the specified blocking queue, waiting up to the specified time for space to become available if the queue is full.

Q

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

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
recombIntensity() - Method in class phase.ParamEstimates: Returns the estimated recombination intensities.
recombIntensity() - Method in class phase.PhaseData: Returns the recombination intensity.
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 optional phased, nonmissing reference genotypes.
refGT() - Method in class vcf.Window: Returns the optional phased, nonmissing input genotypes for the reference samples in this window.
RefGT - Class in vcf: Class RefGT stores a list of samples and a haplotype pair for each sample.
RefGT(Markers, Samples, RefGTRec[]) - Constructor for class vcf.RefGT: Constructs a new RefGT 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.
refHaps() - Method in class phase.CodedSteps: Returns the reference haplotypes
RefIt - Class in vcf: Class RefIt represents an iterator whose next() method returns an object storing data from a VCF record with phased, non-missing genotypes.
RefTargSlidingWindow - Class in vcf: Class RefTargSlidingWindow represents a sliding window of reference and target VCF records.
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.BlockLineReader: The remove method is not supported by this iterator.
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.
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 blbutil.BitArray: Returns a new BitArray of size (from - to) that is a copy of the specified bit indices of this BitArray.
restrict(int, int) - Method in class vcf.BasicGT
restrict(int, int) - Method in interface vcf.GT: Returns a new GT instance restricted to genotype data for the specified markers.
restrict(int, int) - Method in class vcf.Markers: Returns a Markers instance that represents the specified range of marker indices.
restrict(int, int) - Method in class vcf.RefGT
restrict(int, int) - Method in class vcf.RestrictedGT
restrict(int, int) - Method in class vcf.SplicedGT
restrict(int, int) - Method in class vcf.XRefGT
restrict(IntArray) - Method in class vcf.MarkerMap: Return a marker map restricted to the specified markers
restrict(BasicGT, int[]) - Static method in class vcf.BasicGT: Returns a BasicGT instance restricted to genotype data for the specified markers.
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.RefGT
restrict(Markers, int[]) - Method in class vcf.RestrictedGT
restrict(Markers, int[]) - Method in class vcf.SplicedGT
restrict(Markers, int[]) - Method in class vcf.XRefGT
restrict(RefGT, int[]) - Static method in class vcf.RefGT: Returns a RefGT instance restricted to genotype data for the specified markers.
RestrictedGT - Class in vcf: Class RestrictedGT is a wrapper for a GT instance that restricts the data to a subset of the VCF records.
RestrictedGT(GT, Markers, int[]) - Constructor for class vcf.RestrictedGT: Constructs a new RestrictedGT 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.Window: Returns the optional phased, nonmissing input genotypes for the reference samples restricted to the target data markers in this window.
RevPbwtPhaser - Class in phase: Class RevPbwtPhaser phases input genotype data and imputes missing alleles using the Positional Burrows-Wheeler Transform (PBWT).
RevPbwtPhaser(FixedPhaseData, int, int, long) - Constructor for class phase.RevPbwtPhaser: Creates a new RevPbwtPhaser for the specified data.
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.HmmStateProbs: Stores the HMM reference haplotypes and states probabilities for the specified target haplotype, and returns the number of HMM states per marker.
runStage1(PhaseData) - Static method in class phase.PhaseLS: Updates genotype phase estimates 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.
sampleComp() - Static method in class phase.SampleSeg: Returns a comparator that orders first by this.sample(), then by this.start(), and finally by this.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 the excludeSamplesFile parameter is null
sampleIds() - Method in class vcf.VcfHeader: Returns this.sample().ids().
SampleIds - Class in beagleutil: Class SampleIds is a singleton class that represents a list of sample identifiers.
SamplePhase - Class in phase: Each instance of class SamplePhase stores an estimated haplotype pair for a sample, the list of markers with missing genotypes for the sample, a list of markers whose genotype phase with respect to the preceding heterozygote genotype is considered to be uncertain for the sample, and a set of marker clusters for the sample.
SamplePhase(Markers, DoubleArray, int[], int[], IntArray, IntArray) - Constructor for class phase.SamplePhase: Constructs a new SamplePhase instance from the specified data.
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.BasicGTRec
samples() - Method in class vcf.BitArrayGTRec
samples() - Method in class vcf.BitArrayRefGTRec
samples() - Method in interface vcf.GT: Returns the list of samples.
samples() - Method in interface vcf.GTRec: Returns the list of samples.
samples() - Method in class vcf.IntervalVcfIt
samples() - Method in class vcf.LowMafDiallelicGTRec
samples() - Method in class vcf.LowMafGTRec
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.HapListRep: Returns the samples.
samples() - Method in class vcf.VcfRecGTParser: Returns the list of samples.
samples() - Method in class vcf.XRefGT
Samples - Class in vcf: Class Samples stores a list of samples.
Samples(int[], boolean[]) - Constructor for class vcf.Samples: Constructs a new instance of Samples corresponding to the specified list of diploid sample identifier indices.
SampleSeg - Class in phase: Class SampleSeg represents a segment of genotype data in a sample.
SampleSeg(int, int, int) - Constructor for class phase.SampleSeg: Constructs a new SampleSeg instance from the specified data.
scaleFactor() - Method in class vcf.PositionMap: Returns the scale factor that is multiplied by the chromosome position to obtain the corresponding genetic map position
seed() - Method in class main.Par: Returns the seed parameter.
seed() - Method in class phase.PhaseData: Returns an iteration-dependent seed for generating pseudorandom numbers.
segList(int) - Method in class phase.Ibs2Sets: Returns the detected IBS2 sample segments.
semicolon - Static variable in class blbutil.Const: The semicolon character: ';'
SENTINAL - Static variable in class blbutil.BlockLineReader: The string array returned by next() after all blocks of lines have been read.
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-coded RefGTRec objects.
SeqCoder3(Samples) - Constructor for class bref.SeqCoder3: Constructs a new SeqCoder3 for the specified samples.
SeqCoder3(Samples, int) - Constructor for class bref.SeqCoder3: Constructs a new SeqCoder3 for the specified samples.
set(int) - Method in class blbutil.BitArray: Sets the specified bit.
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.
set(int, int) - Method in class ints.SynchedIntList: Replaces the element at the specified position in this list with the specified element.
set(int, SamplePhase) - Method in class phase.EstPhase: Sets the specified phased genotypes for the specified sample.
setAllele(int, int, BitArray) - Method in class vcf.Markers: Stores the specified alleles in the specified bitList
setAllele1(int, int) - Method in class phase.SamplePhase: Sets the allele on the first haplotype for the specified marker to the specified allele
setAllele2(int, int) - Method in class phase.SamplePhase: Sets the allele on the second haplotype for the specified marker to the specified allele
setAlleles(int, int[]) - Method in class imp.RefHapHash: Copies the alleles between this.start() (inclusive) and this.end() (exclusive) of the specified haplotype in the sublist of reference haplotypes to the specified array.
setPhasedGT(int, int, int, int) - Method in class phase.Stage2Haps: Sets the phased genotype if the specified marker was not phased in the first stage.
setUnphased(IntArray) - Method in class phase.SamplePhase: Sets the list of markers whose genotype phase with respect to the preceding non-missing heterozygote genotype is unknown.
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} elements from the array are the first ${code nElements} elements.
shuffle(int[], Random) - Static method in class blbutil.Utilities: Randomly shuffles the elements of the specified array.
shutdownExecService(ExecutorService) - Static method in class blbutil.MultiThreadUtils: Shuts down and awaits termination of the specified ExecutorService.
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.BitArray: Returns the number of bits in this BitArray.
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.PackedIntArray
size() - Method in class ints.SynchedIntList: Returns the number of elements in this list.
size() - Method in class ints.UnsignedByteArray
size() - Method in class ints.WrappedIntArray
size() - Method in class vcf.BasicGTRec
size() - Method in class vcf.BitArrayGTRec
size() - Method in class vcf.BitArrayRefGTRec
size() - Method in interface vcf.DuplicatesGTRec: Returns the number of haplotypes.
size() - Method in class vcf.LowMafDiallelicGTRec
size() - Method in class vcf.LowMafGTRec
size() - Method in class vcf.LowMafRefDiallelicGTRec
size() - Method in class vcf.LowMafRefGTRec
size() - Method in class vcf.Markers: Returns the number of markers.
size() - Method in class vcf.Samples: Returns the number of samples in this list.
size() - Method in class vcf.SeqCodedRefGTRec
size() - Method in class vcf.Steps: Returns the number of steps.
size() - Method in class vcf.VcfRec
SlidingWindow - Interface in vcf: Interface SlidingWindow represents a sliding window of VCF records.
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 one GT instance with phased genotypes from another GT instance.
SplicedGT(GT, GT) - Constructor for class vcf.SplicedGT: Constructs a new SplicedGL instance.
src() - Method in class vcf.VcfHeader: Returns the source from which data are read.
stage1Ibs2() - Method in class phase.FixedPhaseData: Returns the IBS2 data for the stage1 markers.
stage1Maf() - Method in class phase.FixedPhaseData: Returns a list whose j-th element is the estimated minor allele frequency of the j-th the stage1 marker.
stage1Map() - Method in class phase.FixedPhaseData: Returns the genetic map for the stage1 markers.
stage1Overlap() - Method in class phase.FixedPhaseData: Returns the number of stage1 markers that have phased target genotypes due to overlap with the previous window.
stage1RefGT() - Method in class phase.FixedPhaseData: Returns the optional phased, nonmissing reference genotypes for the stage1 markers.
stage1Steps() - Method in class phase.FixedPhaseData: Returns a partition of the stage1 markers into a sequence of sets of consecutive markers (the steps).
stage1TargGT() - Method in class phase.FixedPhaseData: Returns the input target genotypes at the stage1 markers.
stage1To2() - Method in class phase.FixedPhaseData: Returns a map from stage1 marker index to marker index
stage1XRefGT() - Method in class phase.FixedPhaseData: Returns the optional phased, nonmissing reference genotypes for the stage1 markers.
Stage2Baum - Class in phase: Class Stage2Baum 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.
Stage2Baum(LowFreqPhaseIbs, Stage2Haps) - Constructor for class phase.Stage2Baum: Creates a ImputeBaum instance from the specified data.
Stage2Haps - Class in phase: Class Stage2Haps stores phased genotypes.
Stage2Haps(PhaseData) - Constructor for class phase.Stage2Haps: Constructs a new Stage2Haps instance from the specified data.
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.FwdPbwtPhaser: Return the inclusive start marker index.
start() - Method in class phase.RevPbwtPhaser: Return the inclusive start marker index.
start() - Method in class phase.SampleSeg: Returns the start marker index (inclusive).
start(int) - Method in class vcf.Steps: Returns the index of the first marker in the specified step.
startMarker() - Method in class beagleutil.CompHapSegment: Returns the first marker in the haplotype segment
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_scale() - Method in class main.Par: Returns the step-scale parameter.
steps() - Method in class phase.CodedSteps: Returns the partition of the markers into non-overlapping intervals.
Steps - Class in vcf: Class Steps represents a partition of a list of markers into a sequence of sets of consecutive markers (the steps).
Steps(MarkerMap, float) - Constructor for class vcf.Steps: Constructs a new Steps instance from the specified data.
stepsPerBatch() - Method in class phase.PbwtIbsData: Returns the number of steps per batch
stepStart(int) - Method in class imp.CodedSteps: Returns the first marker index in the specified step.
stepStarts() - Method in class phase.Ibs2Markers: Returns the first marker index in each step in increasing order.
storeAlleles(int[], boolean[]) - Method in class vcf.VcfRecGTParser: Stores the genotypes and per-genotype phase data in the specified arrays and returns true if all genotypes are phased and non-missing.
storeAlleles(BitArray, BitArray) - Method in class vcf.VcfRecGTParser: Stores the genotypes genotypes in the specified BitLists.
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.
sumHapBits() - Method in class vcf.Markers: Returns this.sumHaplotypeBits(this.nMarkers()).
sumHapBits(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.
sumSwitchProbs() - Method in class phase.HmmParamData: Returns the sum of the probabilities of switching reference haplotypes between consecutive markers obtained from the generated data.
swapBits(BitArray, BitArray, int, int) - Static method in class blbutil.BitArray: Swaps the specified bits of the two specified Bitlist objects.
swapHaps(int, int) - Method in class phase.SamplePhase: Swaps the alleles of the two haplotypes in the specified range of markers.
SynchedIntList - Class in ints: Class SynchedIntList represents a list of integers.
SynchedIntList() - Constructor for class ints.SynchedIntList: Constructs an SynchedIntList object with the default initial capacity.
SynchedIntList(int) - Constructor for class ints.SynchedIntList: Constructs an SynchedIntList object with the specified initial capacity.
SynchedIntList(int[]) - Constructor for class ints.SynchedIntList: Constructs an SynchedIntList by cloning the specified array.
SynchedIntList(SynchedIntList) - Constructor for class ints.SynchedIntList: Constructs an SynchedIntList by copying the specified SynchedIntList.

T

tab - Static variable in class blbutil.Const: The tab character: '\t'
takeFromBlockingQ(BlockingQueue<E>) - Static method in class blbutil.MultiThreadUtils: Removes and returns the element at the head of the specified blocking queue, waiting if necessary for an element to become available.
takeFromQ(BlockingQueue<E>) - Static method in interface vcf.SlidingWindow: Takes and returns an element from the specified queue.
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.
targGT() - Method in class imp.ImpData: Return the phased target genotype data.
targGT() - Method in class phase.FixedPhaseData: Returns the input target genotypes.
targGT() - Method in class phase.FwdPbwtPhaser: Returns the input target genotypes.
targGT() - Method in class phase.PbwtRecPhaser: Returns the input target genotypes.
targGT() - Method in class phase.RevPbwtPhaser: Returns the input target genotypes.
targGT() - Method in class vcf.Window: Returns the input genotypes for the target samples in this window.
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 the k-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.
targOverlapEnd() - Method in class vcf.MarkerIndices: Returns the end marker index (exclusive) of the overlap with the previous window in the target data.
targOverlapStart() - Method in class vcf.MarkerIndices: Returns the first marker index of the overlap between this marker window and the next marker window in the target data.
targSamples() - Method in class imp.ImpData: Returns the list of target samples.
targSamples() - Method in class phase.CodedSteps: Returns the target samples.
targSamples() - Method in class vcf.RefTargSlidingWindow
targSamples() - Method in interface vcf.SlidingWindow: Returns the target samples.
targSamples() - Method in class vcf.TargSlidingWindow
TargSlidingWindow - Class in vcf: Class TargSlidingWindow represents a sliding window of target VCF records.
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 ThreadSafeIndexerinstance with the specified initial capacity.
timeStamp() - Static method in class blbutil.Utilities: Returns the current local time as a string.
TO_BASIC_GT_REC - Static variable in class vcf.VcfIt: A function mapping a string VCF record with GT format fields to a GTRec object.
TO_LOWMEM_GT_REC - Static variable in class vcf.VcfIt: A function mapping a string VCF record with GT format fields to a memory-efficient GTRec object.
TO_VCF_REC - Static variable in class vcf.VcfIt: A function mapping a string VCF record with GT or GL format fields to a VcfRecord object.
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() - Method in class ints.SynchedIntList: Returns an integer array containing the sequence of elements in this list.
toArray() - Method in class ints.WrappedIntArray: Returns the list of integers.
toArray(IntArray) - Static method in interface ints.IntArray: Returns a copy of the specified array.
toBasicGT(int, int) - Method in class phase.Stage2Haps: Returns a BasicGT instance containing phased genotypes for the specified markers.
toBitArrayRefGTRecs(EstPhase) - Static method in class vcf.BitArrayRefGTRec: Returns the current estimated phased, non-missing genotypes.
toBitArrayRefGTRecs(XRefGT, int) - Static method in class vcf.BitArrayRefGTRec: Returns the phased, non-missing genotypes as a BitArrayRefGTRec[] array.
toBitLists(int) - Method in class vcf.XRefGT: Returns the phased, non-missing genotypes as a BitArray[].
toBitLists(EstPhase) - Static method in class phase.SamplePhase: Returns the current estimated phased genotypes.
toGTRecs() - Method in class phase.EstPhase: Returns the current estimated phased genotypes for the target samples.
toGTRecs(int, int) - Method in class phase.Stage2Haps: Returns a GTRec[] instance containing phased genotypes for the specified markers.
toLongArray() - Method in class blbutil.BitArray: Returns this BitArray as a long array.
toString() - Method in class beagleutil.ChromIds: Returns java.util.Arrays.toString(this.ids()).
toString() - Method in class beagleutil.ChromInterval: Returns a string describing this.
toString() - Method in class beagleutil.SampleIds: Returns java.util.Arrays.toString(this.ids()).
toString() - Method in class beagleutil.ThreadSafeIndexer: Returns this.items().toString().
toString() - Method in class blbutil.BitArray: Returns a string representation of this BitArray.
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 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.SynchedIntList: 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.BasicGT: Returns a string representation of this.
toString() - Method in class vcf.BasicGTRec: Returns the data represented by this as a VCF record with a GT format field.
toString() - Method in class vcf.BasicMarker
toString() - Method in class vcf.BitArrayGTRec: Returns the data represented by this as a VCF record with a GT format field.
toString() - Method in class vcf.BitArrayRefGTRec: 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.LowMafDiallelicGTRec: Returns the data represented by this as a VCF record with a GT format field.
toString() - Method in class vcf.LowMafGTRec: Returns the data represented by this as a VCF record with a GT format field.
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.RefTargSlidingWindow: Returns a string representation of this.
toString() - Method in class vcf.RestrictedGT
toString() - Method in class vcf.RestrictedVcfWindow: Returns a string representation of this.
toString() - Method in class vcf.Samples: Returns java.util.Arrays.toString(this.ids()).
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.TargSlidingWindow: Returns a string representation of this.
toString() - Method in class vcf.VcfHeader: Returns the VCF meta-information lines and the VCF header line after applying sample exclusions.
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.XRefGT
toVcfRec(GTRec) - Static method in interface vcf.GTRec: Returns a VCF record corresponding to the specified GTRec 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 original list of samples before sample exclusions.
unphased() - Method in class phase.SamplePhase: Returns a list of marker indices in increasing order whose genotype phase with respect to the preceding non-missing heterozygote genotype is unknown.
unphasedSep - Static variable in class blbutil.Const: The unphased allele separator: '/'
unphClusters() - Method in class phase.MarkerCluster: Returns a sorted list of cluster indices in increasing order for which the cluster contains an unphased heterozygote.
UnsignedByteArray - Class in ints: Class UnsignedByteIndexArray represents an immutable array of integer values between 0 and 255 inclusive that is stored as a byte[] 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.
UnsignedByteArray(ByteArrayOutputStream) - Constructor for class ints.UnsignedByteArray: Constructs a new UnsignedByteArray instance from the specified data.
update(int) - Method in class phase.HmmParamData: Uses the specified sample to generate data for estimating the allele mismatch and recombination intensity HMM parameters.
update(int[], int, int[]) - Method in class beagleutil.PbwtUpdater: Update the specified prefix and divergence arrays using the forward Positional Burrows-Wheeler Transform.
update(IntArray, int, int[]) - Method in class beagleutil.PbwtUpdater: Update the specified prefix and divergence arrays using the forward Positional Burrows-Wheeler Transform.
updatePMismatch(float) - Method in class phase.PhaseData: Sets the allele mismatch probability to the specified value.
updateRecombIntensity(float) - Method in class phase.PhaseData: Updates the recombination intensity.
updateSegment(int, int, int) - Method in class beagleutil.CompHapSegment: Update the haplotype, the first marker in the haplotype segment, and the last recorded IBS ibsStep.
updateStep(int) - Method in class beagleutil.CompHapSegment: Updates the last recorded IBS ibsStep 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.
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(String, String[], boolean[]) - Constructor for class vcf.VcfHeader: Returns a VCF header object for the specified VCF meta information lines and header line.
VcfHeader(String, String[], boolean[], Filter<String>) - Constructor for class vcf.VcfHeader: Returns a VCF header object for the specified VCF meta information lines and header line.
VcfIt<E extends GTRec> - Class in vcf: Class VcfIt represents an iterator whose next() method returns an object storing data from a VCF record.
VcfMetaInfo - Class in vcf: Class VcfMetaInfo represents a VCF meta-information line.
VcfMetaInfo(String) - Constructor for class vcf.VcfMetaInfo: Constructs a VcfMetaInfo instance representing the specified VCF meta-information line.
VcfRec - Class in vcf: Class VcfRec 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.
VcfRecGTParser.HapListRep - Class in vcf
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.

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 - Class in vcf: Interface Window1 represents a sliding window of target VCF records or a sliding window of reference and target VCF records.
Window(GeneticMap, int, boolean, MarkerIndices, RefGT, BasicGT) - Constructor for class vcf.Window: Constructs a new Window1 instance from the specified data.
windowIndex() - Method in class vcf.Window: Returns the index of this window.
WindowWriter - Class in main: Class WindowWriter writes VCF and IBD output data.
WindowWriter(Par, Samples) - Constructor for class main.WindowWriter: Constructs a new WindowWriter object.
WrappedIntArray - Class in ints: Class WrappedIntArray represents an immutable int[] 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.
WrappedIntArray(IntStream) - Constructor for class ints.WrappedIntArray: Constructs an WrappedIntrray object with the specified values.
write(byte[]) - Method in class blbutil.BGZIPOutputStream
write(byte[], int, int) - Method in class blbutil.BGZIPOutputStream
write(int) - Method in class blbutil.BGZIPOutputStream
write(OutputStream) - Method in class ints.UnsignedByteArray: Write this byte array to the specified output stream.
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
writeEmptyBlock(OutputStream) - Static method in class blbutil.BGZIPOutputStream: Write an empty BGZIP block to the specified output stream.
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

XRefGT - Class in vcf: Class XRefGT represents phased, non-missing genotypes for a list of samples that are stored in column-major (i.e.

Z

ZERO_FREQ_ARRAY - Static variable in class vcf.Window: An array that replaces an array of allele counts for a monomorphic marker.

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