Index

A B C D E F G H I K L M N O P Q R S T U V W X
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(double, double) - Method in class math.Regress: Records the specified values of the dependent and independent variables.
add(float) - Method in class blbutil.FloatList: Adds the specified integer to the end of this list.
add(int) - Method in class ints.IntList: Adds the specified integer to the end of this list.
add(int) - Method in class ints.IntSet: Adds the specified element to this set.
add(int, double[]) - Method in interface main.GenotypeValues: Adds the specified genotype values to the stored genotype values for the specified sample.
add(int, int, int, double) - Method in interface main.GenotypeValues: Adds the specified genotype value to the stored genotype value.
add(RefGTRec) - Method in class bref.SeqCoder3: Attempts to add the specified RefGTRec object to the list of compressed RefGTRec objects, and returns true if the RefGTRec object was added.
addRecords(List<E>, int, int) - Method in class vcf.Window: Adds the specified records to he specified list.
addRestrictedRefHapPairs(List<BitHapPair>) - Method in class main.CurrentData: Returns a list with the specified haplotypes following by the reference haplotype pairs that are restricted to the target data markers.
addSampleData(double[]) - Method in class vcf.R2Estimator: Adds the specified allele dose probabilities for a genotype to the stored allele dose data.
addSampleData(double[]) - Method in class vcf.VcfRecBuilder: Adds the FORMAT field for a sample to the VCF record for the current marker.
addSampleData(double[], double[]) - Method in class vcf.VcfRecBuilder: Adds the FORMAT field for a sample to the VCF record for the current marker.
addSampleData(float[], float[]) - Method in class imp.ImputedRecBuilder: Scales the specified probabilities for each allele to each sum to 1.0, and adds the sample data to the VCF record.
addToElement(int, float) - Method in class blbutil.FloatList: Adds the specified value to the specified element.
advanceWindow(Markers) - Method in class vcf.RestrictedVcfWindow: Advances the sliding marker window, and returns the advanced window as a GTRec[] object.
advanceWindowCm() - Method in class vcf.AllData
advanceWindowCm() - Method in interface vcf.Data: Advances the sliding window of VCF records.
advanceWindowCm() - Method in class vcf.TargetData
allData(Supplier<SampleFileIt<RefGTRec>>, SampleFileIt<GTRec>, Par) - Static method in class vcf.AllData: Constructs and returns a new AllData instance from VCF recList returned by the specified SampleFileIt objects.
AllData - Class in vcf: Class AllData represents a sliding window of reference and target VCF recList.
allele(int) - Method in class vcf.BasicMarker
allele(int) - Method in interface vcf.Marker: Returns the specified allele.
allele(int, int) - Method in class haplotype.HapPairPhasedGT
allele(int, int) - Method in class imp.ImpData: Returns the specified target marker cluter alleles for the reference and target haplotypes.
allele(int, int) - Method in class phase.EstPhase.HapsGT
allele(int, int) - Method in class phase.PhaseData
allele(int, int) - Method in class vcf.BasicGT
allele(int, int) - Method in class vcf.BasicRefGT
allele(int, int) - Method in interface vcf.GT: Returns the allele on the specified haplotype for the specified marker or return -1 if the allele is missing.
allele(int, int) - Method in class vcf.SplicedGT
allele(int, int) - Method in class vcf.XBasicGT
ALLELE_CODED - Static variable in class bref.AsIsBref3Writer: The byte value denoting an allele coded record
allele1(int) - Method in class haplotype.BitHapPair
allele1(int) - Method in interface haplotype.HapPair: Returns the first allele for the specified marker.
allele1(int) - Method in class haplotype.WrappedHapPair
allele1(int) - Method in class vcf.BitSetGT
allele1(int) - Method in interface vcf.DuplicatesGTRec: Returns the first allele for the specified sample or -1 if the allele is missing.
allele1(int) - Method in class vcf.LowMafRefDiallelicGT
allele1(int) - Method in class vcf.LowMafRefGT
allele1(int) - Method in class vcf.SeqCodedRefGT
allele1(int) - Method in class vcf.VcfRecord
allele1(int) - Method in class vcf.XBasicGT1
allele1(int) - Method in interface vcf.XGT1: Returns the first allele for the specified marker if the observed data include a non-missing allele, and returns -1 otherwise.
allele1(int, int) - Method in class haplotype.HapPairPhasedGT
allele1(int, int) - Method in class phase.EstPhase.HapsGT
allele1(int, int) - Method in class vcf.BasicGT
allele1(int, int) - Method in class vcf.BasicRefGT
allele1(int, int) - Method in interface vcf.GT: Returns the first allele for the specified marker and sample or return -1 if the allele is missing.
allele1(int, int) - Method in class vcf.SplicedGT
allele1(int, int) - Method in class vcf.XBasicGT
allele2(int) - Method in class haplotype.BitHapPair
allele2(int) - Method in interface haplotype.HapPair: Returns the second allele for the specified marker.
allele2(int) - Method in class haplotype.WrappedHapPair
allele2(int) - Method in class vcf.BitSetGT
allele2(int) - Method in interface vcf.DuplicatesGTRec: Returns the second allele for the specified sample or -1 if the allele is missing.
allele2(int) - Method in class vcf.LowMafRefDiallelicGT
allele2(int) - Method in class vcf.LowMafRefGT
allele2(int) - Method in class vcf.SeqCodedRefGT
allele2(int) - Method in class vcf.VcfRecord
allele2(int) - Method in class vcf.XBasicGT1
allele2(int) - Method in interface vcf.XGT1: Returns the second allele for the specified marker if the observed data include a non-missing allele, and returns -1 otherwise.
allele2(int, int) - Method in class haplotype.HapPairPhasedGT
allele2(int, int) - Method in class phase.EstPhase.HapsGT
allele2(int, int) - Method in class vcf.BasicGT
allele2(int, int) - Method in class vcf.BasicRefGT
allele2(int, int) - Method in interface vcf.GT: Returns the second allele for the specified marker and sample or return -1 if the allele is missing.
allele2(int, int) - Method in class vcf.SplicedGT
allele2(int, int) - Method in class vcf.XBasicGT
alleleCodedInstance(Marker, Samples, int[][]) - Static method in interface vcf.RefGTRec: Constructs and returns a new allele-coded RefGTRec instance from the specified data.
alleleCodedInstance(RefGTRec) - Static method in interface vcf.RefGTRec: Returns an allele-coded RefGTRec instance for the specified data.
alleleCodedInstance(VcfRecGTParser) - Static method in interface vcf.RefGTRec: Constructs and returns a new allele-coded RefGTRec instance from the specified data.
alleleCount(int) - Method in class vcf.LowMafRefDiallelicGT
alleleCount(int) - Method in class vcf.LowMafRefGT
alleleCount(int) - Method in interface vcf.RefGTRec: Returns the number of haplotypes that carry the specified allele.
alleleCount(int) - Method in class vcf.SeqCodedRefGT
alleles() - Method in class vcf.BasicMarker
alleles() - Method in class vcf.BitSetGT
alleles() - Method in interface vcf.DuplicatesGTRec: Returns an array of length this.size() whose j-th element is equal to this.allele(j}
alleles() - Method in class vcf.LowMafRefDiallelicGT
alleles() - Method in class vcf.LowMafRefGT
alleles() - Method in interface vcf.Marker: Returns the alleles.
alleles() - Method in class vcf.SeqCodedRefGT
alleles() - Method in class vcf.VcfRecord
allelesToBits(int[]) - Method in class vcf.Markers: Returns a bit array storing the specified haplotype.
allelicR2() - Method in class vcf.R2Estimator: Returns the estimated squared correlation between the most probable ALT allele dose and the true ALT allele dose for the current genotype data.
allSamples() - Method in class main.CurrentData: Returns a list of all target and reference samples.
allSamples() - Method in class vcf.AllData
allSamples() - Method in interface vcf.Data: Returns a list of all target and reference samples.
allSamples() - Method in class vcf.TargetData
ap() - Method in class main.Par: Returns the ap parameter.
appendRecords(AtomicReferenceArray<StateProbs>, PrintWriter) - Method in class imp.ImputedVcfWriter: Writes the VCF records to the specified PrintWriter.
appendRecords(GenotypeValues, int, int, PrintWriter) - Static method in class vcf.VcfWriter: Writes the specified genotype data as VCF records to the specified PrintWriter.
appendRecords(GT, int, int, boolean, boolean, PrintWriter) - Static method in class vcf.VcfWriter: Writes the data in phased genotypes for the specified markers to the specified PrintWriter.
args() - Method in class main.Par: Returns the command line arguments.
argsToMap(String[], char) - Static method in class blbutil.Validate: Returns a map with one (key, value) pair for each element of the specified array.
AsIsBref3Writer - Class in bref: Class AsIsBref3Writer writes VCF data with phased, non-missing genotypes to a binary reference format v3 (bref) file.
AsIsBref3Writer(String, Samples, File) - Constructor for class bref.AsIsBref3Writer: Constructs a new AsIsBref4Writer for the specified data.
asString(IntArray) - Static method in interface ints.IntArray: Returns a string representation of this IntArray by applying java.utils.Arrays.toString() to an equivalent int[] object.
asString(LongArray) - Static method in class ints.LongArray: Returns a string representation of this LongArray by applying java.utils.Arrays.toString() to an equivalent int[] object.

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.MarkerMap
basePos(int, double) - Method in class vcf.PlinkGenMap
basePos(int, double) - Method in class vcf.PositionMap
BasicGT - Class in vcf: Class BasicGT represents genotype emission probabilities for a set of samples.
BasicGT(Samples, GTRec[]) - Constructor for class vcf.BasicGT: Constructs a BasicGT instance.
BasicMarker - Class in vcf: Class BasicMarker represents a genetic marker.
BasicMarker(int, int, String[], String[]) - Constructor for class vcf.BasicMarker: Constructs a new BasicMarker instance from the specified data.
BasicMarker(int, int, String[], String[], int) - Constructor for class vcf.BasicMarker: Constructs a new BasicMarker instance from the specified data.
BasicMarker(String) - Constructor for class vcf.BasicMarker: Constructs a new BasicMarker instance from the specified string VCF record prefix.
BasicRefGT - Class in vcf: Class BasicRefGT stores a list of samples and a haplotype pair for each sample.
BasicRefGT(Markers, Samples, RefGTRec[]) - Constructor for class vcf.BasicRefGT: Constructs a new RefHapPairs instance.
BasicRefGT(RefGTRec[]) - Constructor for class vcf.BasicRefGT: Constructs a new RefHapPairs instance.
beagleutil - package beagleutil
beta() - Method in class math.Regress: Returns the regression coefficient for the recorded values of the independent and dependent variables.
BGZIPOutputStream - Class in blbutil: Class BGZIPOutputStream is an output stream filter that performs BGZIP compression.
BGZIPOutputStream(OutputStream, boolean) - Constructor for class blbutil.BGZIPOutputStream: Creates a new BGZIPOutputStream instance that writes to the specified output stream.
bgzipPrintWriter(File) - Static method in class blbutil.FileUtil: Returns a buffered java.io.PrintWriter that compresses data using the BGZIP algorithm and writes the compressed data to the specified file.
bgzipPrintWriter(File, boolean) - Static method in class blbutil.FileUtil: Returns a buffered java.io.PrintWriter that compresses data using the BGZIP algorithm and writes the compressed data to the specified file.
binarySearch(int) - Method in class ints.IntList: Returns an index associated with the specified value, or (-insertionPoint - 1) if the value is not found.
BitHapPair - Class in haplotype: Class BitHapPair represents a pair of haplotypes for a sample.
BitHapPair(Markers, int, int[], int[]) - Constructor for class haplotype.BitHapPair: Constructs a new BitHapPair instance.
BitSetGT - Class in vcf: Class BitSetGT represents genotype emission probabilities for a list of samples at a single marker.
BitSetGT(VcfHeader, String) - Constructor for class vcf.BitSetGT: Constructs a new BitSetGT instance representing the specified VCF record's GT format field data.
bitsToAllele(LongArray, int) - Method in class vcf.Markers: Returns the specified allele stored in the specified hapBits array.
blbutil - package blbutil
booleanArg(String, Map<String, String>, boolean, boolean) - Static method in class blbutil.Validate: Removes the specified key from the specified map, and returns the boolean value corresponding to the specified key.
bref - package bref
Bref3 - Class in bref: Class Bref3 converts files in VCF format into bref version 3 format.
Bref3() - Constructor for class bref.Bref3
Bref3It - Class in bref: Class Bref3It represents an iterator whose next() which returns records from a bref version 3 file.
Bref3It(File) - Constructor for class bref.Bref3It: Constructs a new Bref3It instance.
Bref3It(File, Filter<Marker>) - Constructor for class bref.Bref3It: Constructs a new Bref4It instance.
Bref3Reader - Class in bref: Class Bref3Reader contains methods for reading a bref 3 (binary reference format) file.
Bref3Reader(DataInput, Filter<Marker>) - Constructor for class bref.Bref3Reader: Constructs a new Bref3Reader instance.
BrefBlock - Class in bref: Class BrefBlock represents starting chromosome coordinates and file offset for the start of a binary reference format (bref) data block.
BrefBlock(int, int, long) - Constructor for class bref.BrefBlock: Constructs a BrefBlock for the specified data.
BrefWriter - Interface in bref: Interface BrefWrites writes phased, non-missing genotypes to a binary reference format (bref) file.
bufferedInputStream(File) - Static method in class blbutil.FileUtil: Returns an buffered java.io.InputStream with default buffer size reading from the specified file.
bufferedOutputStream(File) - Static method in class blbutil.FileUtil: Returns an buffered java.io.OutputStream with default buffer size writing to the specified file.
bufferedOutputStream(File, boolean) - Static method in class blbutil.FileUtil: Returns an buffered java.io.OutputStream with default buffer size writing to the specified file.
buildNanos(long) - Method in class main.RunStats: Increases the cumulative time to build the DAG models by the specified number of nanoseconds.
burnin() - Method in class main.Par: Returns the burnin parameter.
burnin() - Method in class phase.PhaseData: Returns true if the current phasing iteration is a burnin iteration and returns false otherwise.

C

canAdvanceWindow() - Method in class vcf.AllData
canAdvanceWindow() - Method in interface vcf.Data: Returns true if the sliding window of VCF records can advance and returns false otherwise.
canAdvanceWindow() - Method in class vcf.TargetData
capacity() - Method in class ints.IntSet: Returns the capacity of this set.
cd() - Method in class imp.ImpData: Returns the current data.
CharArray - Class in ints: /**
CharArray(byte[]) - Constructor for class ints.CharArray: Constructs a new CharArray instance from the specified data.
CharArray(char[]) - Constructor for class ints.CharArray: Constructs a new CharArray instance from the specified data.
CharArray(int[]) - Constructor for class ints.CharArray: Constructs a new CharArray instance from the specified data.
CharArray(int[], int) - Constructor for class ints.CharArray: Constructs a new CharArray instance from the specified data.
CharArray(int[], int, int) - Constructor for class ints.CharArray: Constructs a new CharArray instance from the specified data.
CharArray(IntList) - Constructor for class ints.CharArray: Constructs a new UnsignedByteArray instance from the specified data.
CharArray(IntList, int) - Constructor for class ints.CharArray: Constructs a new CharArray instance from the specified data.
CharArray(IntList, int, int) - Constructor for class ints.CharArray: Constructs a new CharArray instance from the specified data.
chrom() - Method in class beagleutil.ChromInterval: Returns the chromosome identifier.
chrom() - Method in class vcf.BasicMarker
chrom() - Method in interface vcf.Marker: Returns the chromosome.
chrom() - Method in class vcf.MarkerMap: Returns the chromosome corresponding to the list of markers.
ChromIds - Class in beagleutil: Class ChromIds is a singleton class that represents a list of chromosome identifiers.
chromIndex() - Method in class beagleutil.ChromInterval: Returns the chromosome index.
chromIndex() - Method in class bref.BrefBlock: Returns the chromosome index of the first marker in this bref block.
chromIndex() - Method in class vcf.BasicMarker
chromIndex() - Method in interface vcf.Marker: Returns the chromosome index.
chromIndex() - Method in class vcf.MarkerMap: Returns the index of the chromosome corresponding to the list of markers.
chromIndex() - Method in class vcf.Window: Returns the chromosome index of the first maker in the window.
chromInt() - Method in class main.Par: Returns the chromosome interval or null if no chrom parameter was specified.
ChromInterval - Class in beagleutil: Class ChromInterval represents a chromosome interval whose end points are genome coordinates.
ChromInterval(String, int, int) - Constructor for class beagleutil.ChromInterval: Constructs a new ChromInterval instance.
ChromInterval(Marker, Marker) - Constructor for class beagleutil.ChromInterval: Constructs a new ChromInterval instance.
clear() - Method in class blbutil.FloatList: Removes all elements from this list.
clear() - Method in class ints.IntList: Removes all elements from this list.
clear() - Method in class ints.IntMap: Removes all keys from this map.
clear() - Method in class ints.IntSet: Removes all elements from this set.
clear() - Method in class vcf.R2Estimator: Clears all genotype data and sets the number of genotype with allele dose data to 0.
close() - Method in class blbutil.BGZIPOutputStream
close() - Method in interface blbutil.FileIt: Terminates the iteration and releases any system resources that are held by this object.
close() - Method in class blbutil.InputIt
close() - Method in class bref.AsIsBref3Writer
close() - Method in class bref.Bref3It
close() - Method in interface bref.BrefWriter: Flushes any buffered output and releases any system resources that are held by this BrefWriter.
close() - Method in class bref.CompressBref3Writer
close() - Method in class main.WindowWriter
close() - Method in class vcf.AllData
close() - Method in interface vcf.Data: Releases any I/O resources controlled by this object.
close() - Method in class vcf.IntervalVcfIt
close() - Method in class vcf.RefIt
close() - Method in class vcf.RestrictedVcfWindow: Releases any I/O resources controlled by this object.
close() - Method in class vcf.TargetData
close() - Method in class vcf.VcfIt
close() - Method in class vcf.WindowIt: Releases any I/O resources controlled by this object.
closestIndex(int, int) - Method in class vcf.PlinkGenMap: Returns the index of the genetic map position that is closest to the specified base position.
cluster() - Method in class main.Par: Returns the cluster parameter.
cnt() - Method in class math.Regress: Returns the number of recorded values of the independent variable.
colon - Static variable in class blbutil.Const: The colon character: ':'
comma - Static variable in class blbutil.Const: The comma character: ','
COMMAND - Static variable in class main.Main
commandLine(String, String[]) - Static method in class blbutil.Utilities: Returns a string representation of the command line arguments.
comparator(Samples) - Static method in interface haplotype.HapPair: Returns a Comparator<HapPairInterface> whose compare(hp1, hp2) method returns -1, 0, or 1 depending on whether samples.index(hp1.idIndex()) is less than, equal, or greater than samples.index(hp2.idIndex()).
compareTo(ChromInterval) - Method in class beagleutil.ChromInterval: Compares this ChromInteval with the specified ChromInterval instance for order, and returns -1, 0, or 1 depending on whether this is less than, equal or greater than the specified instance.
compareTo(Marker) - Method in class vcf.BasicMarker
compareTo(Marker) - Method in interface vcf.Marker: Compares this marker with the specified marker for order, and returns a negative integer, 0, or a positive integer depending on whether this marker is less than, equal to, or greater than the specified marker.
COMPRESS_FREQ_THRESHOLD - Static variable in class bref.SeqCoder3: The major allele frequency threshold for allele coding.
CompressBref3Writer - Class in bref: Class CompressBref3Writer writes phased, non-missing genotypes to a binary reference format v3 (bref) file.
CompressBref3Writer(String, Samples, int, File) - Constructor for class bref.CompressBref3Writer: Constructs a new CompressBref3fWriter for the specified data.
confirmEmptyMap(Map<String, String>) - Static method in class blbutil.Validate: Checks whether the specified map of key-value pairs is empty.
Const - Class in blbutil: Class Const provides public static final fields with string and character constants.
contains(int) - Method in class ints.IntMap: Returns true if the map contains the specified key, and returns false otherwise.
contains(int) - Method in class ints.IntSet: Returns true if the set contains the specified element, and returns false otherwise.
contains(Marker) - Method in class beagleutil.ChromInterval: Returns true if the specified marker is in this chromosome interval and returns false otherwise.
contains(Marker) - Method in class vcf.Markers: Returns true if the specified marker is not null and is an element in the list of markers represented by this, and returns false otherwise.
copyOf(int) - Method in class ints.IntList: Copies and returns this list of integers, truncating or padding with 0 as necessary so that the copy has the specified length.
COPYRIGHT - Static variable in class main.Main: The copyright string.
countFields(String) - Static method in class blbutil.StringUtil: Returns the number of white-space delimited fields in the specified string.
countFields(String, char) - Static method in class blbutil.StringUtil: Returns the number of delimited fields in the specified string.
countFields(String, char, int) - Static method in class blbutil.StringUtil: Returns Math.min(countFields(s, delimiter), max).
create(int[], int) - Static method in interface ints.IntArray: Returns a new IntArray instance that has the same sequence of integers as the specified array.
create(FileIt<String>) - Static method in class vcf.RefIt: Create and returns a new RefIt instance from the specified iterator.
create(FileIt<String>, Filter<String>, Filter<Marker>, int) - Static method in class vcf.RefIt: Create and returns a new RefIt instance from the specified objects.
create(FileIt<String>, Filter<String>, Filter<Marker>, BiFunction<VcfHeader, String, R>) - Static method in class vcf.VcfIt: Create and returns a new VcfIt instance from the specified objects.
create(FileIt<String>, Filter<String>, Filter<Marker>, BiFunction<VcfHeader, String, R>, int) - Static method in class vcf.VcfIt: Create and returns a new VcfIt instance from the specified objects.
create(FileIt<String>, Filter<String>, BiFunction<VcfHeader, String, R>) - Static method in class vcf.VcfIt: Create and returns a new VcfIt instance from the specified objects.
create(FileIt<String>, BiFunction<VcfHeader, String, R>) - Static method in class vcf.VcfIt: Create and returns a new VcfIt instance from the specified objects.
create(IntList, int) - Static method in interface ints.IntArray: Returns a new IntArray instance that has the same sequence of integers as the specified list.
create(GeneticMap, Markers) - Static method in class vcf.MarkerMap: Returns a new MarkerMap instance that is constructed from the specified data
create(Marker[]) - Static method in class vcf.Markers: Returns a new Markers instance that is constructed from the specified data.
cumMarkerCnt() - Method in class vcf.RestrictedVcfWindow: Returns the number of VCF records in the union of the current window and all previous windows.
CurrentData - Class in main: Class CurrentData represents input data for the current marker window.
CurrentData(Par, GeneticMap, Data, GT) - Constructor for class main.CurrentData: Constructs a new CurrentData instance from the specified data.

D

Data - Interface in vcf: Interface Data represents a sliding window of target VCF records or a sliding window of reference and target VCF records.
decEndComp() - Static method in interface beagleutil.IntInterval: Returns a Comparator<IntInterval> which orders IntInterval objects in order of increasing this.start() value and orders IntInterval objects with the same this.start() value in order of decreasing this.end() value.
decrementAndGet(int) - Method in class ints.IntList: Decrements by one the element at the specified position in this list.
DEFAULT_BUFFER_SIZE - Static variable in class blbutil.InputIt: The default buffer size, which is 4,194,304 bytes.
DEFAULT_INIT_CAPACITY - Static variable in class beagleutil.ThreadSafeIndexer: The default initial capacity, which is 500.
DEFAULT_INIT_CAPACITY - Static variable in class blbutil.FloatList: The default initial capacity of an FloatList, which is 10.
DEFAULT_INIT_CAPACITY - Static variable in class ints.IntList: The default initial capacity of an IntList, which is 16.
DEFAULT_INIT_SIZE - Static variable in class vcf.VcfRecBuilder: The default initial size for the string buffer, which is 50 characters.
defaultMaxNSeq(int) - Static method in class bref.SeqCoder3: Returns the default maximum number of sequences for the specified number of samples.
DELIMITER - Static variable in class vcf.VcfMetaInfo: The VCF meta-information line key-value delimiter: '='
doseR2() - Method in class vcf.R2Estimator: Returns the estimated squared correlation between the expected ALT allele dose and the true ALT allele dose for the current genotype data.
doubleArg(String, Map<String, String>, boolean, double, double, double) - Static method in class blbutil.Validate: Removes the specified key from the specified map, and returns the double value corresponding to the specified key.
duoOffspring(int) - Method in class main.Pedigree: Returns the sample index of the offspring of the specified parent-offspring duo.
duoParent(int) - Method in class main.Pedigree: Returns the sample index of the parent of the specified parent-offspring duo.
duoPrint(PrintWriter, CharSequence) - Static method in class blbutil.Utilities: Prints the specified string to the specified PrintWriter and to standard out.
duoPrintln(PrintWriter, CharSequence) - Static method in class blbutil.Utilities: Prints the specified string to the specified PrintWriter and to standard out.
duoPrintNanos(String, long) - Method in class main.RunStats: Print the specified message followed by the human elapsed time as formatted by blbutil.Utilities.elapsedNanos(nanos)
DuplicatesGTRec - Interface in vcf: Interface DuplicatesGTRec represents marker alleles for a list of samples.

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".
elementWithIndex(int) - Method in class ints.IntSet: Returns the specified element.
end() - Method in class beagleutil.ChromInterval: Returns the last genome coordinate in this chromosome interval.
end() - Method in interface beagleutil.IntInterval: Returns the end of the interval (inclusive).
end() - Method in class imp.RefHapHash: Returns the ending reference marker index (exclusive) for the reference haplotype allele sequences.
end() - Method in class vcf.BasicMarker
end() - Method in interface vcf.Marker: Returns the INFO END field, or -1 if there is no INFO END field.
END_OF_DATA - Static variable in class bref.AsIsBref3Writer: The end of file code for a bref file.
END_OF_INDEX - Static variable in class bref.AsIsBref3Writer: The integer denoting denoting the end of the index in a bref file
equals(IntArray, IntArray) - Static method in interface ints.IntArray: Returns true if the specified IntArray objects represent the same sequence of integer values, and returns false otherwise.
equals(LongArray, LongArray) - Static method in class ints.LongArray: Returns true if the specified LongArray objects represent the same sequence of long values, and returns false otherwise.
equals(Object) - Method in class beagleutil.ChromInterval: Returns true if the specified object is a ChromInterval instance representing the same interval of genome coordinates as this, and returns false otherwise.
equals(Object) - Method in class beagleutil.Samples: Returns true if the specified object is a Samples object which represents the same ordered list of samples as this, and returns false otherwise.
equals(Object) - Method in class blbutil.Pair: Returns true if the specified object is a Pair instance representing the same ordered pair of objects as this, and returns false otherwise.
equals(Object) - Method in class vcf.BasicMarker
equals(Object) - Method in interface vcf.Marker: Returns true if the specified object is a Marker with the same chromosome, position, allele lists, and INFO END field, and returns false otherwise.
equals(Object) - Method in class vcf.Markers: Returns true if the specified object is a Markers instance which represents the same list of markers as this, and returns false otherwise.
err() - Method in class main.Par: Returns the err parameter.
errProb(int) - Method in class imp.ImpData: Returns the probability that the allele carried by the specified target marker cluster matches the allele labeling the latent HMM state.
EstPhase - Class in phase: Class EstPhase stores haplotype pairs, missing genotypes, and unphased, nonmissing heteroygote genotypes for a list of samples.
EstPhase(GT, List<LongArray>) - Constructor for class phase.EstPhase: Constructs a new EstPhase instance from the specified data.
EstPhase.HapsGT - Class in phase
excludeFilter(Collection<E>) - Static method in interface blbutil.Filter: Returns a filter that accepts all non-null objects that are not contained in the specified collection.
excludemarkers() - Method in class main.Par: Returns the excludemarkers parameter or null if no excludemarkers parameter was specified.
excludesamples() - Method in class main.Par: Returns the excludesamples parameter or null if no excludesamples parameter was specified.
exit(String) - Static method in class blbutil.Utilities: Prints the specified string to standard error and then terminates the Java virtual machine.
exit(String, Throwable) - Static method in class blbutil.Utilities: Prints the specified exception, its stack trace, and the specified string to standard error and then terminates the Java virtual machine.
exit(Throwable) - Static method in class blbutil.Utilities: Prints the specified exception, its stack trace, and the specified string to standard error and then terminates the Java virtual machine.

F

father(int) - Method in class main.Pedigree: Returns the sample index of the father of the specified sample, or returns -1 if the father is unknown or is not present in the list of samples.
file() - Method in interface blbutil.FileIt: Returns the file from which the data are read, or null if the data are read from standard input or are computed data.
file() - Method in class blbutil.InputIt
file() - Method in class bref.Bref3It
file() - Method in class vcf.IntervalVcfIt
file() - Method in class vcf.RefIt
file() - Method in class vcf.RestrictedVcfWindow: Returns the file from which VCF records are read, or returns null if the source is standard input.
file() - Method in class vcf.VcfHeader: Returns the file from which data are read, or returns null if the source is standard input.
file() - Method in class vcf.VcfIt
file() - Method in class vcf.WindowIt: Returns the file from which VCF recList are read, or returns null if the source is standard input.
FileIt<E> - Interface in blbutil: An iterator for data elements in a file.
FileUtil - Class in blbutil: Class FileUtil contains static methods for working with files.
filter() - Method in class vcf.VcfRecord: Returns the FILTER field.
Filter<E> - Interface in blbutil: A filter for accepting or rejecting objects.
FilterUtil - Class in vcf: Class FilterUtil contains static methods for constructing marker filters.
first() - Method in class blbutil.Pair: Returns the first object in the ordered pair of objects.
flipStrand(String) - Static method in class vcf.BasicMarker: Returns the string allele obtained by changing the specified allele to the opposite chromosome strand
flipStrand(Marker) - Static method in class vcf.BasicMarker: Constructs and returns a new marker obtained from the specified marker by changing the marker's non-symbolic alleles to the alleles on the opposite chromosome strand.
floatArg(String, Map<String, String>, boolean, float, float, float) - Static method in class blbutil.Validate: Removes the specified key from the specified map, and returns the float value corresponding to the specified key.
FloatArray - Class in blbutil: Class FloatArray represents an immutable list of float floating point values.
FloatArray(float[]) - Constructor for class blbutil.FloatArray: Constructs an FloatArray object with the specified values.
FloatList - Class in blbutil: Class FloatList represents a list of floats.
FloatList() - Constructor for class blbutil.FloatList: Constructs an FloatList object with the default initial capacity.
FloatList(int) - Constructor for class blbutil.FloatList: Constructs an FloatList object with the specified initial capacity.
flush() - Method in class blbutil.BGZIPOutputStream
format() - Method in class vcf.VcfRecord: Returns the FORMAT field.
formatData(String) - Method in class vcf.VcfRecord: Returns an array of length this.nSamples() containing the specified FORMAT subfield data for each sample.
formatIndex(String) - Method in class vcf.VcfRecord: Returns the index of the specified FORMAT subfield if the specified subfield is defined for this VCF record, and returns -1 otherwise.
formatSubfield(int) - Method in class vcf.VcfRecord: Returns the specified FORMAT subfield.
fromGL(VcfHeader, String, float) - Static method in class vcf.VcfRecord: Constructs and returns a new VcfRecord instance from a VCF record and its GL or PL format subfield data.
fromGT(VcfHeader, String) - Static method in class vcf.VcfRecord: Constructs and returns a new VcfRecord instance from a VCF record and its GT format subfield data
fromGTGL(VcfHeader, String, float) - Static method in class vcf.VcfRecord: Constructs and returns a new VcfRecord instance from a VCF record and its GT, GL, and PL format subfield data.
fromGzipFile(File) - Static method in class blbutil.InputIt: Constructs and returns an InputIt instance with the default buffer size that iterates through lines of the specified compressed or uncompressed text file.
fromGzipFile(File, int) - Static method in class blbutil.InputIt: Constructs and returns an InputIt instance with the specified buffer size that iterates through lines of the specified compressed or uncompressed text file.
fromIds(String[]) - Static method in class beagleutil.Samples: Constructs and returns a Samples instance corresponding to the specified list of sample identifiers.
fromPlinkMapFile(File) - Static method in class vcf.PlinkGenMap: Constructs and returns a new PlinkGenMap instance from the data in the specified file.
fromPlinkMapFile(File, String) - Static method in class vcf.PlinkGenMap: Constructs and returns a new PlinkGenMap instance from the data in the specified file.
fromSignedByteArray(byte[], int) - Static method in class ints.PackedIntArray: Constructs and returns a new PackedIntArray instance from the specified data.
fromSignedByteArray(byte[], int, int, int) - Static method in class ints.PackedIntArray: Constructs a new PackedIntArray instance from the specified data.
fromStdIn() - Static method in class blbutil.InputIt: Constructs and returns an InputIt instance with the default buffer size that iterates through lines of text read from standard input.
fromStdIn(int) - Static method in class blbutil.InputIt: Constructs and returns an InputIt instance with the specified buffer size that iterates through lines of text read from standard input.
fromTextFile(File) - Static method in class blbutil.InputIt: Constructs and returns an InputIt instance with the default buffer size that iterates through lines of the specified text file.
fromTextFile(File, int) - Static method in class blbutil.InputIt: Constructs and returns an InputIt instance with the specified buffer size that iterates through lines of the specified text file.
fromUnsignedByteArray(byte[], int) - Static method in class ints.PackedIntArray: Constructs a new PackedIntArray instance from the specified data.
fromUnsignedByteArray(byte[], int, int, int) - Static method in class ints.PackedIntArray: Constructs a new PackedIntArray instance from the specified data.
fromUnsignedTwoByteArray(byte[], int) - Static method in class ints.PackedIntArray: Constructs a new PackedIntArray instance from the specified data.

G

genDist() - Method in class main.CurrentData: Return a FloatArray of size this.nTargMarkers() whose k-th element is the genetic distance between the k-th target marker and the previous marker, or 0.0 if (k == 0).
genDist() - Method in class phase.PhaseData: Return a FloatArray of size this.nTargMarkers() whose k-th element is the genetic distance between the k-th target marker and the previous marker, or 0.0 if (k == 0).
geneticMap(File, ChromInterval) - Static method in interface vcf.GeneticMap: Constructs and returns a genetic map from the specified data.
GeneticMap - Interface in vcf: Interface GeneticMap represents a genetic map for one or more chromosomes.
genMap() - Method in class vcf.AllData
genMap() - Method in interface vcf.Data: Returns the genetic map.
genMap() - Method in class vcf.TargetData
genMap() - Method in class vcf.WindowIt: Returns the genetic map.
genotype(int, int) - Static method in class vcf.BasicGT: Returns the genotype index corresponding to the specified unordered alleles.
GenotypeValues - Interface in main: Interface GenotypeValues represents a value for each possible genotype for each sample at each marker.
genPos() - Method in class vcf.MarkerMap: Returns the array of genetic map positions whose k-th element equals this.genPos(k).
genPos(int) - Method in class vcf.MarkerMap: Returns the genetic map position of the specified marker.
genPos(int, int) - Method in interface vcf.GeneticMap: Returns the genetic map position of the specified genome coordinate.
genPos(int, int) - Method in class vcf.MarkerMap
genPos(int, int) - Method in class vcf.PlinkGenMap
genPos(int, int) - Method in class vcf.PositionMap
genPos(Marker) - Method in interface vcf.GeneticMap: Returns the genetic map position of the specified marker.
genPos(Marker) - Method in class vcf.MarkerMap
genPos(Marker) - Method in class vcf.PlinkGenMap
genPos(Marker) - Method in class vcf.PositionMap
genPos(Markers) - Method in interface vcf.GeneticMap: Returns the an array of length hapPairs.nMarkers() whose whose j-th element is the genetic map position of the j-th marker.
get(int) - Method in class blbutil.FloatArray: Returns the float at the specified position in this list.
get(int) - Method in class blbutil.FloatList: Returns the float at the specified position in this list.
get(int) - Method in class ints.CharArray
get(int) - Method in class ints.IndexArray
get(int) - Method in interface ints.IntArray: Returns the specified array element.
get(int) - Method in class ints.IntList: Returns the element at the specified position in this list.
get(int) - Method in class ints.IntMap: Returns the value for the specified key or null if the specified key is not present in this map.
get(int) - Method in class ints.LongArray: Returns the specified array element.
get(int) - Method in class ints.PackedIntArray
get(int) - Method in class ints.UnsignedByteArray
get(int) - Method in class ints.WrappedIntArray
get(int) - Method in class vcf.BasicRefGT
get(int) - Method in class vcf.BitSetGT
get(int) - Method in interface vcf.DuplicatesGTRec: Returns the specified allele for the specified haplotype or -1 if the allele is missing.
get(int) - Method in class vcf.LowMafRefDiallelicGT
get(int) - Method in class vcf.LowMafRefGT
get(int) - Method in interface vcf.RefGT: Returns the RefGTRec for the specified marker.
get(int) - Method in class vcf.SeqCodedRefGT
get(int) - Method in class vcf.VcfRecord
getAndDecrement(int) - Method in class ints.IntList: Decrements by one the element at the specified position in this list.
getAndIncrement(int) - Method in class ints.IntList: Increments by one the element at the specified position in this list.
getCompressedList() - Method in class bref.SeqCoder3: Returns and clears the stored list of compressed RefGTRec objects.
getFields(String) - Static method in class blbutil.StringUtil: Returns an array obtained by trimming white-space from the beginning and end of the specified string, and splitting the resulting string around white space.
getFields(String, char) - Static method in class blbutil.StringUtil: Returns an array obtained by splitting the specified string around the specified delimiter.
getFields(String, char, int) - Static method in class blbutil.StringUtil: Returns an array obtained by splitting the specified string around the first (limit - 1) occurrences of the specified delimiter.
getFields(String, int) - Static method in class blbutil.StringUtil: Returns an array obtained by trimming white-space from the beginning and end of the specified string, and splitting the resulting string around the first (limit-1) white-space delimiters.
getFile(String) - Static method in class blbutil.Validate: Returns a File object corresponding to the specified filename or null if filename == null
getIndex(String) - Method in class beagleutil.ChromIds: Returns the index of the specified chromosome identifier.
getIndex(String) - Method in class beagleutil.SampleIds: Returns the index of the specified sample identifier.
getIndex(T) - Method in class beagleutil.ThreadSafeIndexer: Returns the index of the specified object.
getIndexIfIndexed(String) - Method in class beagleutil.ChromIds: Returns the index of the specified chromosome identifier, or returns -1 if the specified chromosome identifier is not indexed.
getIndexIfIndexed(String) - Method in class beagleutil.SampleIds: Returns the index of the specified sampled identifier, or returns -1 if the specified sample identifier is not indexed.
getIndexIfIndexed(T) - Method in class beagleutil.ThreadSafeIndexer: Returns the index of the specified object, or returns -1 if the specified object is not indexed.
getIndices(String[]) - Method in class beagleutil.ChromIds: Returns an array of chromosome identifier indices corresponding to the specified array of chromosome identifiers.
getIndices(String[]) - Method in class beagleutil.SampleIds: Returns an array of sample identifier indices corresponding to the specified array of sample identifiers.
getIndices(T[]) - Method in class beagleutil.ThreadSafeIndexer: Returns an array of object indices corresponding to the specified object array.
getMissing(int) - Method in class phase.EstPhase: Returns a list of marker indices in increasing order for which the specified sample has a missing genotype.
getMissing(int, boolean[]) - Method in class phase.EstPhase: Sets the k-th entry of the specified isMissing array to true if the specified sample's genotype at the k-th marker is missing, and to false otherwise.
getUnphasedHets(int) - Method in class phase.EstPhase: Returns a list of marker indices in increasing order for which the specified sample has an unphased, non-missing heterozygote genotype.
getUnphasedHets(int, boolean[]) - Method in class phase.EstPhase: Sets the k-th entry of the specified isUnphased array to true if the specified sample's genotype at the k-th marker is an unphased, nonmissing heterozygote, and to false otherwise.
giga - Static variable in class blbutil.Const: The value 1,000,000,000
gl(int, int, int) - Method in class vcf.BitSetGT
gl(int, int, int) - Method in interface vcf.GTRec: Returns the probability of the observed data for the specified sample if the specified pair of ordered alleles is the true ordered genotype.
gl(int, int, int) - Method in class vcf.LowMafRefDiallelicGT
gl(int, int, int) - Method in class vcf.LowMafRefGT
gl(int, int, int) - Method in class vcf.SeqCodedRefGT
gl(int, int, int) - Method in class vcf.VcfRecord
gl(int, int, int) - Method in class vcf.XBasicGT1
gl(int, int, int) - Method in interface vcf.XGT1: Returns the probability of the observed data for the specified marker if the specified pair of ordered alleles is the true ordered genotype.
gl(int, int, int, int) - Method in class vcf.BasicGT
gl(int, int, int, int) - Method in interface vcf.GT: Returns the probability of the observed data for the specified marker and sample if the specified pair of ordered alleles is the true ordered genotype.
gl(int, int, int, int) - Method in class vcf.SplicedGT
gl(int, int, int, int) - Method in class vcf.XBasicGT
GL_FORMAT - Static variable in class vcf.VcfRecord: The VCF FORMAT code for log-scaled genotype likelihood data: "GL".
gp() - Method in class main.Par: Returns the gp parameter.
gt() - Method in class main.Par: Returns the gt parameter or null if no gt parameter was specified.
GT - Interface in vcf: Interface GT represents genotype data for a list of markers and a list of samples.
GT_FORMAT - Static variable in class vcf.BitSetGT: The VCF FORMAT code for genotype data: "GT".
gtIndex(int, int) - Static method in class vcf.VcfRecord: Returns the VCF genotype index for the specified pair of alleles.
GTRec - Interface in vcf: Interface GTRec represents represents genotype data for one marker.
gzipPrintWriter(File) - Static method in class blbutil.FileUtil: Returns a buffered java.io.PrintWriter writing to the specified file.
gzipPrintWriter(File, boolean) - Static method in class blbutil.FileUtil: Returns a buffered java.io.PrintWriter writing to the specified file.

H

hap(int) - Method in class imp.RefHapHash: Return the specified haplotype in the sublist of reference haplotypes.
hap2Index(int) - Method in class imp.RefHapHash: Returns the index of the specified haplotype in the sublist of reference haplotypes.
hapIndex(int, int) - Method in class vcf.LowMafRefDiallelicGT
hapIndex(int, int) - Method in class vcf.LowMafRefGT
hapIndex(int, int) - Method in interface vcf.RefGTRec: Returns index of the haplotype that carries the specified copy of the specified allele.
hapIndex(int, int) - Method in class vcf.SeqCodedRefGT
hapIndices() - Method in class vcf.LowMafRefDiallelicGT
hapIndices() - Method in class vcf.LowMafRefGT
hapIndices() - Method in interface vcf.RefGTRec: Returns an array whose j-th element is null if j is the major allele with lowest index, and otherwise is an array of indices of haplotypes that carry the j-th allele sorted in increasing order
hapIndices() - Method in class vcf.SeqCodedRefGT
haplotype - package haplotype
HaplotypeCoder - Class in imp: Class HaplotypeCoder indexes the observed allele sequences in phased reference and target genotype data in a chromosome interval.
HaplotypeCoder(RefGT, GT) - Constructor for class imp.HaplotypeCoder: Constructs a new HaplotypeCoder instance from the specified data.
HapPair - Interface in haplotype: Interface HapPair represents a pair of haplotypes for a sample.
HapPairPhasedGT - Class in haplotype: Class HapPairPhasedGT stores a list of samples and a haplotype pair for each sample.
HapPairPhasedGT(Samples, List<BitHapPair>) - Constructor for class haplotype.HapPairPhasedGT: Constructs a new BasicPhasedGT instance from the specified data.
hapsGT() - Method in class phase.EstPhase
hapToSeq(int) - Method in class imp.ImpData: Returns the specified target marker cluster alleles for the reference and target haplotypes.
hasFormat(String) - Method in class vcf.VcfRecord: Returns true if the specified FORMAT subfield is present, and returns false otherwise.
hash(int) - Method in class imp.RefHapHash: Return a hash code computed from the allele sequence of the specified haplotype in the sublist of reference haplotypes.
hashCode() - Method in class beagleutil.ChromInterval: Returns a hash code value for the object.
hashCode() - Method in class beagleutil.Samples: Returns a hash code value for the object.
hashCode() - Method in class blbutil.Pair: Returns a hash code value for the object.
hashCode() - Method in class vcf.BasicMarker
hashCode() - Method in interface vcf.Marker: Returns the hash code value for this object.
hashCode() - Method in class vcf.Markers: Returns a hash code value for the object.
hasMissingGT(int) - Method in class phase.EstPhase: Returns true if the specified sample has a missing genotype, and returns false otherwise.
hasNext() - Method in class blbutil.InputIt: Returns true if the iteration has more elements.
hasNext() - Method in class bref.Bref3It: Returns true if the iteration has more elements, and returns false otherwise.
hasNext() - Method in class vcf.IntervalVcfIt: Returns true if the iteration has more elements.
hasNext() - Method in class vcf.RefIt: Returns true if the iteration has more elements, and returns false otherwise.
hasNext() - Method in class vcf.VcfIt: Returns true if the iteration has more elements, and returns false otherwise.
hasNext() - Method in class vcf.WindowIt: Returns true if the sliding window of VCF recList can advance and returns false otherwise.
hasUnphasedHets(int) - Method in class phase.EstPhase: Returns true if the specified sample has an unphased heterozygote genotype, and returns false otherwise.
HEADER_PREFIX - Static variable in class vcf.VcfHeader: A string equal to the first nine tab-delimited fields of a VCF header line that contains sample data.
headerLine() - Method in class vcf.VcfHeader: Returns the VCF header line.
hyphen - Static variable in class blbutil.Const: The hyphen character: '-'

I

ibsHaps(int, int) - Method in class imp.ImpIbs: Returns an array containing reference haplotype indices that that are IBS with the specified target haplotype in an interval beginning with the specified step.
ibsHaps(int, int, int) - Method in class phase.PhaseIbs: Returns a set containing the specified number of haplotype indices that are IBS with haplotype h1 in the specified step.
ibsStates(int, int[][]) - Method in class phase.PhaseStates: Identifies the HMM state alleles for the specified sample.
ibsStates(int, int[][], boolean[][]) - Method in class imp.ImpStates: Stores the reference haplotype for the j-th state at the m-th marker in hapIndices[m][j], and stores the equality of the allele carried by the reference haplotype for the j-th state and the allele carried by the target haplotype at the m-th marker in alMatch[m][j].
id() - Method in class vcf.BasicMarker
id() - Method in interface vcf.Marker: Returns the first marker identifier if there is at least one identifier in the VCF record ID field, and returns this.chr() + ":" + this.pos() otherwise.
id(int) - Method in class beagleutil.ChromIds: Returns the chromosome identifier with the specified index.
id(int) - Method in class beagleutil.SampleIds: Returns the sample identifier with the specified index.
id(int) - Method in class beagleutil.Samples: Returns the identifier for the sample with the specified index in this list of samples.
id(int) - Method in class vcf.BasicMarker
id(int) - Method in interface vcf.Marker: Returns the specified marker identifier.
IDENTICAL - beagleutil.Phase
idFilter(Collection<String>) - Static method in class vcf.FilterUtil: Returns a filter that accepts all markers which do not have an identifier or chromomsome position present in the specified collection.
idIndex() - Method in class haplotype.BitHapPair
idIndex() - Method in interface haplotype.HapPair: Returns the sample identifier index.
idIndex() - Method in class haplotype.WrappedHapPair
idIndex() - Method in class vcf.XBasicGT1
idIndex() - Method in interface vcf.XGT1: Returns the sample identifier index.
idIndex(int) - Method in class beagleutil.Samples: Returns the sample identifier index corresponding to the sample with the specified index in this list of samples.
ids() - Method in class beagleutil.ChromIds: Returns the list of chromosome identifiers as an array.
ids() - Method in class beagleutil.SampleIds: Returns the list of indexed sample identifiers as an array.
ids() - Method in class beagleutil.Samples: Returns this list of samples as an array of sample identifiers.
ids(int[]) - Method in class beagleutil.SampleIds: Returns a list of sample identifiers with the specified indices.
idSet(File) - Static method in class blbutil.Utilities: Returns a set of identifiers found in a text file that has one identifier per line.
imp - package imp
imp_segment() - Method in class main.Par: Returns the imp-segment parameter.
imp_states() - Method in class main.Par: Returns the imp-states parameter.
impData() - Method in class imp.ImpIbs: Return the data for genotype imputation in the marker window.
impData() - Method in class imp.ImpLSBaum: Return the input data for genotype imputation
ImpData - Class in imp: Class ImpData contains the input data for imputation of ungenotyped markers.
ImpData(Par, CurrentData, GT, GeneticMap) - Constructor for class imp.ImpData: Constructs a new ImpData instance from the specified data.
ImpIbs - Class in imp: Class ImpIbs identifies haplotypes that share a long IBS segment with a specified haplotype.
ImpIbs(ImpData) - Constructor for class imp.ImpIbs: Constructs a new ImpIbs object from the specified data.
ImpLS - Class in imp: Class ImpLS computes HMM state probabilities at genotyped markers in the target haplotypes.
ImpLSBaum - Class in imp: Class ImpLSBaum implements a Baum hidden Markov model forward and backward algorithms for computing HMM state probabilities at genotyped markers using IBS-matched reference haplotypes.
ImpLSBaum(ImpData, ImpIbs) - Constructor for class imp.ImpLSBaum: Creates a LSHapBaum instance from the specified data.
ImpStates - Class in imp: Class ImpStates identifies a list of pseudo-reference haplotypes for a target haplotype.
ImpStates(ImpIbs) - Constructor for class imp.ImpStates: Constructs a new ImpStates object from the specified data.
imputationNanos(long) - Method in class main.RunStats: Stores the time for imputing ungenotyped marker and increases the cumulative imputation time by the specified number of nanoseconds.
impute() - Method in class main.Par: Returns the impute parameter.
impute(int) - Method in class imp.ImpLSBaum: Returns HMM state probabilities at genotyped markers for the specified target haplotype.
ImputedRecBuilder - Class in imp: Class ImputeRecBuilder contains methods for constructing and printing a VCF record in VCF 4.3 format.
ImputedRecBuilder(Marker, int, boolean, boolean) - Constructor for class imp.ImputedRecBuilder: Constructs a new ImputedRecBuilder instance for the specified number of samples.
ImputedVcfWriter - Class in imp: Class ImputedVcfWriter writes observed and imputed genotypes to a VCF output file.
ImputedVcfWriter(ImpData, int, int, int) - Constructor for class imp.ImputedVcfWriter: Constructs a new ImputedVcfWriter instance from the specified data.
incEndComp() - Static method in interface beagleutil.IntInterval: Returns a Comparator<IntInterval> which orders IntInterval objects in order of increasing this.start() value and orders IntInterval objects with the same this.start() value in order of increasing this.end() value.
includeFilter(Collection<E>) - Static method in interface blbutil.Filter: Returns a filter that accepts all non-null objects that are contained in the specified collection.
INCONSISTENT - beagleutil.Phase
incrementAndGet(int) - Method in class ints.IntList: Increments by one the element at the specified position in this list.
index(int) - Method in class beagleutil.Samples: Returns the index of the sample that corresponds to the specified sample identifier index, or returns -1 if there is no corresponding sample in this list of samples.
index(String) - Method in class beagleutil.Samples: Returns the index of the sample that corresponds to the specified sample identifier, or returns -1 if there is no corresponding sample in this list of samples.
index2BasePos(int, int) - Method in class vcf.PlinkGenMap: Returns the specified base position
index2GenPos(int, int) - Method in class vcf.PlinkGenMap: Returns the specified genetic map position
IndexArray - Class in ints: Class IndexArray stores an array whose entries are elements of a bounded set of non-negative integers along with an upper bound.
IndexArray(IntArray, int) - Constructor for class ints.IndexArray: Constructs a new IndexArray instance from the specified data.
info() - Method in class vcf.VcfRecord: Returns the INFO field.
InitTargHapPairs - Class in sample: Class InitTargHapPairs has a static method for returning initial target haplotype pairs.
InputIt - Class in blbutil: Class InputIt is a buffered iterator whose next() method returns lines of a text input stream.
instance() - Static method in class beagleutil.ChromIds: Returns the singleton ChromIds instance.
instance() - Static method in class beagleutil.SampleIds: Returns the singleton SampleIds instance.
intArg(String, Map<String, String>, boolean, int, int, int) - Static method in class blbutil.Validate: Removes the specified key from the specified map, and returns the integer value corresponding to the specified key.
intArray() - Method in class ints.IndexArray: Returns the wrapped IntArray object.
IntArray - Interface in ints: Interface IntArray represents an immutable int[] array.
intensity() - Method in class main.CurrentData: Returns the intensity used to generate the pRecomb values.
IntervalVcfIt<E extends MarkerContainer> - Class in vcf: Class IntervalVcfIterator is a sample file iterator whose next() method returns a marker container.
IntervalVcfIt(SampleFileIt<E>, ChromInterval) - Constructor for class vcf.IntervalVcfIt: Constructs a new IntervalVcfIterator instance.
IntInterval - Interface in beagleutil: Interface IntInterval represents an interval of consecutive integers.
IntList - Class in ints: Class IntList represents a list of integers.
IntList() - Constructor for class ints.IntList: Constructs an IntList object with the default initial capacity.
IntList(int) - Constructor for class ints.IntList: Constructs an IntList object with the specified initial capacity.
IntList(int[]) - Constructor for class ints.IntList: Constructs an IntList by cloning the specified array.
IntList(IntList) - Constructor for class ints.IntList: Constructs an IntList by copying the specified IntList.
IntMap<E> - Class in ints: Class IntMap represents a map with integer keys and generic type values.
IntMap(int) - Constructor for class ints.IntMap: Creates a new IntMap instance.
ints - package ints
IntSet - Class in ints: Class IntSet represents an indexed set of integers.
IntSet(int) - Constructor for class ints.IntSet: Creates a new IntSet instance.
isAlleleCoded() - Method in class vcf.LowMafRefDiallelicGT
isAlleleCoded() - Method in class vcf.LowMafRefGT
isAlleleCoded() - Method in interface vcf.RefGTRec: Returns true if this instance stores the indices of haplotypes that carry non-major alleles, and returns false otherwise.
isAlleleCoded() - Method in class vcf.SeqCodedRefGT
isCarrier(int, int) - Method in class vcf.LowMafRefDiallelicGT
isCarrier(int, int) - Method in class vcf.LowMafRefGT
isCarrier(int, int) - Method in interface vcf.RefGTRec: Returns true if the specified haplotype carries the specified allele and return false otherwise.
isCarrier(int, int) - Method in class vcf.SeqCodedRefGT
isEmpty() - Method in class blbutil.FloatArray: Returns true if this list has no elements, and returns false otherwise.
isEmpty() - Method in class blbutil.FloatList: Returns true if this list has no elements, and returns false otherwise.
isEmpty() - Method in class ints.IntList: Returns true if this list has no elements, and returns false otherwise.
isGTData() - Method in class vcf.BasicGT
isGTData() - Method in class vcf.BitSetGT
isGTData() - Method in interface vcf.GT: Returns true if the value returned by this.gl() is determined by a called or missing genotype, and returns false otherwise.
isGTData() - Method in interface vcf.GTRec: Returns true if the value returned by this.gl() is determined by a called or missing genotype, and returns false otherwise.
isGTData() - Method in class vcf.LowMafRefDiallelicGT
isGTData() - Method in class vcf.LowMafRefGT
isGTData() - Method in class vcf.SeqCodedRefGT
isGTData() - Method in class vcf.SplicedGT
isGTData() - Method in class vcf.VcfRecord
isGTData() - Method in class vcf.XBasicGT
isPhased() - Method in class haplotype.HapPairPhasedGT
isPhased() - Method in class phase.EstPhase.HapsGT
isPhased() - Method in class vcf.BasicGT
isPhased() - Method in class vcf.BasicRefGT
isPhased() - Method in class vcf.BitSetGT
isPhased() - Method in interface vcf.DuplicatesGTRec: Returns true if every genotype for each sample is a phased, non-missing genotype, and returns false otherwise.
isPhased() - Method in interface vcf.GT: Returns true if the genotype for each marker and sample is a phased, non-missing genotype, and returns false otherwise.
isPhased() - Method in class vcf.LowMafRefDiallelicGT: Returns true.
isPhased() - Method in class vcf.LowMafRefGT: Returns true.
isPhased() - Method in interface vcf.RefGTRec: Returns true.
isPhased() - Method in class vcf.SeqCodedRefGT: Returns true.
isPhased() - Method in class vcf.SplicedGT
isPhased() - Method in class vcf.VcfRecord
isPhased() - Method in class vcf.XBasicGT
isPhased(int) - Method in class haplotype.HapPairPhasedGT
isPhased(int) - Method in class phase.EstPhase.HapsGT
isPhased(int) - Method in class vcf.BasicGT
isPhased(int) - Method in class vcf.BasicRefGT
isPhased(int) - Method in class vcf.BitSetGT
isPhased(int) - Method in interface vcf.DuplicatesGTRec: Returns true if the genotype for the specified sample is a phased, nonmissing genotype, and returns false otherwise.
isPhased(int) - Method in interface vcf.GT: Returns true if the genotype for each marker for the specified sample is a phased, nonmissing genotype, and returns false otherwise.
isPhased(int) - Method in class vcf.LowMafRefDiallelicGT
isPhased(int) - Method in class vcf.LowMafRefGT
isPhased(int) - Method in interface vcf.RefGTRec: Returns true.
isPhased(int) - Method in class vcf.SeqCodedRefGT
isPhased(int) - Method in class vcf.SplicedGT
isPhased(int) - Method in class vcf.VcfRecord
isPhased(int) - Method in class vcf.XBasicGT
isPhased(int) - Method in class vcf.XBasicGT1
isPhased(int) - Method in interface vcf.XGT1: Returns true if the observed data for the specified marker includes a phased genotype, and returns false otherwise.
isPhased(int, int) - Method in class haplotype.HapPairPhasedGT
isPhased(int, int) - Method in class phase.EstPhase.HapsGT
isPhased(int, int) - Method in class vcf.BasicGT
isPhased(int, int) - Method in class vcf.BasicRefGT
isPhased(int, int) - Method in interface vcf.GT: Returns true if the genotype for the specified marker and sample is a phased, nonmissing genotype, and returns false otherwise.
isPhased(int, int) - Method in class vcf.SplicedGT
isPhased(int, int) - Method in class vcf.XBasicGT
isRefSample() - Method in class vcf.XBasicGT1
isRefSample() - Method in interface vcf.XGT1: Returns true if the observed data for each marker includes a phased genotype that has no missing alleles, and returns false otherwise.
item(int) - Method in class beagleutil.ThreadSafeIndexer: Returns the object with the specified index.
items() - Method in class beagleutil.ThreadSafeIndexer: Returns an listed of all indexed objects.
items(int[]) - Method in class beagleutil.ThreadSafeIndexer: Returns a list of objects with the specified indices.
iter() - Method in class phase.PhaseData: Returns the iteration index.
iterationNanos(long) - Method in class main.RunStats: Stores the time for updating the haplotype estimates and increases the cumulative phasing time by the specified number of nanoseconds.
iterations() - Method in class main.Par: Returns the iterations parameter.

K

key() - Method in class vcf.VcfMetaInfo: Returns the VCF meta-information line key.
key(int) - Method in class ints.IntMap: Returns the specified key.
keys() - Method in class ints.IntMap: Returns an array containing the keys in this map.

L

lastWindow() - Method in class vcf.Window: Returns true if the sliding window of genotype records is the last window and returns false otherwise.
lastWindowOnChrom() - Method in class vcf.AllData
lastWindowOnChrom() - Method in interface vcf.Data: Returns true if the current window of VCF records is the last window for the chromosome and returns false otherwise.
lastWindowOnChrom() - Method in class vcf.TargetData
lastWindowOnChrom() - Method in class vcf.Window: Returns true if the sliding window of genotype records is the last window for its chromosome and returns false otherwise.
longArg(String, Map<String, String>, boolean, long, long, long) - Static method in class blbutil.Validate: Removes the specified key from the specified map, and returns the long value corresponding to the specified key.
LongArray - Class in ints: Interface LongArray represents an immutable long[] array.
LongArray(long[]) - Constructor for class ints.LongArray: Constructs a LongArray instance from the specified values.
LowMafRefDiallelicGT - Class in vcf: Class LowMafRefDiallelicGT represent represents phased, non-missing genotypes for a list of reference samples at a single diallelic marker.
LowMafRefDiallelicGT(Marker, Samples, int[][]) - Constructor for class vcf.LowMafRefDiallelicGT: Constructs a new LowMafRefDiallelicGT instance from the specified data.
LowMafRefDiallelicGT(RefGTRec) - Constructor for class vcf.LowMafRefDiallelicGT: Constructs a new LowMafRefDiallelicGT instance with phased non-missing genotypes from the specified data.
LowMafRefDiallelicGT(VcfRecGTParser) - Constructor for class vcf.LowMafRefDiallelicGT: Constructs a new LowMafRefDiallelicGT instance with phased non-missing genotypes from the specified data.
LowMafRefGT - Class in vcf: Class LowMafRefGT represent represents phased, non-missing genotypes for a list of reference samples at a single marker.
LowMafRefGT(Marker, Samples, int[][]) - Constructor for class vcf.LowMafRefGT: Constructs a new LowMafRefGT instance from the specified data.
LowMafRefGT(RefGTRec) - Constructor for class vcf.LowMafRefGT: Constructs a new LowMafRefGT instance with phased non-missing genotypes from the specified data.
LowMafRefGT(VcfRecGTParser) - Constructor for class vcf.LowMafRefGT: Constructs a new LowMafRefGT instance with phased non-missing genotypes from the specified VcfRecGTParser object.

M

MAGIC_NUMBER_V3 - Static variable in class bref.AsIsBref3Writer: The initial integer in a bref version 3 file.
main - package main
main(String[]) - Static method in class blbutil.BGZIPOutputStream: Applies BGZIP compression on the specified files.
main(String[]) - Static method in class bref.Bref3: The main() method is the entry point to the bref program.
main(String[]) - Static method in class bref.UnBref3: The main() method is the entry point to the bref program.
main(String[]) - Static method in class main.Main: Entry point to Beagle program.
main(String[]) - Static method in class math.Regress
Main - Class in main: Class Main is the entry class for the Beagle program.
MainHelper - Class in main: Class MainHelper is an auxiliary class with methods called by the main.Main class.
majorAllele() - Method in class vcf.LowMafRefDiallelicGT
majorAllele() - Method in class vcf.LowMafRefGT
majorAllele() - Method in interface vcf.RefGTRec: Returns the index of the major allele.
majorAllele() - Method in class vcf.SeqCodedRefGT
map() - Method in class main.CurrentData: Returns the genetic map.
map() - Method in class main.Par: Returns the map parameter.
map(int) - Method in class vcf.LowMafRefDiallelicGT
map(int) - Method in class vcf.LowMafRefGT
map(int) - Method in interface vcf.RefGTRec: Returns this.maps()[index].
map(int) - Method in class vcf.SeqCodedRefGT
maps() - Method in class vcf.LowMafRefDiallelicGT
maps() - Method in class vcf.LowMafRefGT
maps() - Method in interface vcf.RefGTRec: Returns an array of maps, which when composed map haplotype indices to values.
maps() - Method in class vcf.SeqCodedRefGT
marker() - Method in class imp.ImputedRecBuilder: Returns the marker in the VCF record.
marker() - Method in class vcf.BitSetGT
marker() - Method in class vcf.LowMafRefDiallelicGT
marker() - Method in class vcf.LowMafRefGT
marker() - Method in interface vcf.MarkerContainer: Returns the marker.
marker() - Method in class vcf.SeqCodedRefGT
marker() - Method in class vcf.VcfRecBuilder: Returns the current marker.
marker() - Method in class vcf.VcfRecGTParser: Returns the marker.
marker() - Method in class vcf.VcfRecord
marker(int) - Method in class haplotype.BitHapPair
marker(int) - Method in interface haplotype.HapPair: Returns the specified marker.
marker(int) - Method in class haplotype.HapPairPhasedGT
marker(int) - Method in class haplotype.WrappedHapPair
marker(int) - Method in interface main.GenotypeValues: Returns the specified marker.
marker(int) - Method in class phase.EstPhase.HapsGT
marker(int) - Method in class phase.PhaseData: Returns the specified marker.
marker(int) - Method in class vcf.BasicGT
marker(int) - Method in class vcf.BasicRefGT
marker(int) - Method in interface vcf.GT: Returns the specified marker.
marker(int) - Method in class vcf.MarkerMap: Returns the specified marker.
marker(int) - Method in class vcf.Markers: Returns the specified marker.
marker(int) - Method in class vcf.SplicedGT
marker(int) - Method in class vcf.XBasicGT
marker(int) - Method in class vcf.XBasicGT1
marker(int) - Method in interface vcf.XGT1: Returns the specified marker.
Marker - Interface in vcf: Interface Marker represents a genetic marker.
MarkerContainer - Interface in vcf: Interface MarkerContainer represents an object that stores a unique vcf.Marker instance.
markerFilter(File) - Static method in class vcf.FilterUtil: Returns a filter that excludes markers that have an identifier or genome coordinates that matches a line of the specified file, or returns null if the excludeMarkersFile parameter is null.
markerIndex(int) - Method in class main.CurrentData: Returns the index of the specified marker in the reference data markers.
markerIndex(int) - Method in class vcf.AllData
markerIndex(int) - Method in interface vcf.Data: Returns the marker index corresponding to the specified target data marker.
markerIndex(int) - Method in class vcf.TargetData
markerIndices() - Method in class main.CurrentData: Returns an array of length this.nTargMarkers() which maps the k-th marker in the list of target data markers to the index of the marker in the list of reference data markers.
markerIsInSet(Marker, Set<String>) - Static method in class vcf.FilterUtil: Returns true if the specified marker has an identifier is in the specified set, or if ("marker.chrom()" + ":" + "marker.pos()") is in the specified set, and returns false otherwise.
MarkerMap - Class in vcf: Class MarkerMap represents genetic map positions for a list of markers.
markers() - Method in class haplotype.BitHapPair
markers() - Method in interface haplotype.HapPair: Returns the markers.
markers() - Method in class haplotype.HapPairPhasedGT
markers() - Method in class haplotype.WrappedHapPair
markers() - Method in class main.CurrentData: Returns the list of reference data markers.
markers() - Method in interface main.GenotypeValues: Returns the list of markers.
markers() - Method in class phase.EstPhase.HapsGT
markers() - Method in class phase.EstPhase: Returns the list of markers.
markers() - Method in class phase.PhaseData: Returns the list of target markers.
markers() - Method in class vcf.AllData
markers() - Method in class vcf.BasicGT
markers() - Method in class vcf.BasicRefGT
markers() - Method in interface vcf.Data: Returns the list of markers in the current window.
markers() - Method in interface vcf.GT: Returns the list of markers.
markers() - Method in class vcf.MarkerMap: Returns the list of markers.
markers() - Method in class vcf.Markers: Returns the list of markers.
markers() - Method in class vcf.SplicedGT
markers() - Method in class vcf.TargetData
markers() - Method in class vcf.XBasicGT
markers() - Method in class vcf.XBasicGT1
markers() - Method in interface vcf.XGT1: Returns the list of markers.
Markers - Class in vcf: Class Markers represent a list of markers in chromosome order.
math - package math
max(IntArray) - Static method in interface ints.IntArray: Returns the maximum element, or Integer.MIN_VALUE if this.size() == 0.
MAX_EM_BUFFER_SIZE - Static variable in class vcf.RefIt: The default number of GTRec objects that are stored in a buffer.
MAX_EM_BUFFER_SIZE - Static variable in class vcf.VcfIt: The default number of VCF records stored in a buffer, which is 1000.
MAX_NALLELES - Static variable in class bref.SeqCoder3: The maximum number of alleles are that permitted in order for the add() method to return true
MAX_SAMPLES - Variable in class bref.AsIsBref3Writer
maxNSeq() - Method in class bref.SeqCoder3: Returns the maximum number of distinct allele sequences.
mega - Static variable in class blbutil.Const: The value 1,000,000
merge(ChromInterval, ChromInterval) - Static method in class beagleutil.ChromInterval: Returns the union of the specified overlapping chromosome intervals.
metaInfoLine(int) - Method in class vcf.VcfHeader: Returns the specified VCF meta-information line.
min(IntArray) - Static method in interface ints.IntArray: Returns the minimum element, or Integer.MAX_VALUE if this.size() == 0.
minutesAndSeconds() - Static method in class blbutil.Utilities: Returns the current minutes and seconds as a string.
MISSING_DATA_CHAR - Static variable in class blbutil.Const: The VCF missing-data symbol as a character: '.'
MISSING_DATA_STRING - Static variable in class blbutil.Const: The VCF missing-data symbol as a string: "."
mother(int) - Method in class main.Pedigree: Returns the sample index of the mother of the specified sample, or returns -1 if the mother is unknown or is not present in the list of samples.

N

nAlleles() - Method in class vcf.BasicMarker
nAlleles() - Method in class vcf.BitSetGT
nAlleles() - Method in class vcf.LowMafRefDiallelicGT
nAlleles() - Method in class vcf.LowMafRefGT
nAlleles() - Method in interface vcf.Marker: Returns the number of alleles for the marker, including the REF allele.
nAlleles() - Method in interface vcf.MarkerContainer: Returns the number of marker alleles.
nAlleles() - Method in class vcf.SeqCodedRefGT
nAlleles() - Method in class vcf.VcfRecGTParser: Returns this.marker().nAlleles().
nAlleles() - Method in class vcf.VcfRecord
nAllSamples() - Method in class main.CurrentData: Returns the number of reference and target samples.
nAllSamples() - Method in class vcf.AllData
nAllSamples() - Method in interface vcf.Data: Returns the total number of reference and target samples.
nAllSamples() - Method in class vcf.TargetData
nClusters() - Method in class imp.ImpData: Return the number of target marker clusters.
nDuos() - Method in class main.Pedigree: Returns the number of parent-offspring duos in the list of samples.
ne() - Method in class main.Par: Returns the ne parameter
newInstance(Supplier<SampleFileIt<E>>, GeneticMap, float, float) - Static method in class vcf.WindowIt: Constructs and returns a new WindowIt instance for the specified data.
next() - Method in class blbutil.InputIt: Returns the next element in the iteration.
next() - Method in class bref.Bref3It: Returns the next element in the iteration.
next() - Method in class vcf.IntervalVcfIt: Returns the next element in the iteration.
next() - Method in class vcf.RefIt: Returns the next element in the iteration.
next() - Method in class vcf.VcfIt: Returns the next element in the iteration.
next() - Method in class vcf.WindowIt: Advances the sliding window of VCF recList, and returns the advanced window as a RefGTRec[] object.
nextOverlapStart() - Method in class main.CurrentData: Returns the first marker index in the overlap between this marker window and the next marker window, or returns this.nMarkers() the next marker window is from a different chromosome.
nextOverlapStart() - Method in class vcf.AllData
nextOverlapStart() - Method in interface vcf.Data: Returns the first marker index in the overlap between this marker window and the next marker window.
nextOverlapStart() - Method in class vcf.TargetData
nextSpliceStart() - Method in class main.CurrentData: Returns the first marker index after the splice point between this marker window and the next marker window, or returns this.nMarkers() if there is no overlap or if there are no markers after the splice point.
nextTargetOverlapStart() - Method in class main.CurrentData: Returns the first target marker index in the overlap between this marker window and the next marker window, or returns this.nMarkers() if there is no overlap or if there are no target markers in the overlap.
nextTargetSpliceStart() - Method in class main.CurrentData: Returns the first target marker index after the splice point between this marker window and the next marker window, or returns this.nTargMarkers() if there is no overlap or if there are no target markers after the splice point
nFormatSubfields() - Method in class vcf.VcfRecord: Returns the number of FORMAT subfields.
nGenotypes() - Method in class vcf.BasicMarker
nGenotypes() - Method in interface vcf.Marker: Returns the number of distinct genotypes, which equals this.nAlleles()*(1 + this.nAlleles())/2.
nGenotypes() - Method in class vcf.R2Estimator: Returns the current number of genotypes with allele dose data.
nHaps() - Method in class haplotype.HapPairPhasedGT
nHaps() - Method in class imp.ImpData: Return the total number of reference and target haplotypes.
nHaps() - Method in class imp.RefHapHash: Returns the size of the sublist of reference haplotypes.
nHaps() - Method in class main.CurrentData
nHaps() - Method in class phase.EstPhase.HapsGT
nHaps() - Method in class phase.PhaseData: Returns the number of reference and target haplotypes.
nHaps() - Method in class vcf.BasicGT
nHaps() - Method in class vcf.BasicRefGT
nHaps() - Method in interface vcf.GT: Returns the number of haplotypes.
nHaps() - Method in class vcf.SplicedGT
nHaps() - Method in class vcf.XBasicGT
nHeaderFields() - Method in class vcf.VcfHeader: Returns the number of fields in the VCF header line before sample exclusions.
nIds() - Method in class vcf.BasicMarker
nIds() - Method in interface vcf.Marker: Returns the number of marker identifiers.
nItsRemaining() - Method in class phase.PhaseData: Returns the number of iterations remaining.
nl - Static variable in class blbutil.Const: The system-dependent string representing a new line-line: System.getProperty("line.separator")
nMapPositions(int) - Method in class vcf.PlinkGenMap: Returns the number of mapped loci in this genetic map.
nMaps() - Method in class vcf.LowMafRefDiallelicGT
nMaps() - Method in class vcf.LowMafRefGT
nMaps() - Method in interface vcf.RefGTRec: Returns this.maps().length
nMaps() - Method in class vcf.SeqCodedRefGT
nMarkers() - Method in class haplotype.BitHapPair
nMarkers() - Method in interface haplotype.HapPair: Returns the number of markers.
nMarkers() - Method in class haplotype.HapPairPhasedGT
nMarkers() - Method in class haplotype.WrappedHapPair
nMarkers() - Method in class main.CurrentData: Returns the number of reference data markers.
nMarkers() - Method in interface main.GenotypeValues: Returns the number of markers.
nMarkers() - Method in class phase.EstPhase.HapsGT
nMarkers() - Method in class phase.EstPhase: Returns the number of markers.
nMarkers() - Method in class phase.PhaseData: Returns the number of target markers
nMarkers() - Method in class vcf.AllData
nMarkers() - Method in class vcf.BasicGT
nMarkers() - Method in class vcf.BasicRefGT
nMarkers() - Method in interface vcf.Data: Returns the number of markers in the current window.
nMarkers() - Method in interface vcf.GT: Returns the number of markers.
nMarkers() - Method in class vcf.MarkerMap: Returns the number of markers.
nMarkers() - Method in class vcf.Markers: Returns the number of markers.
nMarkers() - Method in class vcf.SplicedGT
nMarkers() - Method in class vcf.TargetData
nMarkers() - Method in class vcf.Window: Returns the number of markers in this window.
nMarkers() - Method in class vcf.XBasicGT
nMarkers() - Method in class vcf.XBasicGT1
nMarkers() - Method in interface vcf.XGT1: Returns the number of markers.
nMarkersSoFar() - Method in class vcf.AllData
nMarkersSoFar() - Method in interface vcf.Data: Returns the number of markers in the union of the current window and all previous windows.
nMarkersSoFar() - Method in class vcf.TargetData
nMetaInfoLines() - Method in class vcf.VcfHeader: Returns the number of VCF meta-information lines.
nOffspring(int) - Method in class main.Pedigree: Returns the number of offspring of the specified sample.
nonBufferedPrintWriter(File, boolean) - Static method in class blbutil.FileUtil: Returns an unbuffered java.io.PrintWriter writing to the specified file.
nonMajRefIndices() - Method in class vcf.VcfRecGTParser: Returns an array of length this.nAlleles() whose k-th element is the list of haplotype indices carrying the k-th allele if k is a non-major allele, and whose k-th element is null if k is the major allele.
nRecs() - Method in class bref.SeqCoder3: Returns the number of compressed RefGTRec objects.
nRefHaps() - Method in class imp.ImpData: Return the number of reference haplotypes.
nRefHaps() - Method in class main.CurrentData: Returns the number of reference haplotypes.
nRefHaps() - Method in class phase.PhaseData: Return the number of reference haplotypes.
nRefSamples() - Method in class main.CurrentData: Returns the number of reference samples.
nRefSamples() - Method in class vcf.AllData
nRefSamples() - Method in interface vcf.Data: Returns the number of reference samples.
nRefSamples() - Method in class vcf.TargetData
nSamples() - Method in class beagleutil.Samples: Returns the number of samples in this list.
nSamples() - Method in class haplotype.HapPairPhasedGT
nSamples() - Method in class imp.ImputedRecBuilder: Returns the required number of samples in the VCF record.
nSamples() - Method in interface main.GenotypeValues: Returns the number of samples.
nSamples() - Method in class main.Pedigree: Returns the number of samples.
nSamples() - Method in class phase.EstPhase.HapsGT
nSamples() - Method in class phase.EstPhase: Returns the number of samples.
nSamples() - Method in class vcf.BasicGT
nSamples() - Method in class vcf.BasicRefGT
nSamples() - Method in class vcf.BitSetGT
nSamples() - Method in interface vcf.DuplicatesGTRec: Returns the number of samples.
nSamples() - Method in interface vcf.GT: Returns the number of samples.
nSamples() - Method in class vcf.LowMafRefDiallelicGT
nSamples() - Method in class vcf.LowMafRefGT
nSamples() - Method in class vcf.RestrictedVcfWindow: Returns the number of samples.
nSamples() - Method in class vcf.SeqCodedRefGT
nSamples() - Method in class vcf.SplicedGT
nSamples() - Method in class vcf.VcfHeader: Returns the number of samples after sample exclusions.
nSamples() - Method in class vcf.VcfRecGTParser: Returns the number of samples.
nSamples() - Method in class vcf.VcfRecord
nSamples() - Method in class vcf.XBasicGT
nSingles() - Method in class main.Pedigree: Returns the number of single individuals in the list of samples.
nStates() - Method in class imp.ImpIbs: Returns the number of HMM states per marker.
nStates() - Method in class imp.ImpStates: Returns the number of HMM states per marker.
nStates() - Method in class phase.PhaseIbs: Returns the number of HMM states per marker.
nStates() - Method in class phase.PhaseStates: Returns the number of HMM states per marker.
nStates(int) - Method in interface imp.StateProbs: Returns the number of stored HMM states at the specified target marker.
nsteps() - Method in class main.Par: Returns the nsteps parameter.
nSteps() - Method in class imp.ImpIbs: Returns the number of IBS steps in the marker window.
nSteps() - Method in class phase.PhaseIbs: Returns the number of IBS steps in the marker window.
nTargetMarkers() - Method in class vcf.AllData
nTargetMarkers() - Method in interface vcf.Data: Returns the number of target data markers in the current window.
nTargetMarkers() - Method in class vcf.TargetData
nTargetMarkersSoFar() - Method in class vcf.AllData
nTargetMarkersSoFar() - Method in interface vcf.Data: Returns the number of target VCF records in the union of the current window and all previous windows.
nTargetMarkersSoFar() - Method in class vcf.TargetData
nTargetSamples() - Method in class main.CurrentData: Returns the number of target samples.
nTargetSamples() - Method in class vcf.AllData
nTargetSamples() - Method in interface vcf.Data: Returns the number of target samples.
nTargetSamples() - Method in class vcf.TargetData
nTargHaps() - Method in class imp.ImpData: Return the number of target haplotypes.
nTargHaps() - Method in class main.CurrentData: Returns the number of target haplotypes.
nTargHaps() - Method in class phase.PhaseData: Return the number of target haplotypes.
nTargMarkers() - Method in interface imp.StateProbs: Returns the number of target markers.
nTargMarkers() - Method in class imp.StateProbsFactory: Returns the number of target marker.
nTargMarkers() - Method in class main.CurrentData: Returns the number of target data markers.
nTargSamples() - Method in class imp.ImpData: Returns the number of target samples.
nTargSamples() - Method in class phase.PhaseData: Returns the number of target samples.
nthreads() - Method in class main.Par: Returns the nthreads parameter.
nTrios() - Method in class main.Pedigree: Returns the number of parent-offspring trios in the list of samples.
nUnfilteredSamples() - Method in class vcf.VcfHeader: Returns the number of samples before sample exclusions.
nUnphasedHets(int) - Method in class phase.EstPhase: Returns the number of unphased, non-missing heterozygote genotypes.

O

offset() - Method in class bref.BrefBlock: Returns the file offset of the first marker in this bref block.
offspring(int, int) - Method in class main.Pedigree: Returns the sample index of the offspring of the specified sample.
OPPOSITE - beagleutil.Phase
out() - Method in class main.Par: Returns the out parameter.
outPrefix() - Method in class main.WindowWriter: Returns the output file prefix.
overlap() - Method in class main.Par: Return the overlap parameter.
overlap() - Method in class vcf.AllData
overlap() - Method in interface vcf.Data: Returns the number of VCF records in the overlap between the current window and the previous window.
overlap() - Method in class vcf.RestrictedVcfWindow: Returns the number of VCF records in the overlap between the current window and the previous window.
overlap() - Method in class vcf.TargetData
overlap(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.Window: Returns the index of the first marker after the overlap with the preceding marker window.
overlapStart() - Method in class vcf.Window: Returns the index of the first marker in the overlap with the next marker window.

P

PackedIntArray - Class in ints: Class PackedIntArray represents an immutable array of nonnegative integer values, which are stored in compressed form.
PackedIntArray(int[], int) - Constructor for class ints.PackedIntArray: Constructs a new PackedIntArray instance from the specified data.
PackedIntArray(IntList, int) - Constructor for class ints.PackedIntArray: Constructs a new PackedIntArray instance from the specified data.
Pair<F,S> - Class in blbutil: Class Pair represents a pair of ordered objects.
Pair(F, S) - Constructor for class blbutil.Pair: Constructs a Pair instance representing the specified ordered pair of objects.
par() - Method in class imp.ImpData: Returns the command line parameters
par() - Method in class main.CurrentData: Return the analysis parameters.
par() - Method in class phase.PhaseData: Returns the command line parameters
Par - Class in main: Class Parameters represents the parameters for a Beagle analysis.
Par(String[]) - Constructor for class main.Par: Constructs a new Parameters instance from the specified command line arguments.
parse(String) - Static method in class beagleutil.ChromInterval: Returns a ChromInterval instance corresponding to the specified string, or returns null if the specified string does not represent a valid chromosome interval or if the specified string is null.
ped() - Method in class main.CurrentData: Returns the parent-offspring relationships.
ped() - Method in class main.Par: Returns the ped parameter or null if no ped parameter was specified.
ped() - Method in class vcf.AllData
ped() - Method in interface vcf.Data: Returns the pedigree.
ped() - Method in class vcf.TargetData
Pedigree - Class in main: Class Pedigree stores parent-offspring relationships in a list of samples.
Pedigree(Samples, File) - Constructor for class main.Pedigree: Constructs a new NuclearFamilies instance.
pErr(int) - Method in class phase.PhaseData: Returns the probability that the allele carried by the specified target marker cluster matches the allele labeling the latent HMM state.
phase - package phase
phase(EstPhase, int, Regress) - Method in class phase.PhaseBaum1: Estimates and returns phased haploytpes for the specified sample
Phase - Enum in beagleutil: Class Phase represents the equivalence of two phased genotypes for a marker or for a set of markers.
phase_segment() - Method in class main.Par: Returns the phase-segment parameter.
phase_states() - Method in class main.Par: Returns the phase-states parameter.
PhaseBaum1 - Class in phase: Class PhaseBaum1 implements the forward and backward algorithms for a haploid Li and Stephens hidden Markov model.
PhaseBaum1(PhaseData, PhaseIbs) - Constructor for class phase.PhaseBaum1: Creates a PhaseLSBaum instance from the specified data.
phasedAlleles() - Method in class vcf.VcfRecGTParser: Returns the list of phased alleles in the backing VCF record.
phaseData() - Method in class phase.PhaseIbs: Return the data used to phase genotypes in a marker window.
PhaseData - Class in phase: Class PhaseData contains the input data for phasing genotypes.
PhaseData(CurrentData, EstPhase, double, int, long) - Constructor for class phase.PhaseData: Constructs a new ImpData instance from the specified data.
phasedSep - Static variable in class blbutil.Const: The phased allele separator: '|'
PhaseIbs - Class in phase: Class PhaseIbs identifies haplotypes that share a long IBS segment with a specified haplotype.
PhaseIbs(PhaseData) - Constructor for class phase.PhaseIbs: Constructs a new PhaseIbs object from the specified data.
PhaseLS - Class in phase: Class PhaseLS estimated genotypes phase using a haploid Li and Stephens hidden Markov model.
PhaseStates - Class in phase: Class PhaseStates identifies a rolling window of reference haplotypes for a target sample.
PhaseStates(PhaseIbs) - Constructor for class phase.PhaseStates: Constructs a new PhaseIbs object from the specified data.
PL_FORMAT - Static variable in class vcf.VcfRecord: The VCF FORMAT code for phred-scaled genotype likelihood data: "PL".
PlinkGenMap - Class in vcf: Class PlinkGenMap represents a genetic map derived from a PLINK map file with map positions in cM units for one or more chromosomes.
pop() - Method in class ints.IntList: Removes and returns the last entry of this list.
pos() - Method in class bref.BrefBlock: Returns the chromosome position of the first marker in this bref block.
pos() - Method in class imp.ImpData: Return an array of size this.nClusters() containing the the genetic map positions of the target marker clusters.
pos() - Method in class phase.PhaseData: Returns the array of genetic map positions whose k-th element equals this.pos(k).
pos() - Method in class vcf.BasicMarker
pos() - Method in interface vcf.Marker: Returns the chromosome position coordinate.
pos(int) - Method in class imp.ImpData: Return the genetic map position of the specified target marker cluster.
PositionMap - Class in vcf: Class PositionMap represents a genetic map obtained by multiplying chromosome position by a scale factor.
PositionMap(double) - Constructor for class vcf.PositionMap: Constructs a new PositionMap instance.
pRecomb() - Method in class phase.PhaseData: Return a FloatArray of size this.nTargMarkers() whose k-th element is the factor multiplied by genetic distance to obtain the probability of transitioning to a random HMM state between the k-th target marker and the previous marker.
pRecomb(int) - Method in class imp.ImpData: Return the probability of recombination between the specified target marker cluster and the previous target marker cluster.
pRecomb(Markers, double) - Method in interface vcf.GeneticMap: Returns the an array of length hapPairs.nMarkers() whose whose j-th element for j > 0 is the probability of recombination between marker j - 1 and marker j.
PREFIX - Static variable in class vcf.VcfMetaInfo: The VCF meta-information line prefix: "##"
prevSpliceStart() - Method in class main.CurrentData: Returns the first marker index after the splice point with the previous marker window.
prevTargetSpliceStart() - Method in class main.CurrentData: Returns the first target marker index after the splice point with the previous marker window.
print(ImpData, AtomicReferenceArray<StateProbs>, int, int) - Method in class main.WindowWriter: Prints the data in alProbs for markers with index between refStart (inclusive) and refEnd (exclusive) to the output VCF file: this.outPrefix() + ".vcf.gz".
print(GT, int, int, int) - Method in class main.WindowWriter: Writes the data in phased genotypes for the specified markers to the output VCF file: this.outPrefix() + ".vcf.gz".
printDS() - Method in class vcf.VcfRecBuilder: Returns true if the FORMAT field in the VCF record for this marker includes a DS subfield, and false otherwise
printFixedFieldsGT(Marker, PrintWriter) - Static method in class vcf.VcfWriter: Prints the first 9 VCF record fields for the specified marker to the specified PrintWriter.
printGP() - Method in class vcf.VcfRecBuilder: Returns true if the FORMAT field in the VCF record for this marker includes a GP subfield, and false otherwise
printGV(CurrentData, GenotypeValues) - Method in class main.WindowWriter: Prints VCF records with GT and GP format fields for markers with index between cd.lastSplice() (inclusive) and cd.nextSplice() (exclusive).
printImputationUpdate() - Method in class main.RunStats: Prints run time for most recent imputation to a log file and to standard output.
printIterationUpdate(int, int) - Method in class main.RunStats: Prints information about the specified iteration.
println(String) - Method in class main.RunStats: Prints the specified string to the log file and to standard out.
printMemoryUse(String) - Static method in class blbutil.Utilities: Prints a summary of memory use at the time of method invocation to standard output.
printPhasingIterationUpdate(int, boolean, long) - Method in class main.RunStats
printRec(PrintWriter, boolean) - Method in class imp.ImputedRecBuilder: Prints the VCF record to the specified PrintWriter.
printSampleSummary(Data) - Method in class main.RunStats: Prints information about the samples to a log file and to standard output.
printStartInfo() - Method in class main.RunStats: Prints initial information about the analysis to a log file and to standard output.
printSummaryAndClose(int, int) - Method in class main.RunStats: Prints information about the complete analysis to a log file and to standard output, and closes the log file.
printWindowUpdate(Data) - Method in class main.RunStats: Prints information about the marker window to a log file and to standard output.
printWriter(File) - Static method in class blbutil.FileUtil: Returns a buffered java.io.PrintWriter writing to the specified file.
printWriter(File, boolean) - Static method in class blbutil.FileUtil: Returns a buffered java.io.PrintWriter writing to the specified file.
probs(int, int) - Method in interface imp.StateProbs: Returns the probability of the specified state at the specified target marker.
probsP1(int, int) - Method in interface imp.StateProbs: Returns the probability of the specified state at the marker following the specified target marker.
PROGRAM - Static variable in class main.Main
put(int, E) - Method in class ints.IntMap: Adds the specified key and value to this map.

Q

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

R

R2Estimator - Class in vcf: Class R2Estimator estimates the correlation between the estimated allele dose and true allele dose for a set of genotypes.
R2Estimator() - Constructor for class vcf.R2Estimator: Constructs a new R2Estimator instance.
randomAccessFile(File, String) - Static method in class blbutil.FileUtil: Returns a java.io.RandomAccessFile to read from or optionally to write to the specified file.
rec(int) - Method in class vcf.Window: Returns the specified record.
recList() - Method in class vcf.Window: Returns the list of recList in this window.
recodeIfLowFreq(RefGTRec) - Static method in class vcf.RefIt
ref() - Method in class main.Par: Returns the ref parameter or null if no ref parameter was specified.
refClusterEnd(int) - Method in class imp.ImpData: Returns the index of the reference marker corresponding to the end (exclusive) of the specified target marker cluster.
refClusterStart(int) - Method in class imp.ImpData: Returns the index of the reference marker corresponding to the start (inclusive) of the specified target marker cluster.
refGT() - Method in class imp.ImpData: Return the reference genotype data
refGT() - Method in class imp.RefHapHash: Returns the phased reference genotypes.
refGT() - Method in class main.CurrentData: Returns the phased, nonmissing reference genotype data or null if there are no reference data.
refGT() - Method in class vcf.AllData
refGT() - Method in interface vcf.Data: Returns the phased, nonmissing reference genotype data for the current window, or null if there are no reference data
refGT() - Method in class vcf.TargetData
RefGT - Interface in vcf: Interface RefGT represents phased, compressed, nonmissing genotype data for a list of markers and a list of reference samples.
RefGTRec - Interface in vcf: Interface RefGTRec represents represents phased genotype data for one marker.
refHap(int, int) - Method in interface imp.StateProbs: Returns the specified reference haplotype index.
RefHapHash - Class in imp: Class RefHapHash stores a hash code for each haplotype in a sublist of reference haplotypes.
RefHapHash(AtomicReferenceArray<StateProbs>, int, RefGT, int, int) - Constructor for class imp.RefHapHash: Constructs a new RefHapHash instance for the specified data.
refHapPairs() - Method in class imp.HaplotypeCoder: Returns the phased reference genotypes at the target markers.
refHapPairs() - Method in class vcf.AllData
refHapPairs() - Method in interface vcf.Data: Returns a list of the reference haplotype pairs for the current window.
refHapPairs() - Method in class vcf.TargetData
RefIt - Class in vcf: Class RefIt represents an iterator whose next() method returns an object storing data from a VCF record with phased, non-missing genotypes.
refSamples() - Method in class main.CurrentData: Returns the list of reference samples, or null if there are no reference samples.
refSamples() - Method in class vcf.AllData
refSamples() - Method in interface vcf.Data: Returns the list of reference samples, or null if there are no reference samples.
refSamples() - Method in class vcf.TargetData
Regress - Class in math: Class Regress estimates a regression coefficient.
Regress() - Constructor for class math.Regress: Constructs a new Regress instance.
relateds() - Method in class main.Pedigree: Returns an array of indices of samples with at least one parent or child in the list or samples.
remove() - Method in class blbutil.InputIt: The remove method is not supported by this iterator.
remove() - Method in class vcf.IntervalVcfIt: The remove method is not supported by this iterator.
remove() - Method in class vcf.RefIt: The remove method is not supported by this iterator.
remove() - Method in class vcf.VcfIt: The remove method is not supported by this iterator.
remove(int) - Method in class ints.IntMap: Removes the specified key from this map, and returns the value previously associated with the key or null if no such value exists.
remove(int) - Method in class ints.IntSet: Removes the specified element from this set.
reset(Marker, boolean, boolean) - Method in class vcf.VcfRecBuilder: Clears existing data, and sets the current marker to the specified marker.
restrict(int, int) - Method in class vcf.Markers: Returns a Markers instance that represents the specified range of marker indices.
restrictedRefHapPairs() - Method in class vcf.AllData
restrictedRefHapPairs() - Method in interface vcf.Data: Returns a list of reference haplotype pairs that are restricted to the target data markers in the current window.
restrictedRefHapPairs() - Method in class vcf.TargetData
RestrictedVcfWindow - Class in vcf: Class RestrictedVcfWindow represents a sliding window of VCF records.
RestrictedVcfWindow(SampleFileIt<? extends GTRec>) - Constructor for class vcf.RestrictedVcfWindow: Construct a new RestrictedVcfWindow instance.
restrictRefGT() - Method in class main.CurrentData: Returns the phased, nonmissing reference genotype data for the target data markers or null if there are no reference data.
restrictRefGT() - Method in class vcf.AllData
restrictRefGT() - Method in interface vcf.Data: Returns the phased, nonmissing reference genotype data for the target data markers in the current window.
restrictRefGT() - Method in class vcf.TargetData
run(int, int) - Method in class imp.HaplotypeCoder: Returns an array mapping haplotype indices to allele sequence indices in the specified marker interval.
run(PhaseData, EstPhase, Regress) - Static method in class phase.PhaseLS: Estimates and stores phased haplotypes for the target samples.
run(GT, GT, double, long) - Static method in class sample.InitTargHapPairs: Returns initial target haplotype pairs.
RunStats - Class in main: Class RunStats contains methods for storing and printing statistics describing a Beagle analysis.

S

sample - package sample
sampleCnt() - Method in class imp.ImputedRecBuilder: Returns the number of times the this.addSampleData() method has been invoked.
sampleData(int) - Method in class vcf.VcfRecord: Returns the data for the specified sample.
sampleData(int, int) - Method in class vcf.VcfRecord: Returns the specified data for the specified sample.
sampleData(int, String) - Method in class vcf.VcfRecord: Returns the specified data for the specified sample.
SampleFileIt<E> - Interface in blbutil: An iterator for records in a file.
sampleFilter(File) - Static method in class vcf.FilterUtil: Returns a filter that excludes samples that have an identifier that matches a line of the specified file, or returns null if the excludeSamplesFile parameter is null
sampleIds() - Method in class vcf.VcfHeader: Returns this.sample().ids().
SampleIds - Class in beagleutil: Class SampleIds is a singleton class that represents a list of sample identifiers.
samples() - Method in interface blbutil.SampleFileIt: Returns the list of samples.
samples() - Method in class bref.AsIsBref3Writer
samples() - Method in class bref.Bref3It
samples() - Method in interface bref.BrefWriter: Returns the list of samples.
samples() - Method in class bref.CompressBref3Writer
samples() - Method in class bref.SeqCoder3: Returns the list of samples whose phased genotype data will be compressed.
samples() - Method in class haplotype.HapPairPhasedGT
samples() - Method in interface main.GenotypeValues: Returns the list of samples.
samples() - Method in class main.Pedigree: Returns the list of samples.
samples() - Method in class main.WindowWriter: Returns the samples whose data is written by this.
samples() - Method in class phase.EstPhase.HapsGT
samples() - Method in class phase.EstPhase: Returns the list of target samples.
samples() - Method in class vcf.BasicGT
samples() - Method in class vcf.BasicRefGT
samples() - Method in class vcf.BitSetGT
samples() - Method in interface vcf.GT: Returns the list of samples.
samples() - Method in interface vcf.GTRec: Returns the list of samples.
samples() - Method in class vcf.IntervalVcfIt
samples() - Method in class vcf.LowMafRefDiallelicGT
samples() - Method in class vcf.LowMafRefGT
samples() - Method in class vcf.RefIt
samples() - Method in class vcf.RestrictedVcfWindow: Returns the list of samples.
samples() - Method in class vcf.SeqCodedRefGT
samples() - Method in class vcf.SplicedGT
samples() - Method in class vcf.VcfHeader: Return the list of samples after sample exclusions.
samples() - Method in class vcf.VcfIt
samples() - Method in class vcf.VcfRecGTParser: Returns the list of samples.
samples() - Method in class vcf.VcfRecord
samples() - Method in class vcf.WindowIt: Returns the list of samples.
samples() - Method in class vcf.XBasicGT
Samples - Class in beagleutil: Class Samples stores a list of samples.
Samples(int[]) - Constructor for class beagleutil.Samples: Constructs a new instance of Samples corresponding to the specified list of sample identifier indices.
scaleFactor() - Method in class vcf.PositionMap: Returns the scale factor that is multiplied by the chromosome position to obtain the corresponding genetic map position
second() - Method in class blbutil.Pair: Returns the second object in the ordered pair of objects.
seed() - Method in class main.Par: Returns the seed parameter.
seed() - Method in class phase.PhaseData: Returns the seed for generating random numbers.
semicolon - Static variable in class blbutil.Const: The semicolon character: ';'
SEQ_CODED - Static variable in class bref.AsIsBref3Writer: The byte value denoting a sequence coded record
SeqCodedRefGT - Class in vcf: Class SeqCodedRefGT represents phased, non-missing genotypes for a list of reference samples at a single marker.
SeqCodedRefGT(Marker, Samples, IntArray, IntArray) - Constructor for class vcf.SeqCodedRefGT: Creates a new SeqCodedRefGT instance with phased, non-missing genotypes from the specified marker, samples, and haplotype alleles.
SeqCoder3 - Class in bref: Class SeqCoder3 compresses a sequence of allele-coded RefGTRec objects.
SeqCoder3(Samples) - Constructor for class bref.SeqCoder3: Constructs a new SeqCoder3 for the specified samples.
SeqCoder3(Samples, int) - Constructor for class bref.SeqCoder3: Constructs a new SeqCoder3 for the specified samples.
set(int, float) - Method in class blbutil.FloatList: Replaces the element at the specified position in this list with the specified element.
set(int, int) - Method in class ints.IntList: Replaces the element at the specified position in this list with the specified element.
setAlleles(int, int[]) - Method in class imp.RefHapHash: Copies the alleles between this.start() (inclusive) and this.end() (exclusive) of the specified haplotype in the sublist of reference haplotypes to the specified array.
setCapacity(int) - Method in class ints.IntSet: Sets the capacity of this list to the specified value.
setHapPair(int, int[], int[]) - Method in class phase.EstPhase: Sets the haplotype pair for the specified sample to the specified haplotypes.
setHapsWithMaskedMissingAlleles(int, int[], int[]) - Method in class phase.EstPhase: Sets the k-th element of the specified hap1 and hap2 arrays to the specified sample's phased genotype at the k-th marker if the genotype is nonmissing, and sets the k-th element of hap1 and hap2 to -1 otherwise.
setUnphasedHets(int, IntArray) - Method in class phase.EstPhase: Sets the array with marker indices of unphased, nonmissing heterozygote genotypes to the specified array.
SHORT_HELP - Static variable in class main.Main: The program name and a brief help message.
shuffle(int[], int, Random) - Static method in class blbutil.Utilities: Shuffles the specified array so that a random set of ${code nElements} from the array are the first elements.
shuffle(int[], Random) - Static method in class blbutil.Utilities: Randomly shuffles the elements of the specified array.
single(int) - Method in class main.Pedigree: Returns the sample index of the specified single individual.
singles() - Method in class main.Pedigree: Returns an array of indices of samples with no parents or children in the list of samples.
size() - Method in class beagleutil.ChromIds: Returns the number of indexed chromosomes identifiers.
size() - Method in class beagleutil.SampleIds: Returns the number of indexed sample identifiers.
size() - Method in class beagleutil.ThreadSafeIndexer: Returns the number of indexed objects.
size() - Method in class blbutil.FloatArray: Returns the number of elements in this list.
size() - Method in class blbutil.FloatList: Returns the number of elements in this list.
size() - Method in class ints.CharArray
size() - Method in class ints.IndexArray
size() - Method in interface ints.IntArray: Returns the number of elements in this IntArray.
size() - Method in class ints.IntList: Returns the number of elements in this list.
size() - Method in class ints.IntMap: Returns the number of keys in this map.
size() - Method in class ints.IntSet: Returns the number of elements in this set.
size() - Method in class ints.LongArray: Returns the number of elements in this LongArray.
size() - Method in class ints.PackedIntArray
size() - Method in class ints.UnsignedByteArray
size() - Method in class ints.WrappedIntArray
size() - Method in class vcf.BitSetGT
size() - Method in interface vcf.DuplicatesGTRec: Returns the number of haplotypes.
size() - Method in class vcf.LowMafRefDiallelicGT
size() - Method in class vcf.LowMafRefGT
size() - Method in class vcf.SeqCodedRefGT
size() - Method in class vcf.VcfRecord
sort() - Method in class ints.IntList: Sorts the elements of this list in increasing order
SplicedGT - Class in vcf: Class SplicedGT represents genotype emission probabilities for a set of samples.
SplicedGT(GT, GT) - Constructor for class vcf.SplicedGT: Constructs a new SplicedGL instance.
start() - Method in class beagleutil.ChromInterval: Returns the first genome coordinate in this chromosome interval.
start() - Method in interface beagleutil.IntInterval: Returns the start of the interval (inclusive).
start() - Method in class imp.RefHapHash: Returns the starting reference marker index (inclusive) for the reference haplotype allele sequences.
stateProbs(int, int, int[][], float[][]) - Method in class imp.StateProbsFactory: Stores the reference haplotypes and state probabilities that will be used to imputed missing state probabilities using linear interpolation.
stateProbs(ImpData) - Static method in class imp.ImpLS: Returns estimated HMM state probabilities at genotyped markers for each target haplotype.
StateProbs - Interface in imp: Class StateProbs stores a subset of Li and Stephens HMM states and associated probabilities for a target haplotype.
StateProbsFactory - Class in imp: Class StateProbsFactory stores HMM state probabilities that that can be used to imputed impute missing HMM state probabilities using linear interpolation.
StateProbsFactory(int) - Constructor for class imp.StateProbsFactory: Creates an StateProbsFactory instance from the specified data.
stdOutPrintWriter() - Static method in class blbutil.FileUtil: Returns a java.io.PrintWriter that writes to standard out.
step() - Method in class main.Par: Returns the step parameter.
stepStart(int) - Method in class imp.ImpIbs: Returns the index of the first marker in the specified step.
stepStart(int) - Method in class phase.PhaseIbs: Returns the first marker index in the specified step.
storeAlleles(BitSet, BitSet, BitSet, BitSet, BitSet) - Method in class vcf.VcfRecGTParser: Stores the genotypes genotypes in the specified BitSets.
stream() - Method in class ints.IntList: Returns an IntStream containing the sequence of elements in this list.
stringArg(String, Map<String, String>, boolean, String, String[]) - Static method in class blbutil.Validate: Removes the specified key from the specified map, and returns the string value corresponding to the specified key.
StringUtil - Class in blbutil: Class StringUtil is a utility class with static methods for counting and returning delimited fields in a string.
sumAlleles() - Method in class vcf.Markers: Returns this.sumAlleles(this.nMarkers()).
sumAlleles(int) - Method in class vcf.Markers: Returns the sum of the number of alleles for the markers with index less than the specified index.
sumGenotypes() - Method in class vcf.Markers: Returns this.sumGenotypes(this.nMarkers()).
sumGenotypes(int) - Method in class vcf.Markers: Returns the sum of the number of possible genotypes for the markers with index less than the specified index.
sumHaplotypeBits() - Method in class vcf.Markers: Returns this.sumHaplotypeBits(this.nMarkers()).
sumHaplotypeBits(int) - Method in class vcf.Markers: Returns the number of bits requires to store a haplotype for the markers with index less than the specified index.

T

tab - Static variable in class blbutil.Const: The tab character: '\t'
targClusterEnd(int) - Method in class imp.ImpData: Returns the target marker index corresponding to the end (exclusive) of the specified marker cluster.
targClusterStart(int) - Method in class imp.ImpData: Returns the target marker index corresponding to the start (inclusive) of the specified marker cluster.
targetData(Par, Supplier<SampleFileIt<GTRec>>) - Static method in class vcf.TargetData: Constructs and returns a new TargetData instance from VcfRecords returned by the specified SampleFileIt objects.
TargetData - Class in vcf: Class TargetData represents a sliding window of target VCF records.
targetMarkerIndex(int) - Method in class vcf.AllData
targetMarkerIndex(int) - Method in interface vcf.Data: Returns the target data marker index corresponding to the specified marker, or returns -1 if no corresponding target data marker exists.
targetMarkerIndex(int) - Method in class vcf.TargetData
targetMarkers() - Method in class vcf.AllData
targetMarkers() - Method in interface vcf.Data: Returns the list of target data markers in the current window.
targetMarkers() - Method in class vcf.TargetData
targetOverlap() - Method in class vcf.AllData
targetOverlap() - Method in interface vcf.Data: Returns the number of target data markers in the overlap between the current marker window and the previous marker window.
targetOverlap() - Method in class vcf.TargetData
targetSamples() - Method in class vcf.AllData
targetSamples() - Method in interface vcf.Data: Returns the list of target samples.
targetSamples() - Method in class vcf.TargetData
targGT() - Method in class imp.ImpData: Return the phased target genotype data.
targGT() - Method in class main.CurrentData: Returns the genotype likelihoods for the target samples at the target data markers.
targGT() - Method in class vcf.AllData
targGT() - Method in interface vcf.Data: Returns the genotype likelihoods for the target samples restricted to the target data markers in the current window.
targGT() - Method in class vcf.TargetData
targHap() - Method in interface imp.StateProbs: Returns the target haplotype index.
targHapPairs() - Method in class imp.HaplotypeCoder: Returns the phased target genotypes.
targMarker() - Method in class imp.RefHapHash: Returns the target marker.
targMarkerIndex(int) - Method in class main.CurrentData: Returns the index of the specified marker in the target data, or returns -1 if the marker is not present in the target data.
targMarkerIndices() - Method in class main.CurrentData: Returns an array of length this.nMarkers() whose k-th element is the index of the k-th marker in the list of target markers or is -1 if the marker is not present in the target data.
targMarkers() - Method in class main.CurrentData: Returns the list of target data markers.
targSamples() - Method in class imp.ImpData: Returns the list of target samples.
targSamples() - Method in class main.CurrentData: Returns the list of target samples.
tempFile(String) - Static method in class blbutil.FileUtil: Returns a temporary File that will be deleted when the Java virtual machine exits.
tempFile(String, File) - Static method in class blbutil.FileUtil: Creates and returns a new empty temporary file in the specified directory.
ThreadSafeIndexer<T> - Class in beagleutil: Class ThreadSafeIndexer indexes objects.
ThreadSafeIndexer() - Constructor for class beagleutil.ThreadSafeIndexer: Creates a new ThreadSafeIndexer instance with the default initial capacity.
ThreadSafeIndexer(int) - Constructor for class beagleutil.ThreadSafeIndexer: Creates a new ThreadSafeIndexerinstance with the specified initial capacity.
timeStamp() - Static method in class blbutil.Utilities: Returns the current local time as a string.
toArray() - Method in class blbutil.FloatArray: Returns an integer array containing the sequence of elements in this list.
toArray() - Method in class blbutil.FloatList: Returns an integer array containing the sequence of elements in this list.
toArray() - Method in class ints.IntList: Returns an integer array containing the sequence of elements in this list.
toArray() - Method in class ints.IntSet: Returns an array containing the elements in this set.
toArray(IntArray) - Static method in interface ints.IntArray: Returns a copy of the specified array.
toArray(LongArray) - Static method in class ints.LongArray: Returns a copy of the specified array.
toBitSetGT - Static variable in class vcf.VcfIt: A function mapping a string VCF record with GT format fields to a GTRec object.
toGLRec - Static variable in class vcf.VcfIt: A function mapping a string VCF record with GL format fields to a VcfRecord object.
toGTGLRec - Static variable in class vcf.VcfIt: A function mapping a string VCF record with GT or GL format fields to a VcfRecord object.
toList(AtomicReferenceArray<E>) - Static method in class main.MainHelper
toString() - Method in class beagleutil.ChromIds: Returns java.util.Arrays.toString(this.ids()).
toString() - Method in class beagleutil.ChromInterval: Returns the string: this.chrom() + ":" + this.start() + "-" + this.end()
toString() - Method in class beagleutil.SampleIds: Returns java.util.Arrays.toString(this.ids()).
toString() - Method in class beagleutil.Samples: Returns java.util.Arrays.toString(this.ids()).
toString() - Method in class beagleutil.ThreadSafeIndexer: Returns this.items().toString().
toString() - Method in interface blbutil.FileIt: Returns a string representation of this.
toString() - Method in class blbutil.FloatArray: Returns a string representation of this list that is obtained by calling java.util.Arrays.toString(this.toArray()).
toString() - Method in class blbutil.FloatList: Returns a string representation of this list.
toString() - Method in class blbutil.InputIt: Returns a string representation of this iterator.
toString() - Method in class blbutil.Pair: Returns a string representation of this.
toString() - Method in class bref.Bref3It
toString() - Method in class bref.Bref3Reader
toString() - Method in class bref.BrefBlock: Returns a string description of this.
toString() - Method in class haplotype.BitHapPair: Returns a string representation of this.
toString() - Method in class ints.IntList: Returns java.util.Arrays.toString(this.toArray())
toString() - Method in class ints.IntMap: Returns java.util.Arrays.toString(this.keys()).
toString() - Method in class ints.IntSet: Returns java.util.Arrays.toString(this.toArray()).
toString() - Method in class ints.UnsignedByteArray
toString() - Method in class ints.WrappedIntArray
toString() - Method in interface main.GenotypeValues: Returns a string representation of this.
toString() - Method in class main.Pedigree: Returns a string representation of this.
toString() - Method in class vcf.AllData: Returns a string representation of this.
toString() - Method in class vcf.BasicGT
toString() - Method in class vcf.BasicMarker
toString() - Method in class vcf.BitSetGT: Returns the data represented by this as a VCF record with a GT format field.
toString() - Method in interface vcf.GeneticMap: Returns a string representation of this genetic map.
toString() - Method in class vcf.LowMafRefDiallelicGT: Returns the data represented by this as a VCF record with a GT format field.
toString() - Method in class vcf.LowMafRefGT: Returns the data represented by this as a VCF record with a GT format field.
toString() - Method in interface vcf.Marker: Returns a string equal to the first five tab-delimited fields of a VCF record corresponding to this marker.
toString() - Method in class vcf.Markers: Returns a string representation of this.
toString() - Method in class vcf.PlinkGenMap
toString() - Method in class vcf.RefIt
toString() - Method in class vcf.RestrictedVcfWindow: Returns a string representation of this.
toString() - Method in class vcf.SeqCodedRefGT: Returns the data represented by this as a VCF record with a GT format field.
toString() - Method in class vcf.SplicedGT
toString() - Method in class vcf.TargetData: Returns a string representation of this.
toString() - Method in class vcf.VcfHeader: Returns the VCF meta-information lines and the VCF header line used to construct this.
toString() - Method in class vcf.VcfIt
toString() - Method in class vcf.VcfMetaInfo: Returns the VCF meta-information line represented by this.
toString() - Method in class vcf.VcfRecord: Returns the VCF record.
toString() - Method in class vcf.WindowIt: Returns a string representation of this.
toString() - Method in class vcf.XBasicGT
toString() - Method in class vcf.XBasicGT1
toString() - Method in interface vcf.XGT1: Returns a string representation of this.
toVcfRec(GTRec) - Static method in interface vcf.GTRec: Returns a VCF record corresponding to the specified GTRec object.
toVcfRecord - Static variable in class vcf.VcfIt: A function mapping a string VCF record with GT or GL format fields to a VcfRecord object.
trioFather(int) - Method in class main.Pedigree: Returns the sample index of the father of the specified parent-offspring trio.
trioMother(int) - Method in class main.Pedigree: Returns the sample index of the mother of the specified parent-offspring trio.
trioOffspring(int) - Method in class main.Pedigree: Returns the sample index of the offspring of the specified parent-offspring trio.
truncate(int) - Method in class ints.IntList: Truncates this list of integer by removing all elements whose index is greater than or equal to the specified size.
truth() - Method in class main.Par: Returns the truth parameter

U

UnBref3 - Class in bref: Class UnBref3 converts files in bref version 3 format into VCF format.
UnBref3() - Constructor for class bref.UnBref3
unfilteredSampleIndex(int) - Method in class vcf.VcfHeader: Returns the index of the specified sample in the the list original list of samples before sample exclusions.
UNKNOWN - beagleutil.Phase
unphasedSep - Static variable in class blbutil.Const: The unphased allele separator: '/'
UnsignedByteArray - Class in ints: Class ShiftedByteIndexArray represents an immutable array of integer values between 0 and 255 inclusive that is stored as 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.
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.
value(int, int, int) - Method in interface main.GenotypeValues: Returns the specified genotype value.
valueOf(String) - Static method in enum beagleutil.Phase: Returns the enum constant of this type with the specified name.
values() - Static method in enum beagleutil.Phase: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class ints.IntMap: Returns a list containing the values in this map.
valueSize() - Method in class ints.IndexArray: Returns the value size that was specified at construction.
valueSize(int[]) - Static method in class ints.IndexArray: Returns the minimum integer that is greater than all elements in the specified array of non-negative values.
valueSize(IntArray) - Static method in class ints.IndexArray: Returns the minimum integer that is greater than all elements in the specified list of non-negative values.
vcf - package vcf
vcfHeader() - Method in class vcf.VcfRecGTParser: Returns the VCF meta-information lines and header line for the backing VCF record
vcfHeader() - Method in class vcf.VcfRecord: Returns the VCF meta-information lines and the VCF header line.
VcfHeader - Class in vcf: Class VcfHeader represents the Variant Call Format (VCF) meta-information lines and the Variant Call Format header line that precede the first Variant Call Format record.
VcfHeader(FileIt<String>) - Constructor for class vcf.VcfHeader: Constructs a new VcfHeader object from the VCF meta-information lines and the VCF header line returned by the specified FileIterator<String>.
VcfHeader(FileIt<String>, Filter<String>) - Constructor for class vcf.VcfHeader: Constructs a new VcfHeader object from the VCF meta-information lines and the VCF header line returned by the specified FileIterator<String>.
VcfIt<E extends MarkerContainer> - Class in vcf: Class VcfIt represents an iterator whose next() method returns an object storing data from a VCF record.
VcfMetaInfo - Class in vcf: Class VcfMetaInfo represents a VCF meta-information line.
VcfMetaInfo(String) - Constructor for class vcf.VcfMetaInfo: Constructs a VcfMetaInfo instance representing the specified VCF meta-information line.
VcfRecBuilder - Class in vcf: Class VcfRecBuilder contains methods for constructing and printing a VCF record in VCF 4.2 format.
VcfRecBuilder() - Constructor for class vcf.VcfRecBuilder: Constructs a new VcfRecBuilder instance with initial buffer size equal to VcfRecBuilder.DEFAULT_INIT_SIZE.
VcfRecBuilder(int) - Constructor for class vcf.VcfRecBuilder: Constructs a new VcfRecBuilder instance with the specified initial buffer size.
VcfRecGTParser - Class in vcf: Class VcfRecGTParser parses VCF records and extracts the GT format field.
VcfRecGTParser(VcfHeader, String) - Constructor for class vcf.VcfRecGTParser: Constructs a new VcfRecGTParser object from the specified VCF record.
vcfRecord() - Method in class vcf.VcfRecGTParser: Returns the backing VCF record.
VcfRecord - Class in vcf: Class VcfRecord represents a VCF record.
VcfWriter - Class in vcf: Class VcfWriter contains static methods for writing data in VCF 4.2 format.
VERSION - Static variable in class main.Main: The program name and version.

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.CurrentData: Returns the marker window index.
window() - Method in class main.Par: Returns the window parameter.
Window<E extends GTRec> - Class in vcf: Class Window represents a window of VCF recList.
Window(List<E>, int, int, boolean, boolean) - Constructor for class vcf.Window: Constructs a new Window instance from the specified data.
windowIndex() - Method in class vcf.AllData
windowIndex() - Method in interface vcf.Data: Returns the current window index.
windowIndex() - Method in class vcf.TargetData
WindowIt<E extends GTRec> - Class in vcf: Class WindowIt represents a sliding window of VCF recList.
WindowWriter - Class in main: Class WindowWriter writes VCF and IBD output data.
WindowWriter(Samples, String) - Constructor for class main.WindowWriter: Constructs a new WindowWriter object.
WrappedHapPair - Class in haplotype: Class WrappedHapPair is a HapPair instance that wraps a RefGTWindow object.
WrappedHapPair(GT, int) - Constructor for class haplotype.WrappedHapPair: Creates a WrappedHapPair instance representing the specified haplotype pair.
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.
write(byte[]) - Method in class blbutil.BGZIPOutputStream
write(byte[], int, int) - Method in class blbutil.BGZIPOutputStream
write(int) - Method in class blbutil.BGZIPOutputStream
write(RefGTRec) - Method in class bref.AsIsBref3Writer
write(RefGTRec) - Method in interface bref.BrefWriter: Writes the specified phased genotype data in binary reference format.
write(RefGTRec) - Method in class bref.CompressBref3Writer
writeMetaLines(String[], String, boolean, boolean, boolean, boolean, PrintWriter) - Static method in class vcf.VcfWriter: Writes VCF meta-information lines and header line to the specified PrintWriter.
writeMetaLinesGT(String[], String, PrintWriter) - Static method in class vcf.VcfWriter: Writes VCF meta-information lines and header line to the specified PrintWriter.
writeRec(PrintWriter, boolean) - Method in class vcf.VcfRecBuilder: Prints the current VCF record for the current marker to the specified PrintWriter.

X

XBasicGT - Class in vcf: Class XBasicGT represents genotype and genotype emission probabilities for a set of samples optimized by sample.
XBasicGT(GT, Pedigree) - Constructor for class vcf.XBasicGT: Constructs a XBasicGT instance from the specified data.
XBasicGT1 - Class in vcf: Class XBasicGT1 represents genotype likelihoods for one sample.
XBasicGT1(GT, int) - Constructor for class vcf.XBasicGT1: Constructs a XBasicGL1 instance from the specified data.
XBasicGT1(GT, int, int, int) - Constructor for class vcf.XBasicGT1: Constructs a XBasicGL1 instance from the specified data.
XGT1 - Interface in vcf: Interface XGT1 (Genotype Likelihoods) represents genotype likelihoods for one sample.

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