Package main

Class WindowWriter

java.lang.Object

main.WindowWriter

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable

public class WindowWriter
extends java.lang.Object
implements java.io.Closeable

Class WindowWriter writes VCF and IBD output data.

Instances of class WindowWriter are not thread-safe.

Constructor Summary

Constructors

Constructor	Description
WindowWriter(Samples samples, java.lang.String outPrefix)	Constructs a new WindowWriter object.

Method Summary

Modifier and Type	Method	Description
void	close()
java.lang.String	outPrefix()	Returns the output file prefix.
void	print(ImpData impData, java.util.concurrent.atomic.AtomicReferenceArray<StateProbs> stateProbs, int refStart, int refEnd)	Prints the data in alProbs for markers with index between refStart (inclusive) and refEnd (exclusive) to the output VCF file: this.outPrefix() + ".vcf.gz".
void	print(GT phasedTarg, int start, int end, int nThreads)	Writes the data in phased genotypes for the specified markers to the output VCF file: this.outPrefix() + ".vcf.gz".
void	printGV(CurrentData cd, GenotypeValues gv)	Prints VCF records with GT and GP format fields for markers with index between cd.lastSplice() (inclusive) and cd.nextSplice() (exclusive).
Samples	samples()	Returns the samples whose data is written by this.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

WindowWriter

public WindowWriter(Samples samples,
                    java.lang.String outPrefix)

Constructs a new WindowWriter object.

Parameters:

samples - the sample whose data will be printed

outPrefix - the output file prefix

Throws:

java.lang.IllegalArgumentException - if outPrefix.length() == 0

java.lang.NullPointerException - if samples == null || outPrefix == null

Method Detail

outPrefix

public java.lang.String outPrefix()

Returns the output file prefix.

Returns:

the output file prefix

samples

public Samples samples()

Returns the samples whose data is written by this.

Returns:

the samples whose data is written by this

printGV

public void printGV(CurrentData cd,
                    GenotypeValues gv)

Prints VCF records with GT and GP format fields for markers with index between cd.lastSplice() (inclusive) and cd.nextSplice() (exclusive).

Parameters:

cd - the input data for the current marker window

gv - scaled genotype probabilities for the target samples

Throws:

java.lang.NullPointerException - if cd == null || gv == null

print

public void print(ImpData impData,
                  java.util.concurrent.atomic.AtomicReferenceArray<StateProbs> stateProbs,
                  int refStart,
                  int refEnd)

Prints the data in alProbs for markers with index between refStart (inclusive) and refEnd (exclusive) to the output VCF file: this.outPrefix() + ".vcf.gz".

Parameters:

impData - the input data for genotype imputation

stateProbs - the imputed state probabilities

refStart - the starting ref marker index (inclusive)

refEnd - the ending ref marker index (exclusive)

Throws:

java.lang.IllegalArgumentException - if stateProbs.size() != impData.nTargHaps()

java.lang.IndexOutOfBoundsException - if refStart < 0 || refEnd > impData.refGT().nMarkers()

java.lang.NullPointerException - if impData==null || stateProbs==null

java.lang.NullPointerException - if any element of stateProbs is null

print

public void print(GT phasedTarg,
                  int start,
                  int end,
                  int nThreads)

Writes the data in phased genotypes for the specified markers to the output VCF file: this.outPrefix() + ".vcf.gz".

Parameters:

phasedTarg - the estimated target haplotypes

start - the starting marker index (inclusive)

end - the ending marker index (exclusive)

nThreads - the number of parallel threads to use

Throws:

java.lang.IllegalArgumentException - if isImputed.length != alProbs.nMarkers()

java.lang.IllegalArgumentException - if phasedTarg.isPhased() == false

java.lang.IllegalArgumentException - if nThreads < 1

java.lang.IndexOutOfBoundsException - if start < 0 || end > phasedTarg.nMarkers() || start > end

close

public void close()

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in interface java.io.Closeable