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(Par par, Samples samples)	Constructs a new WindowWriter object.

Method Summary

Modifier and Type	Method	Description
void	close()
java.lang.String	outPrefix()	Returns the output file prefix.
void	printImputed(ImpData impData, int start, int end, java.util.concurrent.atomic.AtomicReferenceArray<StateProbs> stateProbs)	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	printPhased(Stage2Haps stage2Haps, int start, int end)
void	printPhased(GT phasedTarg, int start, int end)	Appends the data in phased genotypes for the specified markers to the output VCF file: this.outPrefix() + ".vcf.gz".
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(Par par,
                    Samples samples)

Constructs a new WindowWriter object.

Parameters:

par - the analysis parameters

samples - the sample whose data will be printed

Throws:

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

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

printImputed

public void printImputed(ImpData impData,
                         int start,
                         int end,
                         java.util.concurrent.atomic.AtomicReferenceArray<StateProbs> stateProbs)

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

start - the starting reference marker index (inclusive)

end - the ending reference 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

printPhased

public void printPhased(GT phasedTarg,
                        int start,
                        int end)

Appends 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)

Throws:

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

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

java.lang.NullPointerException - if phasedTarg == null

printPhased

public void printPhased(Stage2Haps stage2Haps,
                        int start,
                        int end)

close

public void close()

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in interface java.io.Closeable