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

Method Summary

Modifier and Type	Method and Description
void	close()
java.lang.String	outPrefix() Returns the output file prefix.
void	print(AlleleProbs alProbs, boolean[] isImputed, int start, int end, boolean dose, boolean gprobs, int nThreads) Prints the data in alProbs for markers with index between cd.lastSplice() (inclusive) and cd.nextSplice() (exclusive) 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).
void	printIbd(CurrentData cd, java.util.Map<IntPair,java.util.List<IbdSegment>> ibdMap) Prints IBD segments that end between the 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(AlleleProbs alProbs,
                  boolean[] isImputed,
                  int start,
                  int end,
                  boolean dose,
                  boolean gprobs,
                  int nThreads)

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

Parameters:

alProbs - the estimated haplotype allele probabilities

isImputed - an array of length alProbs.nMarkers() whose j-th element is true if the corresponding marker is imputed, and false otherwise

start - the starting marker index (inclusive)

end - the ending marker index (exclusive)

dose - true if the output FORMAT fields should contain a DS subfield, and false otherwise

gprobs - true if the output FORMAT fields should contain a GP subfield, and false otherwise

nThreads - the number of parallel threads to use

Throws:

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

java.lang.IllegalArgumentException - if nThreads < 1

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

java.lang.NullPointerException - if alProbs == null || isImputed == null

printIbd

public void printIbd(CurrentData cd,
                     java.util.Map<IntPair,java.util.List<IbdSegment>> ibdMap)

Prints IBD segments that end between the markers with index between cd.lastSplice() (inclusive) and cd.nextSplice() (exclusive). IBD segments that end on or after the marker with index cd.nextSplice() are saved so that they can be merged with IBD segments from the next marker window.

It is the the caller's responsibility to ensure that the ordered haplotype pairs between adjacent consecutive markers windows are identical for each sample.

Parameters:

cd - the input data for the current window

ibdMap - a map whose keys are pairs of haplotype indices and whose values are lists of IBD segments involving the haplotype pair key

Throws:

java.lang.IllegalArgumentException - if this.samples().equals(cd.targetSamples()) == false

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

close

public void close()

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable