Package imp

Class ImputedRecBuilder

java.lang.Object

imp.ImputedRecBuilder

public final class ImputedRecBuilder
extends java.lang.Object

Class ImputeRecBuilder contains methods for constructing and printing a VCF record in VCF 4.3 format. The sample data in the output VCF record are in the same order that the data were added with the addSampleData() method.

Instances of class ImputeRecBuilder are not thread-safe.

Constructor Summary

Constructors

Constructor	Description
ImputedRecBuilder(Marker marker, int nSamples, boolean ap, boolean gp)	Constructs a new ImputedRecBuilder instance for the specified number of samples.

Method Summary

Modifier and Type	Method	Description
void	addSampleData(float[] a1, float[] a2)	Scales the specified probabilities for each allele to each sum to 1.0, and adds the sample data to the VCF record.
Marker	marker()	Returns the marker in the VCF record.
int	nSamples()	Returns the required number of samples in the VCF record.
void	printRec(java.io.PrintWriter out, boolean isImputed)	Prints the VCF record to the specified PrintWriter.
int	sampleCnt()	Returns the number of times the this.addSampleData() method has been invoked.

Methods inherited from class java.lang.Object

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

Constructor Detail

ImputedRecBuilder

public ImputedRecBuilder(Marker marker,
                         int nSamples,
                         boolean ap,
                         boolean gp)

Constructs a new ImputedRecBuilder instance for the specified number of samples.

Parameters:

marker - the marker corresponding to the VCF record

nSamples - the number of samples

ap - true if posterior allele probabilities are to be printed

gp - true if posterior genotype probabilities are to be printed

Throws:

java.lang.IllegalArgumentException - if nSamples < 1

java.lang.NullPointerException - if marker == null

Method Detail

marker

public Marker marker()

Returns the marker in the VCF record.

Returns:

the marker in the VCF record

nSamples

public int nSamples()

Returns the required number of samples in the VCF record.

Returns:

the required number of samples in the VCF record

sampleCnt

public int sampleCnt()

Returns the number of times the this.addSampleData() method has been invoked.

Returns:

the number of times the this.addSampleData() method has been invoked

addSampleData

public void addSampleData(float[] a1,
                          float[] a2)

Scales the specified probabilities for each allele to each sum to 1.0, and adds the sample data to the VCF record. The contract for this method is undefined if any element of the specified arrays is not a finite non-negative number.

Parameters:

a1 - the allele probabilities for the first allele

a2 - the allele probabilities for the second allele

Throws:

java.lang.IndexOutOfBoundsException - if a1.length < this.marker().nAlleles()

java.lang.IndexOutOfBoundsException - if a2.length < this.marker().nAlleles()

java.lang.NullPointerException - if a1 == null || a2 == null

printRec

public void printRec(java.io.PrintWriter out,
                     boolean isImputed)

Prints the VCF record to the specified PrintWriter. The INFO field of the VCF record will include the DR2 (dose r2) and AF (ALT allele frequency) subfields.

Parameters:

isImputed - true if the INFO field of the VCF record will have an IMP flag and false otherwise

out - the PrintWriter to which the VCF record will be printed

Throws:

java.lang.IllegalStateException - if this.nSamples() != this.sampleCnt()

java.lang.NullPointerException - if out == null