Package vcf

Class VcfRecBuilder

java.lang.Object

vcf.VcfRecBuilder

public final class VcfRecBuilder
extends java.lang.Object

Class VcfRecBuilder contains methods for constructing and printing a VCF record in VCF 4.2 format. The FORMAT field data for each sample is added sequentially to the record via the addSampleData() method.

Instances of class VcfRecBuilder are not thread-safe.

Field Summary

Fields

Modifier and Type	Field	Description
static int	DEFAULT_INIT_SIZE	The default initial size for the string buffer, which is 50 characters.

Constructor Summary

Constructors

Constructor	Description
VcfRecBuilder()	Constructs a new VcfRecBuilder instance with initial buffer size equal to VcfRecBuilder.DEFAULT_INIT_SIZE.
VcfRecBuilder(int initSize)	Constructs a new VcfRecBuilder instance with the specified initial buffer size.

Method Summary

Modifier and Type	Method	Description
void	addSampleData(double[] gtypeProbs)	Adds the FORMAT field for a sample to the VCF record for the current marker.
void	addSampleData(double[] alProbs1, double[] alProbs2)	Adds the FORMAT field for a sample to the VCF record for the current marker.
Marker	marker()	Returns the current marker.
boolean	printDS()	Returns true if the FORMAT field in the VCF record for this marker includes a DS subfield, and false otherwise
boolean	printGP()	Returns true if the FORMAT field in the VCF record for this marker includes a GP subfield, and false otherwise
void	reset(Marker marker, boolean printDS, boolean printGP)	Clears existing data, and sets the current marker to the specified marker.
void	writeRec(java.io.PrintWriter out, boolean isImputed)	Prints the current VCF record for the current marker to the specified PrintWriter.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_INIT_SIZE

public static final int DEFAULT_INIT_SIZE

The default initial size for the string buffer, which is 50 characters.

See Also:

Constant Field Values

Constructor Detail

VcfRecBuilder

public VcfRecBuilder()

Constructs a new VcfRecBuilder instance with initial buffer size equal to VcfRecBuilder.DEFAULT_INIT_SIZE.

VcfRecBuilder

public VcfRecBuilder(int initSize)

Constructs a new VcfRecBuilder instance with the specified initial buffer size.

Parameters:

initSize - the initial buffer size

Throws:

java.lang.NegativeArraySizeException - if initCapacity < 0

Method Detail

reset

public void reset(Marker marker,
                  boolean printDS,
                  boolean printGP)

Clears existing data, and sets the current marker to the specified marker. If the FORMAT field contains a DS or GP subfield, the INFO field will include the AR2 (allele r2), DR2 (dose r2), and AF (ALT allele frequency) subfields.

Parameters:

marker - the marker to which data will be added

printDS - true if the FORMAT field in the VCF record for this marker will include a DS subfield, and false otherwise

printGP - true if the FORMAT field in the VCF record for this marker will include a GP subfield, and false otherwise

Throws:

java.lang.NullPointerException - if marker == null

marker

public Marker marker()

Returns the current marker. Returns null if this.reset() has not been previously invoked.

Returns:

the current marker.

printDS

public boolean printDS()

Returns true if the FORMAT field in the VCF record for this marker includes a DS subfield, and false otherwise

Returns:

true if the FORMAT field in the VCF record for this marker includes a DS subfield

printGP

public boolean printGP()

Returns true if the FORMAT field in the VCF record for this marker includes a GP subfield, and false otherwise

Returns:

true if the FORMAT field in the VCF record for this marker includes a GP subfield

addSampleData

public void addSampleData(double[] gtypeProbs)

Adds the FORMAT field for a sample to the VCF record for the current marker. If the specified posterior genotype probabilities do not sum to 1.0, the specified array will normalized to sum to 1.0.

Parameters:

gtypeProbs - the posterior genotype probabilities

Throws:

java.lang.IllegalArgumentException - if gtProbs.length != this.marker().nGenotypes()

java.lang.IllegalArgumentException - if any element of the specified array is not a finite non-negative number

java.lang.IllegalStateException - if this.marker() == null

java.lang.NullPointerException - if gtProbs == null

addSampleData

public void addSampleData(double[] alProbs1,
                          double[] alProbs2)

Adds the FORMAT field for a sample to the VCF record for the current marker. If either of the specified posterior allele probabilities does not sum to 1.0, it will be normalized to sum to 1.0.

Parameters:

alProbs1 - the posterior allele probabilities for the individual's first allele

alProbs2 - the posterior allele probabilities for the individual's second allele

Throws:

java.lang.IllegalArgumentException - if alProbs1.length != this.marker().nAlleles()

java.lang.IllegalArgumentException - if alProbs2.length != this.marker().nAlleles()

java.lang.IllegalArgumentException - if any element of the specified array is not a finite non-negative number

java.lang.IllegalStateException - if this.marker() == null

java.lang.NullPointerException - if alProbs1 == null || alProbs2 == null

writeRec

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

Prints the current VCF record for the current marker to the specified PrintWriter. If the FORMAT field contains a DS or GP subfield, the INFO field will include the AR2 (allele r2), DR2 (dose r2), and AF (ALT allele frequency) subfields. Invocation of this method has no effect if this.reset() has not previously been invoked.

Parameters:

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

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

Throws:

java.lang.NullPointerException - if out == null