vcf

Class VcfRecGTParser

java.lang.Object

vcf.VcfRecGTParser

public final class VcfRecGTParser
extends java.lang.Object

Class VcfRecGTParser parses VCF records and extracts the GT format field.

Instances of class VcfRecGTParser are not thread-safe.

Constructor Summary

Constructors

Constructor and Description
VcfRecGTParser(VcfHeader vcfHeader, java.lang.String vcfRec) Constructs a new VcfRecGTParser object from the specified VCF record.

Method Summary

Modifier and Type	Method and Description
int	allele1() Returns the first allele of the genotype for the current sample.
int	allele2() Returns the second allele of the genotype for the current sample.
int	currentSample() Returns the index of the current sample, or -1 if this.nextSample() has not yet been invoked.
boolean	isPhased() Returns true if the genotype for the current sample is phased, and returns false otherwise.
Marker	marker() Returns the marker.
void	nextSample() Increases the current sample index by one.
int	nSamples() Returns the number of samples.
Samples	samples() Returns the list of samples.
VcfHeader	vcfHeader() Returns the VCF meta-information lines and header line.
java.lang.String	vcfRecord() Returns the VCF record that is being parsed.

Methods inherited from class java.lang.Object

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

Constructor Detail

VcfRecGTParser

public VcfRecGTParser(VcfHeader vcfHeader,
                      java.lang.String vcfRec)

Constructs a new VcfRecGTParser object from the specified VCF record.

Parameters:

vcfHeader - the VCF meta-information lines and header line

vcfRec - the VCF record

Throws:

java.lang.IllegalArgumentException - if vcfHeader.nSamples() == 0

java.lang.IllegalArgumentException - if a format error is detected in the vcfRecord

java.lang.NullPointerException - if vcfHeader == null || vcfRec == null

Method Detail

vcfHeader

public VcfHeader vcfHeader()

Returns the VCF meta-information lines and header line.

Returns:

the VCF meta-information lines and header line

vcfRecord

public java.lang.String vcfRecord()

Returns the VCF record that is being parsed.

Returns:

the VCF record that is being parsed

marker

public Marker marker()

Returns the marker.

Returns:

the marker

currentSample

public int currentSample()

Returns the index of the current sample, or -1 if this.nextSample() has not yet been invoked.

Returns:

the index of the current sample, or -1 if this.nextSample() has not yet been invoked

allele1

public int allele1()

Returns the first allele of the genotype for the current sample.

Returns:

the first allele of the genotype for the current sample

allele2

public int allele2()

Returns the second allele of the genotype for the current sample.

Returns:

the second allele of the genotype for the current sample

isPhased

public boolean isPhased()

Returns true if the genotype for the current sample is phased, and returns false otherwise.

Returns:

true if the genotype for the current sample is phased

samples

public Samples samples()

Returns the list of samples.

Returns:

the list of samples

nSamples

public int nSamples()

Returns the number of samples.

Returns:

the number of samples

nextSample

public void nextSample()

Increases the current sample index by one.

Throws:

java.lang.IndexOutOfBoundsException - if (this.currentSample() + 1 == this.nSamples()) immediately prior to the invocation of this method

java.lang.IllegalArgumentException - if a format error is detected in this.vcfRecord()