Package vcf

Interface GTRec

All Superinterfaces:

DuplicatesGTRec, IntArray, MarkerContainer

All Known Subinterfaces:

RefGTRec

All Known Implementing Classes:

BitSetGT, LowMafRefDiallelicGT, LowMafRefGT, SeqCodedRefGT, VcfRecord

public interface GTRec
extends DuplicatesGTRec

Interface GTRec represents represents genotype data for one marker.

All instances of GTRec are required to be immutable.

Method Summary

Modifier and Type	Method	Description
float	gl(int sample, int allele1, int allele2)	Returns the probability of the observed data for the specified sample if the specified pair of ordered alleles is the true ordered genotype.
boolean	isGTData()	Returns true if the value returned by this.gl() is determined by a called or missing genotype, and returns false otherwise.
Samples	samples()	Returns the list of samples.
static java.lang.String	toVcfRec(GTRec gtRec)	Returns a VCF record corresponding to the specified GTRec object.

Methods inherited from interface vcf.DuplicatesGTRec

allele1, allele2, alleles, get, isPhased, isPhased, nSamples, size

Methods inherited from interface ints.IntArray

Methods inherited from interface vcf.MarkerContainer

marker, nAlleles

Method Detail

samples

Samples samples()

Returns the list of samples.

Returns:

the list of samples

isGTData

boolean isGTData()

Returns true if the value returned by this.gl() is determined by a called or missing genotype, and returns false otherwise.

Returns:

true if the value returned by this.gl() is determined by a called or missing genotype

gl

float gl(int sample,
         int allele1,
         int allele2)

Returns the probability of the observed data for the specified sample if the specified pair of ordered alleles is the true ordered genotype.

Parameters:

sample - the sample index

allele1 - the first allele index

allele2 - the second allele index

Returns:

the probability of the observed data for the specified sample if the specified pair of ordered alleles is the true ordered genotype.

Throws:

java.lang.IndexOutOfBoundsException - if samples < 0 || samples >= this.nSamples()

java.lang.IndexOutOfBoundsException - if allele1 < 0 || allele1 >= this.marker().nAlleles()

java.lang.IndexOutOfBoundsException - if allele2 < 0 || allele2 >= this.marker().nAlleles()

toVcfRec

static java.lang.String toVcfRec(GTRec gtRec)

Returns a VCF record corresponding to the specified GTRec object. The returned VCF record will have missing QUAL and INFO fields, will have "PASS" in the filter field, and will have a GT format field.

Parameters:

gtRec - the genotype data

Returns:

a VCF record corresponding to the specified GTRec object

Throws:

java.lang.NullPointerException - if gtRec == null