GTRec

All Superinterfaces:

DuplicatesGTRec, IntArray, MarkerContainer

All Known Subinterfaces:

RefGTRec

All Known Implementing Classes:

BasicGTRec, BitArrayGTRec, BitArrayRefGTRec, LowMafDiallelicGTRec, LowMafGTRec, LowMafRefDiallelicGTRec, LowMafRefGTRec, SeqCodedRefGTRec, VcfRec
```
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

All Methods Static Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`static int[]`	`alleleCounts(GTRec rec)`	Returns the allele counts.
`static double[]`	`alleleFreq(GTRec rec)`	Returns the allele frequencies.
`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, size

Methods inherited from interface vcf.MarkerContainer
marker

- Method Detail
  - samples
```
Samples samples()
```
    Returns the list of samples.
    
    Returns:
    
    the list of samples
  - alleleFreq
```
static double[] alleleFreq(GTRec rec)
```
    Returns the allele frequencies. The k-th element of the returned array is the frequency of the k-th allele.
    
    Parameters:
    
    rec - the genotype data for a marker
    
    Returns:
    
    the allele frequencies
  - alleleCounts
```
static int[] alleleCounts(GTRec rec)
```
    Returns the allele counts. The k-th element of the returned array is the count of the k-th allele.
    
    Parameters:
    
    rec - the genotype data for a marker
    
    Returns:
    
    the allele frequencies
  - 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