Package sample

Class InitTargHapPairs

java.lang.Object

sample.InitTargHapPairs

public final class InitTargHapPairs
extends java.lang.Object

Class InitTargHapPairs has a static method for returning initial target haplotype pairs.

Instances of class InitTargHapPairs are immutable.

Method Summary

Modifier and Type	Method	Description
static java.util.List<HapPair>	run(GT gl, HapPairs refHaps, double minFreq, int nCopies, long seed)	Returns initial target haplotype pairs.

Methods inherited from class java.lang.Object

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

Method Detail

run

public static java.util.List<HapPair> run(GT gl,
                                          HapPairs refHaps,
                                          double minFreq,
                                          int nCopies,
                                          long seed)

Returns initial target haplotype pairs. Missing alleles are sampled according from the empirical allele frequency distribution, and input genotypes with unknown phase will have their alleles randomly ordered in the returned haplotype pairs.

Parameters:

gl - the target genotype data

refHaps - the reference haplotype pairs

minFreq - a minimum allele frequency to be enforced

nCopies - the number of haplotype pairs sampled for each target individual

seed - the seed for random number generation

Returns:

initial target haplotype pairs

Throws:

java.lang.IllegalArgumentException - if minFreq <= 0.0 || minFreq >= 0.5 || Double.isNaN(minFreq) == true

java.lang.IllegalArgumentException - if nCopies < 1

java.lang.NullPointerException - if gl == null || refHapPairs == null