haplotype

Class ConsensusPhaser

java.lang.Object

haplotype.ConsensusPhaser

public class ConsensusPhaser
extends java.lang.Object

Class ConsensusPhaser contains a static method for calculating a consensus phasing from multiple estimated haplotype pairs for an individual.

Method Summary

Modifier and Type	Method and Description
static java.util.List<HapPair>	run(java.util.List<HapPair> hapPairs) Returns a list of consensus haplotype pairs (one pair per individual) sorted in order of increasing sample index.

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(java.util.List<HapPair> hapPairs)

Returns a list of consensus haplotype pairs (one pair per individual) sorted in order of increasing sample index. The specified list of haplotype pairs may contain multiple haplotype pairs for each individual.

Parameters:

hapPairs - a list of haplotype pairs

Returns:

a list of consensus haplotype pairs

Throws:

java.lang.IllegalArgumentException - if (hapPairs.get(j).markers().equals(hapPairs.get(k).markers() == false) for any j, k satisfying 0 <= j < k < hapPairs.size()

java.lang.IllegalArgumentException - if (hapPairs.get(j).samples().equals(hapPairs.get(k).samples() == false) for any j, k satisfying 0 <= j < k < hapPairs.size()

java.lang.NullPointerException - if hapPairs == null