htsjdk.variant.utils

Class BinomialCoefficientUtil

java.lang.Object

htsjdk.variant.utils.BinomialCoefficientUtil

public class BinomialCoefficientUtil
extends java.lang.Object

A modified version of the Apache Math implementation of binomial coefficient calculation Derived from code within the CombinatoricsUtils and FastMath classes within Commons Math3 (https://commons.apache.org/proper/commons-math/) Included here for use in Genotype Likelihoods calculation, instead of adding Commons Math3 as a dependency Commons Math3 is licensed using the Apache License 2.0 Full text of this license can be found here: https://www.apache.org/licenses/LICENSE-2.0.txt This product includes software developed at The Apache Software Foundation (http://www.apache.org/). This product includes software developed for Orekit by CS Systèmes d'Information (http://www.c-s.fr/) Copyright 2010-2012 CS Systèmes d'Information

Constructor Summary

Constructors

Constructor and Description
BinomialCoefficientUtil()

Method Summary

Modifier and Type	Method and Description
static long	binomialCoefficient(int n, int k) Binomial Coefficient, "n choose k", the number of k-element subsets that can be selected from an n-element set.

Methods inherited from class java.lang.Object

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

Constructor Detail

BinomialCoefficientUtil

public BinomialCoefficientUtil()

Method Detail

binomialCoefficient

public static long binomialCoefficient(int n,
                                       int k)
                                throws java.lang.ArithmeticException

Binomial Coefficient, "n choose k", the number of k-element subsets that can be selected from an n-element set.

Preconditions:

• 0 <= k <= n (otherwise IllegalArgumentException is thrown)
• The result is small enough to fit into a long. The largest value of n for which all coefficients are < Long.MAX_VALUE is 66. If the computed value exceeds Long.MAX_VALUE an ArithmeticException is thrown.

Parameters:

n - the size of the set

k - the size of the subsets to be counted

Returns:

n choose k

Throws:

java.lang.ArithmeticException - if n < 0 or k > n or the result is too large to be represented by a long integer.