| Class | Description |
|---|---|
| BinomialCoefficientUtil |
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/).
|
| GeneralUtils |
Constants and utility methods used throughout the VCF/BCF/VariantContext classes
|
| SAMSequenceDictionaryExtractor |
Small class for loading a SAMSequenceDictionary from a file
|
| VCFHeaderReader |
Utility class to read a VCF header without being told beforehand whether the input is VCF or BCF.
|