net.maizegenetics.pangenome.fastaExtraction

Class ExtractFastaUtils

java.lang.Object

net.maizegenetics.pangenome.fastaExtraction.ExtractFastaUtils

public class ExtractFastaUtils
extends Object

Class which holds various utilities for extracting fastas Created by zrm22 on 2/8/18.

Constructor Summary

Constructors

Constructor and Description
ExtractFastaUtils()

Method Summary

Modifier and Type	Method and Description
static String	extractFastaSequence(List<htsjdk.variant.variantcontext.VariantContext> variants, ReferenceRange referenceRange) Method to extract out a fasta sequence given a list of variantContexts This will fill in Ns whenever we do not have a variant context record for a given position

Methods inherited from class java.lang.Object

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

Constructor Detail

ExtractFastaUtils

public ExtractFastaUtils()

Method Detail

extractFastaSequence

public static String extractFastaSequence(List<htsjdk.variant.variantcontext.VariantContext> variants,
                                          ReferenceRange referenceRange)

Method to extract out a fasta sequence given a list of variantContexts This will fill in Ns whenever we do not have a variant context record for a given position

Parameters:

variants -

referenceRange -

Returns: