net.maizegenetics.pangenome.hapCalling

Class HapCallingUtils

java.lang.Object

net.maizegenetics.pangenome.hapCalling.HapCallingUtils

public class HapCallingUtils
extends Object

Created by zrm22 on 8/29/17.

Constructor Summary

Constructors

Constructor and Description
HapCallingUtils()

Method Summary

Modifier and Type	Method and Description
static void	callSNPsFromHaplotypeNodes(List<HaplotypeNode> listOfNodes, HashMap<Integer,String> hapIdToFileNameMapping, String vcfFileDir, String exportVCFFileName, String referenceFileName, String taxonName)
static void	callSNPsFromHaplotypePath(HaplotypeGraph graph, HaplotypePath bestPath, String vcfFileDir, String exportVCFFileName, String referenceFileName, String taxonName)
static void	callSNPsFromSomeVCFs(String inputVCFFileDir, String exportVCFFileName, String referenceFileName, String taxonName)
static HashMap<Integer,String>	createHapIdToFileNameMapping(HaplotypeGraph graph, String pangenomeDir)
static List<htsjdk.variant.variantcontext.VariantContext>	getVariantContextFromHaplotypeNodeList(List<HaplotypeNode> nodeList) Method to extract the VCF VariantContexts from a List of HaplotypeNodes
static List<htsjdk.variant.variantcontext.VariantContext>	getVariantContextFromHaplotypePath(HaplotypePath bestPath) Method to extract the VCF VariantContexts from the HaplotypePath.
static void	writeVariantContextsToVCF(List<htsjdk.variant.variantcontext.VariantContext> variantContextList, String exportVCFFileName, String referenceFileName, List<String> taxa)
static void	writeVariantContextsToVCF(List<htsjdk.variant.variantcontext.VariantContext> variantContextList, String exportVCFFileName, String referenceFileName, String taxonName) Method to write the list of VariantContexts out to a vcf file.

Methods inherited from class java.lang.Object

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

Constructor Detail

HapCallingUtils

public HapCallingUtils()

Method Detail

getVariantContextFromHaplotypePath

public static List<htsjdk.variant.variantcontext.VariantContext> getVariantContextFromHaplotypePath(HaplotypePath bestPath)

Method to extract the VCF VariantContexts from the HaplotypePath. TODO remove if we get rid of HaplotypePath

Parameters:

bestPath - HaplotypePath containing one single path through the PHG.

Returns:

list of VariantContext objects which represent the concatenated vcf records for each node on the path

getVariantContextFromHaplotypeNodeList

public static List<htsjdk.variant.variantcontext.VariantContext> getVariantContextFromHaplotypeNodeList(List<HaplotypeNode> nodeList)

Method to extract the VCF VariantContexts from a List of HaplotypeNodes

Parameters:

nodeList - List of HaplotypeNodes which we want the variantContexts from

Returns:

List of VariantContext objects which we can then export to a vcf

writeVariantContextsToVCF

public static void writeVariantContextsToVCF(List<htsjdk.variant.variantcontext.VariantContext> variantContextList,
                                             String exportVCFFileName,
                                             String referenceFileName,
                                             List<String> taxa)

writeVariantContextsToVCF

public static void writeVariantContextsToVCF(List<htsjdk.variant.variantcontext.VariantContext> variantContextList,
                                             String exportVCFFileName,
                                             String referenceFileName,
                                             String taxonName)

Method to write the list of VariantContexts out to a vcf file. If the referenceFileName is not null, it will also index the file on the fly. TODO when we convert TASSEL's VCF reader to use htsjdk, rework this method into ExportUtils TODO use an optional for the referenceFileName

Parameters:

variantContextList - list of VariantContext objects that need to be written to the vcf file

exportVCFFileName - String file name of the exported VCF file

referenceFileName - String name of the reference fasta file name. If null, will not index the vcf. Otherwise you need a fasta index as well to make it work

taxonName - Taxon name

callSNPsFromHaplotypePath

public static void callSNPsFromHaplotypePath(HaplotypeGraph graph,
                                             HaplotypePath bestPath,
                                             String vcfFileDir,
                                             String exportVCFFileName,
                                             String referenceFileName,
                                             String taxonName)

callSNPsFromSomeVCFs

public static void callSNPsFromSomeVCFs(String inputVCFFileDir,
                                        String exportVCFFileName,
                                        String referenceFileName,
                                        String taxonName)

callSNPsFromHaplotypeNodes

public static void callSNPsFromHaplotypeNodes(List<HaplotypeNode> listOfNodes,
                                              HashMap<Integer,String> hapIdToFileNameMapping,
                                              String vcfFileDir,
                                              String exportVCFFileName,
                                              String referenceFileName,
                                              String taxonName)

createHapIdToFileNameMapping

public static HashMap<Integer,String> createHapIdToFileNameMapping(HaplotypeGraph graph,
                                                                   String pangenomeDir)