net.maizegenetics.pangenome.hapcollapse

Class MergeGVCFUtils

java.lang.Object

net.maizegenetics.pangenome.hapcollapse.MergeGVCFUtils

public class MergeGVCFUtils
extends Object

Created by zrm22 on 11/7/17. This class borrows code from GATK. Eventually we should just bring in the GATK jar and use the method directly. Some of this will need to be cleaned up as it uses a lot of extra methods. I just copied them till the class will compile. TODO Clean up this class as it is thrown together to make it work.

Constructor Summary

Constructors

Constructor and Description
MergeGVCFUtils()

Method Summary

Modifier and Type	Method and Description
static net.maizegenetics.dna.snp.GenotypeTable	createGenotypeTableFromGVCFs(ReferenceRange refRange, com.google.common.collect.Multimap<net.maizegenetics.taxa.Taxon,htsjdk.variant.variantcontext.VariantContext> taxonToVariantListMap, net.maizegenetics.dna.map.GenomeSequence referenceSequence) This method takes all the VariantContexts for all of the Taxon we need in our new GenotypeTable and will create a correctly encoded GenotypeTable
static net.maizegenetics.dna.snp.GenotypeTable	createGenotypeTableFromHaplotypeNodes(ReferenceRange refRange, List<HaplotypeNode> nodesWithVariantContexts, net.maizegenetics.dna.map.GenomeSequence referenceSequence) Method to make a genotypeTable from a list of Haplotype Nodes.
static boolean	isRefBlock(htsjdk.variant.variantcontext.VariantContext vc) Simple method to check to see if the Variant is a reference block
static String	removeHaplotypeCaller(String taxonName) Simple method to remove the _Haplotype_Caller from the taxon name
static net.maizegenetics.dna.snp.GenotypeTable	removeIndels(net.maizegenetics.dna.snp.GenotypeTable baseAlign) Method to Remove indels from the GenotypeTable.

Methods inherited from class java.lang.Object

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

Constructor Detail

MergeGVCFUtils

public MergeGVCFUtils()

Method Detail

createGenotypeTableFromHaplotypeNodes

public static net.maizegenetics.dna.snp.GenotypeTable createGenotypeTableFromHaplotypeNodes(ReferenceRange refRange,
                                                                                            List<HaplotypeNode> nodesWithVariantContexts,
                                                                                            net.maizegenetics.dna.map.GenomeSequence referenceSequence)

Method to make a genotypeTable from a list of Haplotype Nodes. This method will simply make the GenotypeTable encoding indels as either + or - depending on what is actually stored in the HaplotypeNode In other steps, the indels will be filtered out and then will be added back in when consensus is made.

Parameters:

refRange -

nodesWithVariantContexts -

referenceSequence -

Returns:

removeHaplotypeCaller

public static String removeHaplotypeCaller(String taxonName)

Simple method to remove the _Haplotype_Caller from the taxon name

Parameters:

taxonName -

Returns:

createGenotypeTableFromGVCFs

public static net.maizegenetics.dna.snp.GenotypeTable createGenotypeTableFromGVCFs(ReferenceRange refRange,
                                                                                   com.google.common.collect.Multimap<net.maizegenetics.taxa.Taxon,htsjdk.variant.variantcontext.VariantContext> taxonToVariantListMap,
                                                                                   net.maizegenetics.dna.map.GenomeSequence referenceSequence)

This method takes all the VariantContexts for all of the Taxon we need in our new GenotypeTable and will create a correctly encoded GenotypeTable

Parameters:

refRange -

taxonToVariantListMap -

referenceSequence -

Returns:

isRefBlock

public static boolean isRefBlock(htsjdk.variant.variantcontext.VariantContext vc)

Simple method to check to see if the Variant is a reference block

Parameters:

vc -

Returns:

removeIndels

public static net.maizegenetics.dna.snp.GenotypeTable removeIndels(net.maizegenetics.dna.snp.GenotypeTable baseAlign)

Method to Remove indels from the GenotypeTable. Basically if it has a + or - in any of the calls, we filter out.

Parameters:

baseAlign -

Returns: