net.maizegenetics.pangenome.hapcollapse

Class FillIndelsIntoConsensus

java.lang.Object

net.maizegenetics.pangenome.hapcollapse.FillIndelsIntoConsensus

public class FillIndelsIntoConsensus
extends Object

This class is created to fill in the agreeing indels removed from the consensus haplotypes during the merge process. There are various merge rules for when the indels disagree.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	FillIndelsIntoConsensus.INDEL_MERGE_RULE

Constructor Summary

Constructors

Constructor and Description
FillIndelsIntoConsensus()

Method Summary

Modifier and Type	Method and Description
static List<List<htsjdk.variant.variantcontext.VariantContext>>	addInIndels(ReferenceRange range, net.maizegenetics.dna.map.GenomeSequence refSequence, List<List<htsjdk.variant.variantcontext.VariantContext>> consensusSequences, List<List<htsjdk.variant.variantcontext.VariantContext>> rawConsensusWithIndels, int minComparableIndels, FillIndelsIntoConsensus.INDEL_MERGE_RULE mergeRule) Method to add in the indels which were removed for the merging process.

Methods inherited from class java.lang.Object

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

Constructor Detail

FillIndelsIntoConsensus

public FillIndelsIntoConsensus()

Method Detail

addInIndels

public static List<List<htsjdk.variant.variantcontext.VariantContext>> addInIndels(ReferenceRange range,
                                                                                   net.maizegenetics.dna.map.GenomeSequence refSequence,
                                                                                   List<List<htsjdk.variant.variantcontext.VariantContext>> consensusSequences,
                                                                                   List<List<htsjdk.variant.variantcontext.VariantContext>> rawConsensusWithIndels,
                                                                                   int minComparableIndels,
                                                                                   FillIndelsIntoConsensus.INDEL_MERGE_RULE mergeRule)

Method to add in the indels which were removed for the merging process. The indels need to be readded in due to the filtering process in MergeGVCFPlugin. There we removed all sites where there was an indel in any of the taxa. Even if it was just one. Because of this, we likely have a lot of reference alleles missing from the consensus for the majority of the taxa. This method will add in any calls which are in agreement by all the taxon in the cluster or in the case of disagreement it will use the INDEL_MERGE_RULE to determine what variantContext record to put back in.

Parameters:

range -

refSequence -

consensusSequences -

rawConsensusWithIndels -

minComparableIndels -

mergeRule -

Returns: