Package 

Class FillIndelsIntoConsensus

  • All Implemented Interfaces:
    
public class FillIndelsIntoConsensus

    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.

    • Field Summary

      Fields 
      Modifier and Type Field Description

    • Constructor Summary

      Constructors 
      Constructor Description

    • Enum Constant Summary

      Enum Constants 
      Enum Constant Description

    • Method Summary

      Modifier and Type Method Description
      static List<List<VariantContext>> addInIndels(ReferenceRange range, GenomeSequence refSequence, List<List<VariantContext>> consensusSequences, List<List<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

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

    • Constructor Detail

    • Method Detail

      • addInIndels

         static List<List<VariantContext>> addInIndels(ReferenceRange range, GenomeSequence refSequence, List<List<VariantContext>> consensusSequences, List<List<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.