Package 

Class GVCFGenotypeSequence

  • All Implemented Interfaces:
    net.maizegenetics.dna.map.GenomeSequence 
    
public class GVCFGenotypeSequence
extends GVCFSequence

    GVCFGenotypeSequence This class should be used instead of GVCFSequence when you want to have diploid calls being returned. Due to the fact that this class will return diploids, you cannot query a range of positions as we cannot separate the two gametes. If you need a range, you will have to loop through each position and retrieve them one at a time.. The Diploids are separated by the / character

    • Nested Class Summary

      Nested Classes 
      Modifier and Type Class Description

    • 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 GenomeSequence instance(String refFileName, String gvcfFileName) Returns an initialized GVCFSequence given the input Reference and GVCF Files.
      static GenomeSequence instance(GenomeSequence referenceSequence, String gvcfFileName) Returns an initialized GVCFSequence given the input Reference and GVCF Files.
      static GenomeSequence instance(GenomeSequence referenceSequence, String gvcfFileName, boolean missingAsRef) Instance method to allow for reference filling in missing for a file
      static GenomeSequence instance(GenomeSequence referenceSequence, List<VariantContext> variantContexts, boolean missingAsRef, String taxonName) Instance method to build the GenomeSequence in memory using a List of VariantContexts
      Array<byte> chromosomeSequence(Chromosome chrom) Unsupported method to get the sequence for the whole chromosome
      Array<byte> chromosomeSequence(Chromosome chrom, int startSite, int endSite)
      Array<byte> genomeSequence(long startSite, long lastSite)
      String genomeSequenceAsString(long startSite, long lastSite)
      byte genotype(Chromosome chrom, int position)
      byte genotype(Chromosome chrom, Position positionObject)
      String genotypeAsString(Chromosome chrom, int position)
      String genotypeAsString(Chromosome chrom, Position positionObject)
      String genotypeAsString(Chromosome chrom, int startSite, int endSite)

      • Methods inherited from class net.maizegenetics.pangenome.fastaExtraction.GVCFSequence

        allTaxonInstance, chromosomeSize, chromosomes, fullRefCoordinateToChromCoordinate, genomeSize, instance, numberOfChromosomes

      • Methods inherited from class net.maizegenetics.dna.map.GenomeSequence

        chromosomeSequence, chromosomeSize, chromosomes, fullRefCoordinateToChromCoordinate, genomeSequence, genomeSequenceAsString, genomeSize, genotype, genotypeAsString, numberOfChromosomes

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

    • Method Detail

      • instance

         static GenomeSequence instance(String refFileName, String gvcfFileName)

        Returns an initialized GVCFSequence given the input Reference and GVCF Files.

        Parameters:
        refFileName - File name of the Reference file used in creating the GVCF.
        gvcfFileName - File name of the GVCF file which defines the variants of the taxon to the reference

      • instance

         static GenomeSequence instance(GenomeSequence referenceSequence, String gvcfFileName)

        Returns an initialized GVCFSequence given the input Reference and GVCF Files. This should be used if you are running multiple GVCFs through using the same Reference File. Currently will speed up processing each GVCF by about a minute.

        Parameters:
        referenceSequence - GenomeSequence object already read into memory.
        gvcfFileName - File name of the GVCF file which defines the variants of the taxon to the reference

      • instance

         static GenomeSequence instance(GenomeSequence referenceSequence, String gvcfFileName, boolean missingAsRef)

        Instance method to allow for reference filling in missing for a file

      • instance

         static GenomeSequence instance(GenomeSequence referenceSequence, List<VariantContext> variantContexts, boolean missingAsRef, String taxonName)

        Instance method to build the GenomeSequence in memory using a List of VariantContexts

      • chromosomeSequence

         Array<byte> chromosomeSequence(Chromosome chrom)

        Unsupported method to get the sequence for the whole chromosome

      • genotype

         byte genotype(Chromosome chrom, int position)

      • genotype

         byte genotype(Chromosome chrom, Position positionObject)