Package 

Class GVCFSequence

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

    GVCFSequence.java

    Simple class to read in a GVCF then get the FASTA encoded sequence taking into account the variants in the GVCF file Uses a RangeMapto hold the GVCF variant calls for a given position range. Will coalesce any overlapping regions by concatenating the calls together in order of gvcf.

    Created by zrm22 on 7/17/17.

    • Nested Class Summary

      Nested Classes 
      Modifier and Type Class Description

    • Field Summary

      Fields 
      Modifier and Type Field Description

    • Constructor Summary

      Constructors 
      Constructor Description
      GVCFSequence()

    • Enum Constant Summary

      Enum Constants 
      Enum Constant Description

    • Constructor Detail

      • GVCFSequence

        GVCFSequence()

    • 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 add in missing as Ref from a file

      • instance

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

        Instance method to create a GenomeSequenc from a List of VariantContexts

      • allTaxonInstance

         static Map<String, GenomeSequence> allTaxonInstance(GenomeSequence referenceSequence, String vcfFileName, boolean missingAsRef)

        Method to get a map of taxon to its genome sequence for all the taxon in the vcf file

      • genotype

         byte genotype(Chromosome chrom, int position)

      • genotype

         byte genotype(Chromosome chrom, Position positionObject)