net.maizegenetics.pangenome.fastaExtraction

Class GVCFGenotypeSequence

java.lang.Object

net.maizegenetics.pangenome.fastaExtraction.GVCFSequence

net.maizegenetics.pangenome.fastaExtraction.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

Method Summary

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

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

allTaxonInstance, chromosomes, chromosomeSize, fullRefCoordinateToChromCoordinate, genomeSize, numberOfChromosomes

Methods inherited from class java.lang.Object

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

Method Detail

instance

public static net.maizegenetics.dna.map.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

Returns:

GenomeSequence which can be used to get sequence out

instance

public static net.maizegenetics.dna.map.GenomeSequence instance(net.maizegenetics.dna.map.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

Returns:

GenomeSequence which can be used to get sequence out

instance

public static net.maizegenetics.dna.map.GenomeSequence instance(net.maizegenetics.dna.map.GenomeSequence referenceSequence,
                                                                String gvcfFileName,
                                                                boolean missingAsRef)

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

Parameters:

referenceSequence -

gvcfFileName -

missingAsRef -

Returns:

instance

public static net.maizegenetics.dna.map.GenomeSequence instance(net.maizegenetics.dna.map.GenomeSequence referenceSequence,
                                                                List<htsjdk.variant.variantcontext.VariantContext> variantContexts,
                                                                boolean missingAsRef,
                                                                String taxonName)

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

Parameters:

referenceSequence -

variantContexts -

missingAsRef -

taxonName -

Returns:

chromosomeSequence

public byte[] chromosomeSequence(net.maizegenetics.dna.map.Chromosome chrom)

Unsupported method to get the sequence for the whole chromosome

Specified by:

chromosomeSequence in interface net.maizegenetics.dna.map.GenomeSequence

Overrides:

chromosomeSequence in class GVCFSequence

Parameters:

chrom -

Returns:

chromosomeSequence

public byte[] chromosomeSequence(net.maizegenetics.dna.map.Chromosome chrom,
                                 int startSite,
                                 int endSite)

Specified by:

chromosomeSequence in interface net.maizegenetics.dna.map.GenomeSequence

Overrides:

chromosomeSequence in class GVCFSequence

genomeSequence

public byte[] genomeSequence(long startSite,
                             long lastSite)

Specified by:

genomeSequence in interface net.maizegenetics.dna.map.GenomeSequence

Overrides:

genomeSequence in class GVCFSequence

genomeSequenceAsString

public String genomeSequenceAsString(long startSite,
                                     long lastSite)

Specified by:

genomeSequenceAsString in interface net.maizegenetics.dna.map.GenomeSequence

Overrides:

genomeSequenceAsString in class GVCFSequence

genotype

public byte genotype(net.maizegenetics.dna.map.Chromosome chrom,
                     int position)

Specified by:

genotype in interface net.maizegenetics.dna.map.GenomeSequence

Overrides:

genotype in class GVCFSequence

genotype

public byte genotype(net.maizegenetics.dna.map.Chromosome chrom,
                     net.maizegenetics.dna.map.Position positionObject)

Specified by:

genotype in interface net.maizegenetics.dna.map.GenomeSequence

Overrides:

genotype in class GVCFSequence

genotypeAsString

public String genotypeAsString(net.maizegenetics.dna.map.Chromosome chrom,
                               int position)

Specified by:

genotypeAsString in interface net.maizegenetics.dna.map.GenomeSequence

Overrides:

genotypeAsString in class GVCFSequence

genotypeAsString

public String genotypeAsString(net.maizegenetics.dna.map.Chromosome chrom,
                               net.maizegenetics.dna.map.Position positionObject)

Specified by:

genotypeAsString in interface net.maizegenetics.dna.map.GenomeSequence

Overrides:

genotypeAsString in class GVCFSequence

genotypeAsString

public String genotypeAsString(net.maizegenetics.dna.map.Chromosome chrom,
                               int startSite,
                               int endSite)

Specified by:

genotypeAsString in interface net.maizegenetics.dna.map.GenomeSequence

Overrides:

genotypeAsString in class GVCFSequence