net.maizegenetics.pangenome.fastaExtraction

Class GVCFSequence

java.lang.Object

net.maizegenetics.pangenome.fastaExtraction.GVCFSequence

All Implemented Interfaces:

net.maizegenetics.dna.map.GenomeSequence

Direct Known Subclasses:

GVCFGenotypeSequence

public class GVCFSequence
extends Object
implements net.maizegenetics.dna.map.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 RangeMap to 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.

Constructor Summary

Constructors

Constructor and Description
GVCFSequence()

Method Summary

Modifier and Type	Method and Description
static Map<String,net.maizegenetics.dna.map.GenomeSequence>	allTaxonInstance(net.maizegenetics.dna.map.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
Set<net.maizegenetics.dna.map.Chromosome>	chromosomes()
byte[]	chromosomeSequence(net.maizegenetics.dna.map.Chromosome chrom)
byte[]	chromosomeSequence(net.maizegenetics.dna.map.Chromosome chrom, int startSite, int endSite)
int	chromosomeSize(net.maizegenetics.dna.map.Chromosome chromosome)
Map<Long,net.maizegenetics.util.Tuple<net.maizegenetics.dna.map.Chromosome,Integer>>	fullRefCoordinateToChromCoordinate(ArrayList<Long> coordinates)
byte[]	genomeSequence(long startSite, long lastSite)
String	genomeSequenceAsString(long startSite, long lastSite)
long	genomeSize()
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 create a GenomeSequenc from 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 add in missing as Ref from a file
static net.maizegenetics.dna.map.GenomeSequence	instance(String refFileName, String gvcfFileName) Returns an initialized GVCFSequence given the input Reference and GVCF Files.
int	numberOfChromosomes()

Methods inherited from class java.lang.Object

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

Constructor Detail

GVCFSequence

public GVCFSequence()

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 add in missing as Ref from 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 create a GenomeSequenc from a List of VariantContexts

Parameters:

referenceSequence -

variantContexts -

missingAsRef -

taxonName -

Returns:

allTaxonInstance

public static Map<String,net.maizegenetics.dna.map.GenomeSequence> allTaxonInstance(net.maizegenetics.dna.map.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

Parameters:

referenceSequence -

vcfFileName -

missingAsRef -

Returns:

chromosomes

public Set<net.maizegenetics.dna.map.Chromosome> chromosomes()

Specified by:

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

chromosomeSequence

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

Specified by:

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

chromosomeSequence

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

Specified by:

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

genomeSequence

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

Specified by:

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

genomeSequenceAsString

public String genomeSequenceAsString(long startSite,
                                     long lastSite)

Specified by:

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

fullRefCoordinateToChromCoordinate

public Map<Long,net.maizegenetics.util.Tuple<net.maizegenetics.dna.map.Chromosome,Integer>> fullRefCoordinateToChromCoordinate(ArrayList<Long> coordinates)

Specified by:

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

chromosomeSize

public int chromosomeSize(net.maizegenetics.dna.map.Chromosome chromosome)

Specified by:

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

genomeSize

public long genomeSize()

Specified by:

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

numberOfChromosomes

public int numberOfChromosomes()

Specified by:

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

genotype

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

Specified by:

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

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

genotypeAsString

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

Specified by:

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

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

genotypeAsString

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

Specified by:

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