net.maizegenetics.dna.map

Interface GenomeSequence

All Known Subinterfaces:

GVCFGenomeSequence

public GenomeSequence

Defines the genome sequence of a chromosome

Method Detail

chromosomes

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

Returns a list of chromosomes whose sequences have been stored in the chromsomeSequence map of the class implementing this interface. Return empty set if empty.

Returns:

org.jetbrains.dokka.NodeRenderContent@8f5660f: a Set of Chromosome objects

chromosomeSequence

kotlin.Array[] chromosomeSequence(Chromosome chrom)

Takes a Chromosome object and returns the stored byte array representing the genomic sequence for the specified chromosome.

Parameters:

chrom - ; a Chromosome object representing the chromosome whose sequence will be returned

Returns:

org.jetbrains.dokka.NodeRenderContent@110720d6: A byte array containing the chromosome alleles in NucleotideAlignmentConstant form packed in half bytes

chromosomeSequence

kotlin.Array[] chromosomeSequence(Chromosome chrom,
                                  int startSite,
                                  int endSite)

Returns the partial genomic sequence for a chromosome, from the specified start position to the specified end position. THe start/end positions are inclusive and the request is 1-based (though the alleles are stored in a 0-based byte array).

Parameters:

chrom - : the chromosome whose partial sequence will be returned.

startSite - : the 1-based position in the sequence to start the pull.

endSite - : the 1-based position in the sequence that will be the last allele in the pull

Returns:

org.jetbrains.dokka.NodeRenderContent@450400f3: A byte array of alleles in NucleotideAlignmentConstant form that is packed into half bytes.

genomeSequence

kotlin.Array[] genomeSequence(long startSite,
                              long lastSite)

Returns the partial genomic sequence from the specified start position to the specified end position. THe start/end positions are inclusive and the request is 0-based (though the alleles are stored in a 0-based byte array). Note the difference with chromosomes, which start with 1. Can only return 2.1 billion sites per call.

Parameters:

startSite - : the 0-based position in the sequence to start the pull.

lastSite - : the 0-based position in the sequence that will be the last allele in the pull

Returns:

org.jetbrains.dokka.NodeRenderContent@5ad5e205: A byte array of alleles in NucleotideAlignmentConstant

genomeSequenceAsString

java.lang.String genomeSequenceAsString(long startSite,
                                        long lastSite)

Returns the partial genomic sequence from the specified start position to the specified end position. The start/end positions are inclusive and the request is 0-based (though the alleles are stored in a 0-based byte array). Note the difference with chromosomes, which start with 1. Can only return 2.1 billion sites per call.

Parameters:

startSite - : the 0-based position in the sequence to start the pull.

lastSite - : the 0-based position in the sequence that will be the last allele in the pull

Returns:

org.jetbrains.dokka.NodeRenderContent@79b3224e: A String of the sequence

fullRefCoordinateToChromCoordinate

java.util.Map<java.lang.Long,net.maizegenetics.util.Tuple> fullRefCoordinateToChromCoordinate(java.util.ArrayList<java.lang.Long> coordinates)

Takes a list of coordinates from the full genome sequence and for each returns the corresponding chromosome and a coordinate relative to the start of that chromosome. The request is 0-based, as are the arrays where the alleles are stored, and the results.

Parameters:

coordinates - : list of coordinates from the full genome sequence to be like mapped

Returns:

org.jetbrains.dokka.NodeRenderContent@519abc3e: A map of > for each global coordinate passed where "Long" is the global ref, and Tuple<> is the chrom/chrom-position to which this relates.

chromosomeSize

int chromosomeSize(Chromosome chromosome)

Returns the length of the current chromsome

Parameters:

chromosome -

Returns:

org.jetbrains.dokka.NodeRenderContent@34fc2d66:

genomeSize

long genomeSize()

Returns the length of the entire genome

numberOfChromosomes

int numberOfChromosomes()

Returns the number of chromosomes

genotype

byte genotype(Chromosome chrom,
              int position)

Returns the allele value in a byte for the specified PHYSICAL position (1-based)

Parameters:

chrom - Chromosome object we wish to query

position - Position on the chromosome whose value will be returned

Returns:

org.jetbrains.dokka.NodeRenderContent@414c2436:

genotype

byte genotype(Chromosome chrom,
              Position positionObject)

Returns the TASSEL encoding for the allele value in a byte for the specified PHYSICAL position

Parameters:

chrom -

positionObject - Position object from which the physical will be obtained.

Returns:

org.jetbrains.dokka.NodeRenderContent@210ddf03:

genotypeAsString

java.lang.String genotypeAsString(Chromosome chrom,
                                  int position)

Returns the haplotype allele value in a String for the specified physical position on the specified chromosome

Parameters:

chrom -

position -

Returns:

org.jetbrains.dokka.NodeRenderContent@25f2fc50:

genotypeAsString

java.lang.String genotypeAsString(Chromosome chrom,
                                  Position positionObject)

Returns the haplotype allele value in a String for the specified physical position on the specified chromosome

Parameters:

chrom -

positionObject -

Returns:

org.jetbrains.dokka.NodeRenderContent@70b07295:

genotypeAsString

java.lang.String genotypeAsString(Chromosome chrom,
                                  int startSite,
                                  int endSite)

Returns a string of haplotype allele values for the specified physical start and physical end positions on the specified chromosome.

Parameters:

chrom -

startSite -

endSite -

Returns:

org.jetbrains.dokka.NodeRenderContent@50fd9521: