net.maizegenetics.dna.map

Class GenomeSequenceBuilder

net.maizegenetics.dna.map.GenomeSequenceBuilder

Direct Known Subclasses:

GVCFGenomeSequenceBuilder

public class GenomeSequenceBuilder

Builder for a chromosome genome sequence that hides the ReferenceGenomeSequence implementation. The sequence is read from a fasta file and stored in a byte array, 2 alleles packed per byte.

Method Detail

instance

public static GenomeSequence instance(java.lang.String fastaFileName)

Builds GenomeSequence from a fasta file.

Parameters:

fastaFileName - full path to fasta file

Returns:

org.jetbrains.dokka.NodeRenderContent@5ee742b: GenomeSequence object

instance

public static GenomeSequence instance(java.lang.String fastaFileName,
                                      java.util.function.Function<java.lang.Character,java.lang.Character> charConversion)

Builds GenomeSequence from a fasta file. The char conversion provide a mechanism to convert upper and lower case or convert one case to N. This is useful if a case if used to define a certain class of bases

Parameters:

fastaFileName - full path to fasta file

charConversion - lambda Function to convert characters

Returns:

org.jetbrains.dokka.NodeRenderContent@a399cdb: GenomeSequence object

instance

public static GenomeSequence instance(Chromosome chromosome,
                                      java.lang.String sequence)

Builds GenomeSequence from a String with one Chromosome.

Parameters:

chromosome - chromosome object

sequence - in upper case character

Returns:

org.jetbrains.dokka.NodeRenderContent@4f8e7344: GenomeSequence object

readReferenceGenomeChr

protected static java.util.Map<net.maizegenetics.dna.map.Chromosome,kotlin.Array[]> readReferenceGenomeChr(java.lang.String fastaFileName,
                                                                                                           java.util.function.Function<java.lang.Character,java.lang.Character> charConversion)