net.maizegenetics.dna.map

Class GVCFGenomeSequenceBuilder

GenomeSequenceBuilder

net.maizegenetics.dna.map.GVCFGenomeSequenceBuilder

public class GVCFGenomeSequenceBuilder
extends GenomeSequenceBuilder

Created by zrm22 on 3/27/17.

Method Detail

instance

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

Builds GenomeSequence from a fasta file and a GVCF file.

Parameters:

fastaFileName - full path to fasta file

Returns:

org.jetbrains.dokka.NodeRenderContent@3125dc20: GenomeSequence object

instance

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

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@47a84532: GenomeSequence object

instance

public static GenomeSequence instance(GVCFGenomeSequence base,
                                      BitSet maskedBitSet,
                                      BitSet filteredBitSet)