net.maizegenetics.dna.snp.io

Class ProjectionGenotypeIO

net.maizegenetics.dna.snp.io.ProjectionGenotypeIO

public class ProjectionGenotypeIO

Methods for reading and writing ProjectionGenotypes to files. ProjectionGenotypes have two parts - one is the Projection file that has the names of high density genotyped taxa and the recombination breakpoints for each of the low density taxa that point to the high density taxa.

Method Detail

getInstance

public static GenotypeTable getInstance(java.lang.String paFile,
                                        java.lang.String baseHighDensityAlignmentFile)

Returns a genotypeTable based on a projection genotype file and high density genotype table

Parameters:

paFile - file name for projection file

baseHighDensityAlignmentFile - file name for high density file

Returns:

org.jetbrains.dokka.NodeRenderContent@355b9bae: GenotypeTable based on both

getInstance

public static GenotypeTable getInstance(java.lang.String paFile,
                                        GenotypeTable baseHighDensityAlignment)

Returns a genotypeTable based on a projection genotype file and high density genotype table

Parameters:

paFile - file name for projection file

baseHighDensityAlignment - GenotypeTable of high density taxa

Returns:

org.jetbrains.dokka.NodeRenderContent@65c9a1ce: Projection GenotypeTable based on both

writeToFile

public static void writeToFile(java.lang.String outfile,
                               GenotypeTable pa)

Exports the ProjectionGenotypes to a file

Parameters:

outfile - the path and name of the projection file

pa - GenotypeTable with a ProjectionGenotypeCallTable