net.maizegenetics.dna.snp

Class ImportUtils

net.maizegenetics.dna.snp.ImportUtils

public class ImportUtils

Methods for importing GenotypeTables from various file formats.

Field Detail

NUM_HAPMAP_NON_TAXA_HEADERS

public static int NUM_HAPMAP_NON_TAXA_HEADERS

See Also:

Constant Field Values

Method Detail

read

public static GenotypeTable read(java.lang.String filename)

This utility attempts to identify the file format(i.e. Hapmap, VCF, HDF5, Fasta, PLINK, Phylip, Numerical Genotype) of the given file and loads it as a Genotype Table.

Parameters:

filename - input file

Returns:

org.jetbrains.dokka.NodeRenderContent@7bdfdad0: genotype table

read

public static GenotypeTable read(java.lang.String filename,
                                 boolean keepDepth,
                                 boolean sortPositions)

This utility attempts to identify the file format(i.e. Hapmap, VCF, HDF5, Fasta, PLINK, Phylip, Numerical Genotype) of the given file and loads it as a Genotype Table.

Parameters:

filename - input file

keepDepth - whether to keep depth (if available)

sortPositions - whether to sort positions (if out of order)

Returns:

org.jetbrains.dokka.NodeRenderContent@17db9fcf: genotype table

readDataSet

public static DataSet readDataSet(java.lang.String filename)

This utility attempts to identify the file format(i.e. Hapmap, VCF, HDF5, Fasta, PLINK, Phylip, Numerical Genotype) of the given file and loads it as a DataSet.

Parameters:

filename -

Returns:

org.jetbrains.dokka.NodeRenderContent@209e7c56:

readGuessFormat

public static GenotypeTable readGuessFormat(java.lang.String fileName)

Deprecated.

readFromVCF

public static GenotypeTable readFromVCF(java.lang.String filename,
                                        ProgressListener listener,
                                        boolean keepDepth,
                                        boolean sortPositions)

readFromVCF

public static GenotypeTable readFromVCF(java.lang.String filename,
                                        ProgressListener listener,
                                        boolean keepDepth)

readFromVCF

public static GenotypeTable readFromVCF(java.lang.String filename,
                                        ProgressListener listener)

readFromVCF

public static GenotypeTable readFromVCF(java.lang.String filename)

readFromHapmap

public static GenotypeTable readFromHapmap(java.lang.String filename)

Read GenotypeTable from HapMap file

Parameters:

filename - input HapMap file name

Returns:

org.jetbrains.dokka.NodeRenderContent@568d79e6: a genotype table

readFromHapmap

public static GenotypeTable readFromHapmap(java.lang.String filename,
                                           ProgressListener listener)

Read GenotypeTable from HapMap file

Parameters:

filename - input HapMap file name

listener - progress listener to track reading rate

Returns:

org.jetbrains.dokka.NodeRenderContent@538130bd: a genotype table

readFromHapmap

public static GenotypeTable readFromHapmap(java.lang.String filename,
                                           ProgressListener listener,
                                           boolean sortPositions)

Read GenotypeTable from HapMap file

Parameters:

filename - input HapMap file name

listener - progress listener to track reading rate

sortPositions - whether to sort positions

Returns:

org.jetbrains.dokka.NodeRenderContent@186fe8e5:

readFromPLink

public static GenotypeTable readFromPLink(java.lang.String pedFilename,
                                          java.lang.String mapFilename,
                                          ProgressListener listener)

readFromPLink

public static GenotypeTable readFromPLink(java.lang.String pedFilename,
                                          java.lang.String mapFilename,
                                          ProgressListener listener,
                                          boolean sortPositions)

readFasta

public static GenotypeTable readFasta(java.lang.String filename)