net.maizegenetics.dna.snp.io

Class BuilderFromVCF

net.maizegenetics.dna.snp.io.BuilderFromVCF

public class BuilderFromVCF

Create an alignment based on VCF format file (either .txt or compressed). Alleles are set as global reference. e.g. code

Alignment a=BuilderFromVCF.getBuilder(infileName).build(); TODO: Add filtering while reading, provide an option to define the alleles as reference and alternate

Method Detail

getBuilder

public static BuilderFromVCF getBuilder(java.lang.String infile)

Create a builder for loading a VCF file into memory

Parameters:

infile - name of the VCF file to be load

Returns:

org.jetbrains.dokka.NodeRenderContent@8312dba: a builder

getBuilder

public static BuilderFromVCF getBuilder(java.lang.String infile,
                                        ProgressListener listener)

Create a builder for loading a VCF file into memory

Parameters:

infile - name of the VCF file to be load

listener - Progress listener for GUI

Returns:

org.jetbrains.dokka.NodeRenderContent@e6058c: a builder

convertToHDF5

public BuilderFromVCF convertToHDF5(java.lang.String hdf5Outfile)

Create a HDF5 version of file from the VCF file. This is useful in many cases where VCF files are too large to load fully into memory.

Parameters:

hdf5Outfile -

Returns:

org.jetbrains.dokka.NodeRenderContent@7a23b9db:

keepDepth

public BuilderFromVCF keepDepth()

buildAndSortInMemory

public GenotypeTable buildAndSortInMemory()

build

public GenotypeTable build()