net.maizegenetics.dna.snp.io

Class BuilderFromVCFUsingHTSJDK

net.maizegenetics.dna.snp.io.BuilderFromVCFUsingHTSJDK

public class BuilderFromVCFUsingHTSJDK

This builder reads a VCF formatted file and creates a interface GenotypeTable

See Also:

interface GenotypeTable

Method Detail

instance

public static BuilderFromVCFUsingHTSJDK instance(java.lang.String vcf)

instance

public static BuilderFromVCFUsingHTSJDK instance(htsjdk.variant.vcf.VCFHeader header,
                                                 java.util.Iterator<htsjdk.variant.variantcontext.VariantContext> variants)

instance

public static BuilderFromVCFUsingHTSJDK instance(htsjdk.variant.vcf.VCFHeader header,
                                                 java.util.List<htsjdk.variant.variantcontext.VariantContext> variants)

read

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

read

public static GenotypeTable read(htsjdk.variant.vcf.VCFHeader header,
                                 java.util.List<htsjdk.variant.variantcontext.VariantContext> variants)

progressListener

public BuilderFromVCFUsingHTSJDK progressListener(ProgressListener listener)

keepDepth

public BuilderFromVCFUsingHTSJDK keepDepth(boolean keep)

build

public GenotypeTable build()