org.bdgenomics.convert.htsjdk

Class GenotypesToVariantContext

java.lang.Object

org.bdgenomics.convert.AbstractConverter<List<org.bdgenomics.formats.avro.Genotype>,htsjdk.variant.variantcontext.VariantContext>

org.bdgenomics.convert.htsjdk.GenotypesToVariantContext

All Implemented Interfaces:

Serializable, Converter<List<org.bdgenomics.formats.avro.Genotype>,htsjdk.variant.variantcontext.VariantContext>

public final class GenotypesToVariantContext
extends AbstractConverter<List<org.bdgenomics.formats.avro.Genotype>,htsjdk.variant.variantcontext.VariantContext>

Convert a list of Genotypes to a VariantContext.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
GenotypesToVariantContext(htsjdk.variant.vcf.VCFHeader header) Create a new list of Genotypes to VariantContext converter with the specified header.

Method Summary

Modifier and Type	Method and Description
htsjdk.variant.variantcontext.VariantContext	convert(List<org.bdgenomics.formats.avro.Genotype> genotypes, ConversionStringency stringency, org.slf4j.Logger logger)

Methods inherited from class org.bdgenomics.convert.AbstractConverter

checkNotNull, checkNotNull, checkNotNull, getSourceClass, getTargetClass, warnOrThrow

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GenotypesToVariantContext

@Inject
public GenotypesToVariantContext(htsjdk.variant.vcf.VCFHeader header)

Create a new list of Genotypes to VariantContext converter with the specified header.

Parameters:

header - header, must not be null

Method Detail

convert

public htsjdk.variant.variantcontext.VariantContext convert(List<org.bdgenomics.formats.avro.Genotype> genotypes,
                                                            ConversionStringency stringency,
                                                            org.slf4j.Logger logger)
                                                     throws ConversionException

Throws:

ConversionException