Package org.bdgenomics.convert.htsjdk

Class VariantToVariantContext

java.lang.Object

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

org.bdgenomics.convert.htsjdk.VariantToVariantContext

All Implemented Interfaces:

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

public final class VariantToVariantContext
extends AbstractConverter<org.bdgenomics.formats.avro.Variant,htsjdk.variant.variantcontext.VariantContext>

Convert a Variant to a VariantContext.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
VariantToVariantContext(htsjdk.variant.vcf.VCFHeader header)	Create a new Variant to VariantContext converter with the specified header.

Method Summary

Modifier and Type	Method	Description
htsjdk.variant.variantcontext.VariantContext	convert(org.bdgenomics.formats.avro.Variant variant, 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

VariantToVariantContext

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

Create a new Variant to VariantContext converter with the specified header.

Parameters:

header - header, must not be null

Method Detail

convert

public htsjdk.variant.variantcontext.VariantContext convert(org.bdgenomics.formats.avro.Variant variant,
                                                            ConversionStringency stringency,
                                                            org.slf4j.Logger logger)
                                                     throws ConversionException

Throws:

ConversionException