Package org.bdgenomics.convert.htsjdk

Class VariantContextToVariants

java.lang.Object

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

org.bdgenomics.convert.htsjdk.VariantContextToVariants

All Implemented Interfaces:

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

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

Convert VariantContext to a list of Variants.

See Also:

Serialized Form

Constructor Summary

Constructors

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

Method Summary

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

VariantContextToVariants

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

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

Parameters:

header - header, must not be null

Method Detail

convert

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

Throws:

ConversionException