Package org.bdgenomics.convert.htsjdk

Class VcfHeaderToReferences

java.lang.Object

org.bdgenomics.convert.AbstractConverter<htsjdk.variant.vcf.VCFHeader,List<org.bdgenomics.formats.avro.Reference>>

org.bdgenomics.convert.htsjdk.VcfHeaderToReferences

All Implemented Interfaces:

Serializable, Converter<htsjdk.variant.vcf.VCFHeader,List<org.bdgenomics.formats.avro.Reference>>

public final class VcfHeaderToReferences
extends AbstractConverter<htsjdk.variant.vcf.VCFHeader,List<org.bdgenomics.formats.avro.Reference>>

Convert a VCFHeader to a list of References.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
VcfHeaderToReferences()	Create a new VCFHeader to a list of References converter.

Method Summary

Modifier and Type	Method	Description
List<org.bdgenomics.formats.avro.Reference>	convert(htsjdk.variant.vcf.VCFHeader header, 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

VcfHeaderToReferences

public VcfHeaderToReferences()

Create a new VCFHeader to a list of References converter.

Method Detail

convert

public List<org.bdgenomics.formats.avro.Reference> convert(htsjdk.variant.vcf.VCFHeader header,
                                                           ConversionStringency stringency,
                                                           org.slf4j.Logger logger)
                                                    throws ConversionException

Throws:

ConversionException