Package htsjdk.beta.codecs.variants.vcf

Class VCFEncoder

java.lang.Object

htsjdk.beta.codecs.variants.vcf.VCFEncoder

All Implemented Interfaces:

HtsEncoder<VCFHeader,VariantContext>, VariantsEncoder, Closeable, AutoCloseable

Direct Known Subclasses:

VCFEncoderV3_2, VCFEncoderV3_3, VCFEncoderV4_0, VCFEncoderV4_1, VCFEncoderV4_2

@InternalAPI
public abstract class VCFEncoder
extends Object
implements VariantsEncoder

InternalAPI Base class for concrete implementations of HtsContentType.VARIANT_CONTEXTS encoders.

Constructor Summary

Constructors

Constructor	Description
VCFEncoder(Bundle outputBundle, VariantsEncoderOptions variantsEncoderOptions)	InternalAPI Create a new VCF encoder from a Bundle.

Method Summary

Modifier and Type	Method	Description
void	close()	Close any resources associated with this decoder.
final String	getDisplayName()	Get a user-friendly display name for this encoder.
final String	getFileFormat()	Get the name of the file format supported by this encoder.
Bundle	getOutputBundle()	Get the output Bundle for this encoder.
VariantsEncoderOptions	getVariantsEncoderOptions()	Get the VariantsEncoderOptions for this encoder.
void	setHeader(VCFHeader vcfHeader)	Set the file format header for this decoder, of type HtsEncoder.
void	write(VariantContext variantContext)	Write a single record to the underlying output.

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.beta.plugin.HtsEncoder

getVersion

Constructor Details

VCFEncoder

@InternalAPI
public VCFEncoder(Bundle outputBundle,
 VariantsEncoderOptions variantsEncoderOptions)

InternalAPI Create a new VCF encoder from a Bundle. NOTE: callers that provide an output stream resource should provide a buffered output stream if buffering is desired, since the encoder does not provide an additional buffering layer.

Parameters:

outputBundle - the output Bundle to encode

variantsEncoderOptions - the VariantsEncoderOptions to use

Method Details

getFileFormat

public final String getFileFormat()

Description copied from interface: HtsEncoder

Get the name of the file format supported by this encoder. The format name defines the underlying format handled by this encoder, and also corresponds to the format of the primary bundle resource that is required when encoding (see BundleResourceType and BundleResource.getFileFormat()).

Specified by:

getFileFormat in interface HtsEncoder<VCFHeader,VariantContext>

Returns:

the name of the underlying file format handled by this encoder

getDisplayName

public final String getDisplayName()

Description copied from interface: HtsEncoder

Get a user-friendly display name for this encoder.

Specified by:

getDisplayName in interface HtsEncoder<VCFHeader,VariantContext>

Returns:

a user-friendly display name for this encoder for use in error and warning messages

setHeader

public void setHeader(VCFHeader vcfHeader)

Description copied from interface: HtsEncoder

Set the file format header for this decoder, of type HtsEncoder. HtsEncoder.setHeader(HtsHeader) must be called before HtsEncoder.write(HtsRecord) can be called.

Specified by:

setHeader in interface HtsEncoder<VCFHeader,VariantContext>

Parameters:

vcfHeader - to use

write

public void write(VariantContext variantContext)

Description copied from interface: HtsEncoder

Write a single record to the underlying output. HtsEncoder.write(HtsRecord) may only called after HtsEncoder.setHeader(HtsHeader) has been called.

Specified by:

write in interface HtsEncoder<VCFHeader,VariantContext>

Parameters:

variantContext - record to write

close

public void close()

Description copied from interface: HtsEncoder

Close any resources associated with this decoder.

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Specified by:

close in interface HtsEncoder<VCFHeader,VariantContext>

getOutputBundle

public Bundle getOutputBundle()

Get the output Bundle for this encoder.

Returns:

the output Bundle for this encoder

getVariantsEncoderOptions

public VariantsEncoderOptions getVariantsEncoderOptions()

Get the VariantsEncoderOptions for this encoder.

Returns:

the VariantsEncoderOptions for this encoder.