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.

Class VCFEncoder

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface htsjdk.beta.plugin.HtsEncoder

Constructor Details

VCFEncoder

Method Details

getFileFormat

getDisplayName

setHeader

write

close

getOutputBundle

getVariantsEncoderOptions