Constructor Detail

• BCF2FieldWriterManager

  public BCF2FieldWriterManager()

Method Detail

• setup

  public void setup(VCFHeader header,
                    BCF2Encoder encoder,
                    Map<String,Integer> stringDictionary)

  Setup the FieldWriters appropriate to each INFO and FORMAT in the VCF header Must be called before any of the getter methods will work

  Parameters:

  header - a VCFHeader containing description for every INFO and FORMAT field we'll attempt to write out to BCF

  encoder - the encoder we are going to use to write out the BCF2 data

  stringDictionary - a map from VCFHeader strings to their offsets for encoding

• getSiteFieldWriter

  public BCF2FieldWriter.SiteWriter getSiteFieldWriter(String field)

  Get a site writer specialized to encode values for site info field

  Parameters:

  field - key found in the VCF header INFO records

  Returns:

  non-null writer if one can be found, or null if none exists for field

• getGenotypeFieldWriter

  public BCF2FieldWriter.GenotypesWriter getGenotypeFieldWriter(String field)

  Get a genotypes writer specialized to encode values for genotypes field

  Parameters:

  field - key found in the VCF header FORMAT records

  Returns:

  non-null writer if one can be found, or null if none exists for field

• getWriter

  public <T> T getWriter(String key,
                         Map<String,T> map)