Constructor Detail

• IntArray

  public IntArray(VCFCompoundHeaderLine headerLine,
                  Map<String,Integer> dict)

Method Detail

• numElementsFromValue

  protected int numElementsFromValue(Object value)

  Description copied from class: BCF2FieldEncoder
  Given a value, return the number of elements we will encode for it. Assumes the value is encoded as a List

  Overrides:

  numElementsFromValue in class BCF2FieldEncoder

  Returns:

  the number of elements we will encode for .

• getDynamicType

  public BCF2Type getDynamicType(Object value)

  Overrides:

  getDynamicType in class BCF2FieldEncoder

• encodeValue

  public void encodeValue(BCF2Encoder encoder,
                          Object value,
                          BCF2Type type,
                          int minValues)
                   throws IOException

  Description copied from class: BCF2FieldEncoder
  Key abstract method that should encode a value of the given type into the encoder. Value will be of a type appropriate to the underlying encoder. If the genotype field is represented as an int[], this will be value, and the encoder needs to handle encoding all of the values in the int[]. The argument should be used, not the getType() method in the superclass as an outer loop might have decided a more general type (int16) to use, even through this encoder could have been done with int8. If minValues > 0, then encodeValue must write in at least minValues items from value. If value is atomic, this means that minValues - 1 MISSING values should be added to the encoder. If minValues is a collection type (int[]) then minValues - values.length should be added. This argument is intended to handle padding of values in genotype fields.

  Specified by:

  encodeValue in class BCF2FieldEncoder

  Throws:

  IOException