Package htsjdk.variant.variantcontext.writer

Class BCF2FieldEncoder

java.lang.Object
htsjdk.variant.variantcontext.writer.BCF2FieldEncoder
Direct Known Subclasses:
BCF2FieldEncoder.AtomicInt, BCF2FieldEncoder.Flag, BCF2FieldEncoder.Float, BCF2FieldEncoder.GenericInts, BCF2FieldEncoder.IntArray, BCF2FieldEncoder.StringOrCharacter
public abstract class BCF2FieldEncoder extends Object
See #BCFWriter for documentation on this classes role in encoding BCF2 files
Since:
06/12

  • Method Details

    • getField

      public final String getField()

    • writeFieldKey

      public final void writeFieldKey(BCF2Encoder encoder) throws IOException
      Write the field key (dictionary offset and type) into the BCF2Encoder stream
      Parameters:
      encoder - where we write our dictionary offset
      Throws:
      IOException

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • getCountType

      protected final VCFHeaderLineCount getCountType()

    • hasConstantNumElements

      public boolean hasConstantNumElements()
      Returns:
      True if this field has a constant, fixed number of elements (such as 1 for an atomic integer)

    • hasValueDeterminedNumElements

      public boolean hasValueDeterminedNumElements()
      Returns:
      True if the only way to determine how many elements this field contains is by inspecting the actual value directly, such as when the number of elements is a variable length list per site or per genotype.

    • hasContextDeterminedNumElements

      public boolean hasContextDeterminedNumElements()
      Returns:
      True if this field has a non-fixed number of elements that depends only on the properties of the current VariantContext, such as one value per Allele or per genotype configuration.

    • numElements

      public int numElements()
      Returns:
      the number of elements, assuming this field has a constant number of elements.

    • numElements

      public int numElements(Object value)
      Returns:
      the number of elements by looking at the actual value provided

    • numElements

      public int numElements(VariantContext vc)
      Returns:
      the number of elements, assuming this field has context-determined number of elements.

    • numElements

      public final int numElements(VariantContext vc, Object value)
      A convenience access for the number of elements.
      Parameters:
      vc -
      value -
      Returns:
      the number of encoded elements, either from the fixed number it has, from the VC, or from the value itself.

    • numElementsFromValue

      protected int numElementsFromValue(Object value)
      Given a value, return the number of elements we will encode for it. Assumes the value is encoded as a List
      Parameters:
      value -
      Returns:
      the number of elements we will encode for .

    • isStaticallyTyped

      public final boolean isStaticallyTyped()
      Is the BCF2 type of this field static, or does it have to be determine from the actual field value itself?
      Returns:
      true if the field is static

    • isDynamicallyTyped

      public final boolean isDynamicallyTyped()
      Is the BCF2 type of this field static, or does it have to be determine from the actual field value itself?
      Returns:
      true if the field is not static

    • getType

      public final BCF2Type getType(Object value)
      Get the BCF2 type for this field, either from the static type of the field itself or by inspecting the value itself.
      Returns:
      the BCF2 type for this field

    • getStaticType

      public final BCF2Type getStaticType()

    • getDynamicType

      public BCF2Type getDynamicType(Object value)

    • encodeValue

      public abstract void encodeValue(BCF2Encoder encoder, Object value, BCF2Type type, int minValues) throws IOException
      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.
      Parameters:
      encoder -
      value -
      type -
      minValues -
      Throws:
      IOException