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 java.lang.Object

See #BCFWriter for documentation on this classes role in encoding BCF2 files

Since:

06/12

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BCF2FieldEncoder.AtomicInt Specialized int encoder for atomic (non-list) integers
static class	BCF2FieldEncoder.Flag
static class	BCF2FieldEncoder.Float
static class	BCF2FieldEncoder.GenericInts
static class	BCF2FieldEncoder.IntArray
static class	BCF2FieldEncoder.StringOrCharacter

Method Summary

Modifier and Type	Method and Description
abstract void	encodeValue(BCF2Encoder encoder, java.lang.Object value, BCF2Type type, int minValues) Key abstract method that should encode a value of the given type into the encoder.
protected VCFHeaderLineCount	getCountType()
BCF2Type	getDynamicType(java.lang.Object value)
java.lang.String	getField()
BCF2Type	getStaticType()
BCF2Type	getType(java.lang.Object value) Get the BCF2 type for this field, either from the static type of the field itself or by inspecting the value itself.
boolean	hasConstantNumElements() True if this field has a constant, fixed number of elements (such as 1 for an atomic integer)
boolean	hasContextDeterminedNumElements() 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.
boolean	hasValueDeterminedNumElements() 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.
boolean	isDynamicallyTyped() Is the BCF2 type of this field static, or does it have to be determine from the actual field value itself?
boolean	isStaticallyTyped() Is the BCF2 type of this field static, or does it have to be determine from the actual field value itself?
int	numElements() Get the number of elements, assuming this field has a constant number of elements.
int	numElements(java.lang.Object value) Get the number of elements by looking at the actual value provided
int	numElements(VariantContext vc) Get the number of elements, assuming this field has context-determined number of elements.
int	numElements(VariantContext vc, java.lang.Object value) A convenience access for the number of elements, returning the number of encoded elements, either from the fixed number it has, from the VC, or from the value itself.
protected int	numElementsFromValue(java.lang.Object value) Given a value, return the number of elements we will encode for it.
java.lang.String	toString()
void	writeFieldKey(BCF2Encoder encoder) Write the field key (dictionary offset and type) into the BCF2Encoder stream

Methods inherited from class java.lang.Object

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

Method Detail

getField

public final java.lang.String getField()

writeFieldKey

public final void writeFieldKey(BCF2Encoder encoder)
                         throws java.io.IOException

Write the field key (dictionary offset and type) into the BCF2Encoder stream

Parameters:

encoder - where we write our dictionary offset

Throws:

java.io.IOException

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getCountType

protected final VCFHeaderLineCount getCountType()

hasConstantNumElements

public boolean hasConstantNumElements()

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

Returns:

hasValueDeterminedNumElements

public boolean hasValueDeterminedNumElements()

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.

Returns:

hasContextDeterminedNumElements

public boolean hasContextDeterminedNumElements()

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.

Returns:

numElements

public int numElements()

Get the number of elements, assuming this field has a constant number of elements.

Returns:

numElements

public int numElements(java.lang.Object value)

Get the number of elements by looking at the actual value provided

Returns:

numElements

public int numElements(VariantContext vc)

Get the number of elements, assuming this field has context-determined number of elements.

Returns:

numElements

public final int numElements(VariantContext vc,
                             java.lang.Object value)

A convenience access for the number of elements, returning the number of encoded elements, either from the fixed number it has, from the VC, or from the value itself.

Parameters:

vc -

value -

Returns:

numElementsFromValue

protected int numElementsFromValue(java.lang.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:

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:

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:

getType

public final BCF2Type getType(java.lang.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:

getStaticType

public final BCF2Type getStaticType()

getDynamicType

public BCF2Type getDynamicType(java.lang.Object value)

encodeValue

public abstract void encodeValue(BCF2Encoder encoder,
                                 java.lang.Object value,
                                 BCF2Type type,
                                 int minValues)
                          throws java.io.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:

java.io.IOException