Package | Description |
---|---|
htsjdk.variant.bcf2 | |
htsjdk.variant.variantcontext.writer |
Modifier and Type | Field and Description |
---|---|
static BCF2Type[] |
BCF2Utils.ID_TO_ENUM |
static BCF2Type[] |
BCF2Utils.INTEGER_TYPES_BY_SIZE |
Modifier and Type | Method and Description |
---|---|
static BCF2Type |
BCF2Utils.decodeType(byte typeDescriptor) |
static BCF2Type |
BCF2Utils.determineIntegerType(int value) |
static BCF2Type |
BCF2Utils.determineIntegerType(int[] values) |
static BCF2Type |
BCF2Utils.determineIntegerType(java.util.List<java.lang.Integer> values) |
static BCF2Type |
BCF2Utils.maxIntegerType(BCF2Type t1,
BCF2Type t2)
Returns the maximum BCF2 integer size of t1 and t2
For example, if t1 == INT8 and t2 == INT16 returns INT16
|
static BCF2Type |
BCF2Type.valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.
|
static BCF2Type[] |
BCF2Type.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
Modifier and Type | Method and Description |
---|---|
int |
BCF2Decoder.decodeInt(BCF2Type type) |
int[] |
BCF2Decoder.decodeIntArray(int size,
BCF2Type type,
int[] maybeDest)
Low-level reader for int[]
Requires a typeDescriptor so the function knows how many elements to read,
and how they are encoded.
|
java.lang.Object |
BCF2Decoder.decodeSingleValue(BCF2Type type) |
static byte |
BCF2Utils.encodeTypeDescriptor(int nElements,
BCF2Type type) |
static BCF2Type |
BCF2Utils.maxIntegerType(BCF2Type t1,
BCF2Type t2)
Returns the maximum BCF2 integer size of t1 and t2
For example, if t1 == INT8 and t2 == INT16 returns INT16
|
Modifier and Type | Method and Description |
---|---|
BCF2Type |
BCF2Encoder.encode(java.lang.Object o)
Totally generic encoder that examines o, determines the best way to encode it, and encodes it
This method is incredibly slow, but it's only used for UnitTests so it doesn't matter
|
BCF2Type |
BCF2FieldEncoder.getDynamicType(java.lang.Object value) |
BCF2Type |
BCF2FieldEncoder.IntArray.getDynamicType(java.lang.Object value) |
BCF2Type |
BCF2FieldEncoder.AtomicInt.getDynamicType(java.lang.Object value) |
BCF2Type |
BCF2FieldEncoder.GenericInts.getDynamicType(java.lang.Object value) |
BCF2Type |
BCF2FieldEncoder.getStaticType() |
BCF2Type |
BCF2FieldEncoder.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.
|
Modifier and Type | Method and Description |
---|---|
void |
BCF2Encoder.encodeRawBytes(int value,
BCF2Type type) |
void |
BCF2Encoder.encodeRawInt(int value,
BCF2Type type) |
void |
BCF2Encoder.encodeRawMissingValue(BCF2Type type) |
void |
BCF2Encoder.encodeRawMissingValues(int size,
BCF2Type type) |
<T> void |
BCF2Encoder.encodeRawValue(T value,
BCF2Type type) |
<T> void |
BCF2Encoder.encodeRawValues(java.util.Collection<T> v,
BCF2Type type) |
void |
BCF2Encoder.encodeType(int size,
BCF2Type type) |
void |
BCF2Encoder.encodeTyped(java.util.List<? extends java.lang.Object> v,
BCF2Type type) |
void |
BCF2Encoder.encodeTyped(java.lang.Object value,
BCF2Type type) |
void |
BCF2Encoder.encodeTypedInt(int v,
BCF2Type type) |
void |
BCF2Encoder.encodeTypedMissing(BCF2Type type) |
abstract void |
BCF2FieldEncoder.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.
|
void |
BCF2FieldEncoder.StringOrCharacter.encodeValue(BCF2Encoder encoder,
java.lang.Object value,
BCF2Type type,
int minValues) |
void |
BCF2FieldEncoder.Flag.encodeValue(BCF2Encoder encoder,
java.lang.Object value,
BCF2Type type,
int minValues) |
void |
BCF2FieldEncoder.Float.encodeValue(BCF2Encoder encoder,
java.lang.Object value,
BCF2Type type,
int minValues) |
void |
BCF2FieldEncoder.IntArray.encodeValue(BCF2Encoder encoder,
java.lang.Object value,
BCF2Type type,
int minValues) |
void |
BCF2FieldEncoder.AtomicInt.encodeValue(BCF2Encoder encoder,
java.lang.Object value,
BCF2Type type,
int minValues) |
void |
BCF2FieldEncoder.GenericInts.encodeValue(BCF2Encoder encoder,
java.lang.Object value,
BCF2Type type,
int minValues) |