htsjdk.variant.variantcontext.writer

Class BCF2Encoder

java.lang.Object

htsjdk.variant.variantcontext.writer.BCF2Encoder

public final class BCF2Encoder
extends java.lang.Object

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

Since:

06/12

Field Summary

Fields

Modifier and Type	Field and Description
static int	WRITE_BUFFER_INITIAL_SIZE

Constructor Summary

Constructors

Constructor and Description
BCF2Encoder()

Method Summary

Modifier and Type	Method and Description
BCF2Type	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
void	encodeRawBytes(int value, BCF2Type type)
void	encodeRawChar(byte c)
void	encodeRawFloat(double value)
void	encodeRawInt(int value, BCF2Type type)
void	encodeRawMissingValue(BCF2Type type)
void	encodeRawMissingValues(int size, BCF2Type type)
void	encodeRawString(java.lang.String s, int sizeToWrite)
<T> void	encodeRawValue(T value, BCF2Type type)
<T> void	encodeRawValues(java.util.Collection<T> v, BCF2Type type)
void	encodeType(int size, BCF2Type type)
void	encodeTyped(java.util.List<? extends java.lang.Object> v, BCF2Type type)
void	encodeTyped(java.lang.Object value, BCF2Type type)
void	encodeTypedFloat(double d)
void	encodeTypedInt(int v)
void	encodeTypedInt(int v, BCF2Type type)
void	encodeTypedMissing(BCF2Type type)
void	encodeTypedString(byte[] s)
void	encodeTypedString(java.lang.String s)
byte[]	getRecordBytes()

Methods inherited from class java.lang.Object

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

Field Detail

WRITE_BUFFER_INITIAL_SIZE

public static final int WRITE_BUFFER_INITIAL_SIZE

See Also:

Constant Field Values

Constructor Detail

BCF2Encoder

public BCF2Encoder()

Method Detail

getRecordBytes

public byte[] getRecordBytes()

encodeTypedMissing

public final void encodeTypedMissing(BCF2Type type)
                              throws java.io.IOException

Throws:

java.io.IOException

encodeTyped

public final void encodeTyped(java.lang.Object value,
                              BCF2Type type)
                       throws java.io.IOException

Throws:

java.io.IOException

encodeTypedInt

public final void encodeTypedInt(int v)
                          throws java.io.IOException

Throws:

java.io.IOException

encodeTypedInt

public final void encodeTypedInt(int v,
                                 BCF2Type type)
                          throws java.io.IOException

Throws:

java.io.IOException

encodeTypedString

public final void encodeTypedString(java.lang.String s)
                             throws java.io.IOException

Throws:

java.io.IOException

encodeTypedString

public final void encodeTypedString(byte[] s)
                             throws java.io.IOException

Throws:

java.io.IOException

encodeTypedFloat

public final void encodeTypedFloat(double d)
                            throws java.io.IOException

Throws:

java.io.IOException

encodeTyped

public final void encodeTyped(java.util.List<? extends java.lang.Object> v,
                              BCF2Type type)
                       throws java.io.IOException

Throws:

java.io.IOException

encodeRawValues

public final <T> void encodeRawValues(java.util.Collection<T> v,
                                      BCF2Type type)
                               throws java.io.IOException

Throws:

java.io.IOException

encodeRawValue

public final <T> void encodeRawValue(T value,
                                     BCF2Type type)
                              throws java.io.IOException

Throws:

java.io.IOException

encodeRawMissingValue

public final void encodeRawMissingValue(BCF2Type type)
                                 throws java.io.IOException

Throws:

java.io.IOException

encodeRawMissingValues

public final void encodeRawMissingValues(int size,
                                         BCF2Type type)
                                  throws java.io.IOException

Throws:

java.io.IOException

encodeRawChar

public final void encodeRawChar(byte c)
                         throws java.io.IOException

Throws:

java.io.IOException

encodeRawFloat

public final void encodeRawFloat(double value)
                          throws java.io.IOException

Throws:

java.io.IOException

encodeType

public final void encodeType(int size,
                             BCF2Type type)
                      throws java.io.IOException

Throws:

java.io.IOException

encodeRawInt

public final void encodeRawInt(int value,
                               BCF2Type type)
                        throws java.io.IOException

Throws:

java.io.IOException

encodeRawBytes

public final void encodeRawBytes(int value,
                                 BCF2Type type)
                          throws java.io.IOException

Throws:

java.io.IOException

encodeRawString

public void encodeRawString(java.lang.String s,
                            int sizeToWrite)
                     throws java.io.IOException

Throws:

java.io.IOException

encode

public final BCF2Type encode(java.lang.Object o)
                      throws java.io.IOException

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

Parameters:

o -

Returns:

Throws:

java.io.IOException