htsjdk.variant.bcf2

Class BCF2Decoder

java.lang.Object

htsjdk.variant.bcf2.BCF2Decoder

public final class BCF2Decoder
extends java.lang.Object

Constructor Summary

Constructors

Modifier	Constructor and Description
	BCF2Decoder()
protected	BCF2Decoder(byte[] recordBytes) Create a new decoder ready to read BCF2 data from the byte[] recordBytes, for testing purposes

Method Summary

Modifier and Type	Method and Description
boolean	blockIsFullyDecoded()
int	decodeInt(BCF2Type type)
int	decodeInt(byte typeDescriptor, int missingValue) Decode an int from the stream.
int[]	decodeIntArray(byte typeDescriptor, int size)
int[]	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.
int	decodeNumberOfElements(byte typeDescriptor)
java.lang.Object	decodeSingleValue(BCF2Type type)
java.lang.Object	decodeTypedValue()
java.lang.Object	decodeTypedValue(byte typeDescriptor)
java.lang.Object	decodeTypedValue(byte typeDescriptor, int size)
int	getBlockSize() The size of the current block in bytes
byte[]	getRecordBytes() Returns the byte[] for the block of data we are currently decoding
int	readBlockSize(java.io.InputStream inputStream) Read the size of the next block from inputStream
void	readNextBlock(int blockSizeInBytes, java.io.InputStream stream) Reads the next record from input stream and prepare this decoder to decode values from it
byte	readTypeDescriptor()
void	setRecordBytes(byte[] recordBytes) Use the recordBytes[] to read BCF2 records from now on
void	skipNextBlock(int blockSizeInBytes, java.io.InputStream stream) Skips the next record from input stream, invalidating current block data

Methods inherited from class java.lang.Object

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

Constructor Detail

BCF2Decoder

public BCF2Decoder()

BCF2Decoder

protected BCF2Decoder(byte[] recordBytes)

Create a new decoder ready to read BCF2 data from the byte[] recordBytes, for testing purposes

Parameters:

recordBytes -

Method Detail

readNextBlock

public void readNextBlock(int blockSizeInBytes,
                          java.io.InputStream stream)

Reads the next record from input stream and prepare this decoder to decode values from it

Parameters:

stream -

skipNextBlock

public void skipNextBlock(int blockSizeInBytes,
                          java.io.InputStream stream)

Skips the next record from input stream, invalidating current block data

Parameters:

stream -

getRecordBytes

public byte[] getRecordBytes()

Returns the byte[] for the block of data we are currently decoding

Returns:

getBlockSize

public int getBlockSize()

The size of the current block in bytes

Returns:

blockIsFullyDecoded

public boolean blockIsFullyDecoded()

setRecordBytes

public void setRecordBytes(byte[] recordBytes)

Use the recordBytes[] to read BCF2 records from now on

Parameters:

recordBytes -

decodeTypedValue

public final java.lang.Object decodeTypedValue()
                                        throws java.io.IOException

Throws:

java.io.IOException

decodeTypedValue

public final java.lang.Object decodeTypedValue(byte typeDescriptor)
                                        throws java.io.IOException

Throws:

java.io.IOException

decodeTypedValue

public final java.lang.Object decodeTypedValue(byte typeDescriptor,
                                               int size)
                                        throws java.io.IOException

Throws:

java.io.IOException

decodeSingleValue

public final java.lang.Object decodeSingleValue(BCF2Type type)
                                         throws java.io.IOException

Throws:

java.io.IOException

decodeNumberOfElements

public final int decodeNumberOfElements(byte typeDescriptor)
                                 throws java.io.IOException

Throws:

java.io.IOException

decodeInt

public final int decodeInt(byte typeDescriptor,
                           int missingValue)
                    throws java.io.IOException

Decode an int from the stream. If the value in the stream is missing, returns missingValue. Requires the typeDescriptor indicate an inline single element event

Parameters:

typeDescriptor -

Returns:

Throws:

java.io.IOException

decodeInt

public final int decodeInt(BCF2Type type)
                    throws java.io.IOException

Throws:

java.io.IOException

decodeIntArray

public final int[] decodeIntArray(int size,
                                  BCF2Type type,
                                  int[] maybeDest)
                           throws java.io.IOException

Low-level reader for int[] Requires a typeDescriptor so the function knows how many elements to read, and how they are encoded. If size == 0 => result is null If size > 0 => result depends on the actual values in the stream -- If the first element read is MISSING, result is null (all values are missing) -- Else result = int[N] where N is the first N non-missing values decoded

Parameters:

maybeDest - if not null we'll not allocate space for the vector, but instead use the externally allocated array of ints to store values. If the size of this vector is < the actual size of the elements, we'll be forced to use freshly allocated arrays. Also note that padded int elements are still forced to do a fresh allocation as well.

Returns:

see description

Throws:

java.io.IOException

decodeIntArray

public final int[] decodeIntArray(byte typeDescriptor,
                                  int size)
                           throws java.io.IOException

Throws:

java.io.IOException

readBlockSize

public final int readBlockSize(java.io.InputStream inputStream)
                        throws java.io.IOException

Read the size of the next block from inputStream

Parameters:

inputStream -

Returns:

Throws:

java.io.IOException

readTypeDescriptor

public final byte readTypeDescriptor()
                              throws java.io.IOException

Throws:

java.io.IOException