htsjdk.samtools.cram.io

Interface BitOutputStream

All Superinterfaces:

java.lang.AutoCloseable, java.io.Closeable, java.io.Flushable

All Known Implementing Classes:

DefaultBitOutputStream

public interface BitOutputStream
extends java.io.Closeable, java.io.Flushable

An interface to describe the requirements for writing out bits as opposed to bytes. Implementors must keep track of the amount of data written similar to OutputStream concept and provide flush/close functionality accordingly.

Method Summary

Modifier and Type	Method and Description
void	write(boolean bit) Write a single bit specified in the boolean argument.
void	write(boolean bit, long repeat) Write a single bit specified in the boolean argument repeatedly.
void	write(byte bitContainer, int nofBits) Write specified number of bits supplied in the byte value.
void	write(int bitContainer, int nofBits) Write specified number of bits supplied in the integer value.
void	write(long bitContainer, int nofBits) Write specified number of bits supplied in the long value.

Methods inherited from interface java.io.Closeable

close

Methods inherited from interface java.io.Flushable

flush

Method Detail

write

void write(int bitContainer,
           int nofBits)
    throws java.io.IOException

Write specified number of bits supplied in the integer value. The method is naturally limited to 32 bits max.

Parameters:

bitContainer - an integer containing the bits to be written out

nofBits - the number of bits to written out, minimum 0, maximum 32.

Throws:

java.io.IOException - as per streaming contract in java.

write

void write(long bitContainer,
           int nofBits)
    throws java.io.IOException

Write specified number of bits supplied in the long value. The method is naturally limited to 64 bits max.

Parameters:

bitContainer - an integer containing the bits to be written out

nofBits - the number of bits to written out, minimum 0, maximum 64.

Throws:

java.io.IOException - as per streaming contract in java.

write

void write(byte bitContainer,
           int nofBits)
    throws java.io.IOException

Write specified number of bits supplied in the byte value. The method is naturally limited to 8 bits max.

Parameters:

bitContainer - an integer containing the bits to be written out

nofBits - the number of bits to written out, minimum 0, maximum 8.

Throws:

java.io.IOException - as per streaming contract in java.

write

void write(boolean bit)
    throws java.io.IOException

Write a single bit specified in the boolean argument.

Parameters:

bit - emit 1 if true, 0 otherwise.

Throws:

java.io.IOException - as per streaming contract in java.

write

void write(boolean bit,
           long repeat)
    throws java.io.IOException

Write a single bit specified in the boolean argument repeatedly.

Parameters:

bit - emit 1 if true, 0 otherwise.

repeat - the number of bits to emit.

Throws:

java.io.IOException - as per streaming contract in java.