htsjdk.samtools.cram.io

Interface BitInputStream

All Known Implementing Classes:

DefaultBitInputStream

public interface BitInputStream

Method Summary

Methods

Modifier and Type	Method and Description
void	alignToByte()
boolean	endOfStream()
boolean	ensureMarker(long marker, int nofBits)
boolean	putBack(long b, int numBits)
int	readAlignedBytes(byte[] array)
boolean	readBit()
int	readBits(int len)
byte	readByte()
long	readLongBits(int len)

Method Detail

readBit

boolean readBit()
                throws java.io.IOException

Throws:

java.io.IOException

readBits

int readBits(int len)
             throws java.io.IOException

Throws:

java.io.IOException

readLongBits

long readLongBits(int len)
                  throws java.io.IOException

Throws:

java.io.IOException

endOfStream

boolean endOfStream()
                    throws java.io.IOException

Throws:

java.io.IOException

putBack

boolean putBack(long b,
              int numBits)

alignToByte

void alignToByte()
                 throws java.io.IOException

Throws:

java.io.IOException

readAlignedBytes

int readAlignedBytes(byte[] array)
                     throws java.io.IOException

Throws:

java.io.IOException

readByte

byte readByte()
              throws java.io.IOException

Throws:

java.io.IOException

ensureMarker

boolean ensureMarker(long marker,
                   int nofBits)
                     throws java.io.IOException

Throws:

java.io.IOException