htsjdk.samtools.util

Class FastLineReader

java.lang.Object

htsjdk.samtools.util.FastLineReader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable

public class FastLineReader
extends java.lang.Object
implements java.io.Closeable

Line-oriented InputStream reader that uses one buffer for disk buffering and line-termination-finding, in order to improve performance. Implementation detail: All public methods must leave the input buffer in a non-empty state, unless at EOF.

Constructor Summary

Constructors

Constructor and Description
FastLineReader(java.io.InputStream in)

Method Summary

Modifier and Type	Method and Description
boolean	atEoln()
void	close()
boolean	eof()
byte	getByte()
byte	peekByte()
int	readToEndOfOutputBufferOrEoln(byte[] outputBuffer, int startOutputIndex) Read from input until input is exhausted, EOLN is seen, or output buffer is filled
boolean	skipNewlines() Advance over any EOLN chars (CR or LF)

Methods inherited from class java.lang.Object

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

Constructor Detail

FastLineReader

public FastLineReader(java.io.InputStream in)

Method Detail

eof

public boolean eof()

Returns:

true if input is exhausted

atEoln

public boolean atEoln()

Returns:

peeks at the next byte in the stream and returns true if it is CR or LF. Returns false if EOF or next byte is not CR or LF.

skipNewlines

public boolean skipNewlines()

Advance over any EOLN chars (CR or LF)

Returns:

true if saw one or more CR or LFs

close

public void close()

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

getByte

public byte getByte()

Returns:

Next byte from the input. Do not call if at EOF.

peekByte

public byte peekByte()

Returns:

Next byte from the input, without advancing over that byte. Do not call if at EOF.

readToEndOfOutputBufferOrEoln

public int readToEndOfOutputBufferOrEoln(byte[] outputBuffer,
                                         int startOutputIndex)

Read from input until input is exhausted, EOLN is seen, or output buffer is filled

Parameters:

outputBuffer - where to put bytes read

startOutputIndex - where to start putting bytes read

Returns:

number of bytes read