org.seqdoop.hadoop_bam

Class LineReader

java.lang.Object

org.seqdoop.hadoop_bam.LineReader

public class LineReader
extends Object

A class that provides a line reader from an input stream. This code started as the org.apache.hadoop.util.LineReader class in Hadoop 0.20.2, to which we added a skip(n) method.

Constructor Summary

Constructors

Constructor and Description
LineReader(InputStream in) Create a line reader that reads from the given stream using the default buffer-size (64k).
LineReader(InputStream in, org.apache.hadoop.conf.Configuration conf) Create a line reader that reads from the given stream using the io.file.buffer.size specified in the given Configuration.
LineReader(InputStream in, int bufferSize) Create a line reader that reads from the given stream using the given buffer-size.

Method Summary

Modifier and Type	Method and Description
void	close() Close the underlying stream.
protected int	loadBuffer()
int	readLine(org.apache.hadoop.io.Text str) Read from the InputStream into the given Text.
int	readLine(org.apache.hadoop.io.Text str, int maxLineLength) Read from the InputStream into the given Text.
int	readLine(org.apache.hadoop.io.Text str, int maxLineLength, int maxBytesToConsume) Read one line from the InputStream into the given Text.
long	skip(long n) Skip n bytes from the InputStream.

Methods inherited from class java.lang.Object

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

Constructor Detail

LineReader

public LineReader(InputStream in)

Create a line reader that reads from the given stream using the default buffer-size (64k).

Parameters:

in - The input stream

Throws:

IOException

LineReader

public LineReader(InputStream in,
                  int bufferSize)

Create a line reader that reads from the given stream using the given buffer-size.

Parameters:

in - The input stream

bufferSize - Size of the read buffer

Throws:

IOException

LineReader

public LineReader(InputStream in,
                  org.apache.hadoop.conf.Configuration conf)
           throws IOException

Create a line reader that reads from the given stream using the io.file.buffer.size specified in the given Configuration.

Parameters:

in - input stream

conf - configuration

Throws:

IOException

Method Detail

close

public void close()
           throws IOException

Close the underlying stream.

Throws:

IOException

readLine

public int readLine(org.apache.hadoop.io.Text str,
                    int maxLineLength,
                    int maxBytesToConsume)
             throws IOException

Read one line from the InputStream into the given Text. A line can be terminated by one of the following: '\n' (LF) , '\r' (CR), or '\r\n' (CR+LF). EOF also terminates an otherwise unterminated line.

Parameters:

str - the object to store the given line (without newline)

maxLineLength - the maximum number of bytes to store into str; the rest of the line is silently discarded.

maxBytesToConsume - the maximum number of bytes to consume in this call. This is only a hint, because if the line cross this threshold, we allow it to happen. It can overshoot potentially by as much as one buffer length.

Returns:

the number of bytes read including the (longest) newline found.

Throws:

IOException - if the underlying stream throws

readLine

public int readLine(org.apache.hadoop.io.Text str,
                    int maxLineLength)
             throws IOException

Read from the InputStream into the given Text.

Parameters:

str - the object to store the given line

maxLineLength - the maximum number of bytes to store into str.

Returns:

the number of bytes read including the newline

Throws:

IOException - if the underlying stream throws

readLine

public int readLine(org.apache.hadoop.io.Text str)
             throws IOException

Read from the InputStream into the given Text.

Parameters:

str - the object to store the given line

Returns:

the number of bytes read including the newline

Throws:

IOException - if the underlying stream throws

skip

public long skip(long n)
          throws IOException

Skip n bytes from the InputStream.

Parameters:

n - the number of bytes to skip.

Returns:

the number of bytes skipped.

Throws:

IOException - if the underlying stream throws.

loadBuffer

protected int loadBuffer()
                  throws IOException

Throws:

IOException