org.seqdoop.hadoop_bam.util

Class WrapSeekable<S extends InputStream & org.apache.hadoop.fs.Seekable>

java.lang.Object

java.io.InputStream

htsjdk.samtools.seekablestream.SeekableStream

org.seqdoop.hadoop_bam.util.WrapSeekable<S>

All Implemented Interfaces:

Closeable, AutoCloseable

public class WrapSeekable<S extends InputStream & org.apache.hadoop.fs.Seekable>
extends htsjdk.samtools.seekablestream.SeekableStream

Wraps Hadoop's "seekable stream" abstraction so that we can give such a one to BlockCompressedInputStream and retain seekability.

This is necessary because Hadoop and the SAM tools each have their own "seekable stream" abstraction.

Constructor Summary

Constructors

Constructor and Description
WrapSeekable(S s, long length, org.apache.hadoop.fs.Path p)

Method Summary

Modifier and Type	Method and Description
void	close()
boolean	eof()
String	getSource()
long	length()
static WrapSeekable<org.apache.hadoop.fs.FSDataInputStream>	openPath(org.apache.hadoop.conf.Configuration conf, org.apache.hadoop.fs.Path path)
static WrapSeekable<org.apache.hadoop.fs.FSDataInputStream>	openPath(org.apache.hadoop.fs.FileSystem fs, org.apache.hadoop.fs.Path p) A helper for the common use case.
long	position()
int	read()
int	read(byte[] buf, int offset, int len)
void	seek(long pos)

Methods inherited from class htsjdk.samtools.seekablestream.SeekableStream

readFully

Methods inherited from class java.io.InputStream

available, mark, markSupported, read, reset, skip

Methods inherited from class java.lang.Object

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

Constructor Detail

WrapSeekable

public WrapSeekable(S s,
                    long length,
                    org.apache.hadoop.fs.Path p)

Method Detail

openPath

public static WrapSeekable<org.apache.hadoop.fs.FSDataInputStream> openPath(org.apache.hadoop.fs.FileSystem fs,
                                                                            org.apache.hadoop.fs.Path p)
                                                                     throws IOException

A helper for the common use case.

Throws:

IOException

openPath

public static WrapSeekable<org.apache.hadoop.fs.FSDataInputStream> openPath(org.apache.hadoop.conf.Configuration conf,
                                                                            org.apache.hadoop.fs.Path path)
                                                                     throws IOException

Throws:

IOException

getSource

public String getSource()

Specified by:

getSource in class htsjdk.samtools.seekablestream.SeekableStream

length

public long length()

Specified by:

length in class htsjdk.samtools.seekablestream.SeekableStream

position

public long position()
              throws IOException

Specified by:

position in class htsjdk.samtools.seekablestream.SeekableStream

Throws:

IOException

close

public void close()
           throws IOException

Specified by:

close in interface Closeable

Specified by:

close in interface AutoCloseable

Specified by:

close in class htsjdk.samtools.seekablestream.SeekableStream

Throws:

IOException

eof

public boolean eof()
            throws IOException

Specified by:

eof in class htsjdk.samtools.seekablestream.SeekableStream

Throws:

IOException

seek

public void seek(long pos)
          throws IOException

Specified by:

seek in class htsjdk.samtools.seekablestream.SeekableStream

Throws:

IOException

read

public int read()
         throws IOException

Specified by:

read in class InputStream

Throws:

IOException

read

public int read(byte[] buf,
                int offset,
                int len)
         throws IOException

Specified by:

read in class htsjdk.samtools.seekablestream.SeekableStream

Throws:

IOException