htsjdk.samtools.util

Class CoordSpanInputSteam

java.lang.Object

java.io.InputStream

htsjdk.samtools.util.CoordSpanInputSteam

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable

public class CoordSpanInputSteam
extends java.io.InputStream

An input stream that wraps a SeekableStream to produce only bytes specified within coordinates. Created by vadim on 25/03/2015.

Constructor Summary

Constructors

Constructor and Description
CoordSpanInputSteam(SeekableStream delegate, long[] coords) Wrap SeekableStream to read only bytes within boundaries specified in the coords array.

Method Summary

Modifier and Type	Method and Description
int	available() Returns how many bytes are left in the current chunk.
void	close()
int	read()
int	read(byte[] buffer, int offset, int length)

Methods inherited from class java.io.InputStream

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

CoordSpanInputSteam

public CoordSpanInputSteam(SeekableStream delegate,
                           long[] coords)
                    throws java.io.IOException

Wrap SeekableStream to read only bytes within boundaries specified in the coords array. The coords array consists of [inclusive; exclusive) pairs of long coordinates. This constructor will throw exception if a start coordinate is beyond stream length. End coordinates are capped at the stream length.

Throws:

java.io.IOException

Method Detail

read

public int read()
         throws java.io.IOException

Specified by:

read in class java.io.InputStream

Throws:

java.io.IOException

read

public int read(byte[] buffer,
                int offset,
                int length)
         throws java.io.IOException

Overrides:

read in class java.io.InputStream

Throws:

java.io.IOException

available

public int available()
              throws java.io.IOException

Returns how many bytes are left in the current chunk.

Overrides:

available in class java.io.InputStream

Returns:

number of unread bytes in the current chunk.

Throws:

java.io.IOException

close

public void close()
           throws java.io.IOException

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

Overrides:

close in class java.io.InputStream

Throws:

java.io.IOException