CoordSpanInputSteam (htsjdk 4.3.0 API)

java.lang.Object

java.io.InputStream

htsjdk.samtools.util.CoordSpanInputSteam

All Implemented Interfaces:: Closeable, AutoCloseable

public class CoordSpanInputSteam extends 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

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

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, nullInputStream, read, readAllBytes, readNBytes, readNBytes, reset, skip, skipNBytes, transferTo

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- CoordSpanInputSteam
  
  public CoordSpanInputSteam(SeekableStream delegate, long[] coords) throws 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:
  
  IOException
Method Details
- read
  
  public int read() throws IOException
  
  Specified by:
  
  read in class InputStream
  
  Throws:
  
  IOException
- read
  
  public int read(byte[] buffer, int offset, int length) throws IOException
  
  Overrides:
  
  read in class InputStream
  
  Throws:
  
  IOException
- available
  
  public int available() throws IOException
  
  Returns how many bytes are left in the current chunk.
  
  Overrides:
  
  available in class InputStream
  
  Returns:
  
  number of unread bytes in the current chunk.
  
  Throws:
  
  IOException
- close
  
  public void close() throws IOException
  
  Specified by:
  
  close in interface AutoCloseable
  
  Specified by:
  
  close in interface Closeable
  
  Overrides:
  
  close in class InputStream
  
  Throws:
  
  IOException