Package htsjdk.samtools.util

Class Md5CalculatingInputStream

java.lang.Object

java.io.InputStream

htsjdk.samtools.util.Md5CalculatingInputStream

All Implemented Interfaces:

Closeable, AutoCloseable

public class Md5CalculatingInputStream
extends InputStream

Class to generate an MD5 string for a file as it is being read

Constructor Summary

Constructors

Constructor	Description
Md5CalculatingInputStream(InputStream is, File digestFile)	Constructor that takes in the InputStream that we are wrapping and creates the MD5 MessageDigest

Method Summary

Modifier and Type	Method	Description
int	available()
void	close()
void	mark(int readlimit)
boolean	markSupported()
String	md5()
int	read()
int	read(byte[] b)
int	read(byte[] b, int off, int len)
void	reset()
long	skip(long n)

Methods inherited from class java.io.InputStream

nullInputStream, readAllBytes, readNBytes, readNBytes, skipNBytes, transferTo

Methods inherited from class java.lang.Object

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

Constructor Details

Md5CalculatingInputStream

public Md5CalculatingInputStream(InputStream is,
 File digestFile)

Constructor that takes in the InputStream that we are wrapping and creates the MD5 MessageDigest

Method Details

read

public int read()
         throws IOException

Specified by:

read in class InputStream

Throws:

IOException

read

public int read(byte[] b)
         throws IOException

Overrides:

read in class InputStream

Throws:

IOException

read

public int read(byte[] b,
 int off,
 int len)
         throws IOException

Overrides:

read in class InputStream

Throws:

IOException

md5

public String md5()

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

markSupported

public boolean markSupported()

Overrides:

markSupported in class InputStream

mark

public void mark(int readlimit)

Overrides:

mark in class InputStream

reset

public void reset()
           throws IOException

Overrides:

reset in class InputStream

Throws:

IOException

skip

public long skip(long n)
          throws IOException

Overrides:

skip in class InputStream

Throws:

IOException

available

public int available()
              throws IOException

Overrides:

available in class InputStream

Throws:

IOException