htsjdk.samtools.util

Class BlockCompressedInputStream

java.lang.Object

java.io.InputStream

htsjdk.samtools.util.BlockCompressedInputStream

All Implemented Interfaces:

LocationAware, java.io.Closeable, java.lang.AutoCloseable

public class BlockCompressedInputStream
extends java.io.InputStream
implements LocationAware

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	BlockCompressedInputStream.FileTermination

Constructor Summary

Constructors

Constructor and Description
BlockCompressedInputStream(java.io.File file) Use this ctor if you wish to call seek()
BlockCompressedInputStream(java.io.InputStream stream) Note that seek() is not supported if this ctor is used.
BlockCompressedInputStream(java.io.InputStream stream, boolean allowBuffering) Note that seek() is not supported if this ctor is used.
BlockCompressedInputStream(SeekableStream strm) For providing some arbitrary data source.
BlockCompressedInputStream(java.net.URL url)

Method Summary

Modifier and Type	Method and Description
static void	assertNonDefectiveFile(java.io.File file)
int	available()
static BlockCompressedInputStream.FileTermination	checkTermination(java.io.File file)
void	close() Closes the underlying InputStream or RandomAccessFile
boolean	endOfBlock()
static long	getFileBlock(long bgzfOffset)
long	getFilePointer()
long	getPosition() The current offset, in bytes, of this stream/writer/file.
static boolean	isValidFile(java.io.InputStream stream)
int	read() Reads the next byte of data from the input stream.
int	read(byte[] buffer) Reads some number of bytes from the input stream and stores them into the buffer array b.
int	read(byte[] buffer, int offset, int length) Reads up to len bytes of data from the input stream into an array of bytes.
java.lang.String	readLine() Reads a whole line.
void	seek(long pos) Seek to the given position in the file.
void	setCheckCrcs(boolean check) Determines whether or not the inflater will re-calculated the CRC on the decompressed data and check it against the value stored in the GZIP header.

Methods inherited from class java.io.InputStream

mark, markSupported, reset, skip

Methods inherited from class java.lang.Object

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

Constructor Detail

BlockCompressedInputStream

public BlockCompressedInputStream(java.io.InputStream stream)

Note that seek() is not supported if this ctor is used.

BlockCompressedInputStream

public BlockCompressedInputStream(java.io.InputStream stream,
                                  boolean allowBuffering)

Note that seek() is not supported if this ctor is used.

BlockCompressedInputStream

public BlockCompressedInputStream(java.io.File file)
                           throws java.io.IOException

Use this ctor if you wish to call seek()

Throws:

java.io.IOException

BlockCompressedInputStream

public BlockCompressedInputStream(java.net.URL url)

BlockCompressedInputStream

public BlockCompressedInputStream(SeekableStream strm)

For providing some arbitrary data source. No additional buffering is provided, so if the underlying source is not buffered, wrap it in a SeekableBufferedStream before passing to this ctor.

Method Detail

setCheckCrcs

public void setCheckCrcs(boolean check)

Determines whether or not the inflater will re-calculated the CRC on the decompressed data and check it against the value stored in the GZIP header. CRC checking is an expensive operation and should be used accordingly.

available

public int available()
              throws java.io.IOException

Overrides:

available in class java.io.InputStream

Returns:

the number of bytes that can be read (or skipped over) from this input stream without blocking by the next caller of a method for this input stream. The next caller might be the same thread or another thread. Note that although the next caller can read this many bytes without blocking, the available() method call itself may block in order to fill an internal buffer if it has been exhausted.

Throws:

java.io.IOException

endOfBlock

public boolean endOfBlock()

Returns:

true if the stream is at the end of a BGZF block, false otherwise.

close

public void close()
           throws java.io.IOException

Closes the underlying InputStream or RandomAccessFile

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

read

public int read()
         throws java.io.IOException

Reads the next byte of data from the input stream. The value byte is returned as an int in the range 0 to 255. If no byte is available because the end of the stream has been reached, the value -1 is returned. This method blocks until input data is available, the end of the stream is detected, or an exception is thrown.

Specified by:

read in class java.io.InputStream

Returns:

the next byte of data, or -1 if the end of the stream is reached.

Throws:

java.io.IOException

read

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

Reads some number of bytes from the input stream and stores them into the buffer array b. The number of bytes actually read is returned as an integer. This method blocks until input data is available, end of file is detected, or an exception is thrown. read(buf) has the same effect as read(buf, 0, buf.length).

Overrides:

read in class java.io.InputStream

Parameters:

buffer - the buffer into which the data is read.

Returns:

the total number of bytes read into the buffer, or -1 is there is no more data because the end of the stream has been reached.

Throws:

java.io.IOException

readLine

public java.lang.String readLine()
                          throws java.io.IOException

Reads a whole line. A line is considered to be terminated by either a line feed ('\n'), carriage return ('\r') or carriage return followed by a line feed ("\r\n").

Returns:

A String containing the contents of the line, excluding the line terminating character, or null if the end of the stream has been reached

Throws:

java.io.IOException - If an I/O error occurs

read

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

Reads up to len bytes of data from the input stream into an array of bytes. An attempt is made to read as many as len bytes, but a smaller number may be read. The number of bytes actually read is returned as an integer. This method blocks until input data is available, end of file is detected, or an exception is thrown.

Overrides:

read in class java.io.InputStream

Parameters:

buffer - buffer into which data is read.

offset - the start offset in array b at which the data is written.

length - the maximum number of bytes to read.

Returns:

the total number of bytes read into the buffer, or -1 if there is no more data because the end of the stream has been reached.

Throws:

java.io.IOException

seek

public void seek(long pos)
          throws java.io.IOException

Seek to the given position in the file. Note that pos is a special virtual file pointer, not an actual byte offset.

Parameters:

pos - virtual file pointer

Throws:

java.io.IOException

getFilePointer

public long getFilePointer()

Returns:

virtual file pointer that can be passed to seek() to return to the current position. This is not an actual byte offset, so arithmetic on file pointers cannot be done to determine the distance between the two.

getPosition

public long getPosition()

Description copied from interface: LocationAware

The current offset, in bytes, of this stream/writer/file. Or, if this is an iterator/producer, the offset (in bytes) of the END of the most recently returned record (since a produced record corresponds to something that has been read already). See class javadoc for more. Note that for BGZF files, this does not represent an actually file position, but a virtual file pointer.

Specified by:

getPosition in interface LocationAware

getFileBlock

public static long getFileBlock(long bgzfOffset)

isValidFile

public static boolean isValidFile(java.io.InputStream stream)
                           throws java.io.IOException

Parameters:

stream - Must be at start of file. Throws RuntimeException if !stream.markSupported().

Returns:

true if the given file looks like a valid BGZF file.

Throws:

java.io.IOException

checkTermination

public static BlockCompressedInputStream.FileTermination checkTermination(java.io.File file)
                                                                   throws java.io.IOException

Throws:

java.io.IOException

assertNonDefectiveFile

public static void assertNonDefectiveFile(java.io.File file)
                                   throws java.io.IOException

Throws:

java.io.IOException