Constructor Detail

• SangerFastqReader

  public SangerFastqReader()

Method Detail

• getVariant

  protected FastqVariant getVariant()

  Return the FASTQ sequence format variant for this reader.

  Returns:

  the FASTQ sequence format variant for this reader

• parse

  public final void parse(java.lang.Readable readable,
                          ParseListener listener)
                   throws java.io.IOException

  Description copied from interface: FastqReader
  Parse the specified readable.

  Specified by:

  parse in interface FastqReader

  Parameters:

  readable - readable, must not be null

  listener - low-level event based parser callback, must not be null

  Throws:

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

• stream

  public final void stream(java.lang.Readable readable,
                           StreamListener listener)
                    throws java.io.IOException

  Description copied from interface: FastqReader
  Stream the specified readable.

  Specified by:

  stream in interface FastqReader

  Parameters:

  readable - readable, must not be null

  listener - event based reader callback, must not be null

  Throws:

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

• read

  public final java.lang.Iterable<Fastq> read(java.io.File file)
                                       throws java.io.IOException

  Description copied from interface: FastqReader
  Read zero or more FASTQ formatted sequences from the specified file.

  Specified by:

  read in interface FastqReader

  Parameters:

  file - file to read from, must not be null

  Returns:

  zero or more FASTQ formatted sequences read from the specified file

  Throws:

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

• read

  public final java.lang.Iterable<Fastq> read(java.net.URL url)
                                       throws java.io.IOException

  Description copied from interface: FastqReader
  Read zero or more FASTQ formatted sequences from the specified url.

  Specified by:

  read in interface FastqReader

  Parameters:

  url - URL to read from, must not be null

  Returns:

  zero or more FASTQ formatted sequences read from the specified url

  Throws:

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

• read

  public final java.lang.Iterable<Fastq> read(java.io.InputStream inputStream)
                                       throws java.io.IOException

  Description copied from interface: FastqReader
  Read zero or more FASTQ formatted sequences from the specified input stream.

  Specified by:

  read in interface FastqReader

  Parameters:

  inputStream - input stream to read from, must not be null

  Returns:

  zero or more FASTQ formatted sequences read from the specified input stream

  Throws:

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