Class IlluminaFastqReader

    • 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​(Readable readable,
                                ParseListener listener)
                         throws 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:
        IOException - if an I/O error occurs
      • stream

        public final void stream​(Readable readable,
                                 StreamListener listener)
                          throws 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:
        IOException - if an I/O error occurs
      • read

        public final Iterable<Fastq> read​(File file)
                                   throws 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:
        IOException - if an I/O error occurs
      • read

        public final Iterable<Fastq> read​(URL url)
                                   throws 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:
        IOException - if an I/O error occurs
      • read

        public final Iterable<Fastq> read​(InputStream inputStream)
                                   throws 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:
        IOException - if an I/O error occurs