Class IlluminaFastqWriter

    • Method Detail

      • convert

        protected Fastq convert​(Fastq fastq)
        Convert the specified FASTQ formatted sequence if necessary.
        Parameters:
        fastq - FASTQ formatted sequence to convert, must not be null
        Returns:
        the specified FASTQ formatted sequence or a new FASTA formatted sequence if conversion is necessary
      • append

        public final <T extends Appendable> T append​(T appendable,
                                                     Fastq... fastq)
                                              throws IOException
        Description copied from interface: FastqWriter
        Append the specified FASTQ formatted sequences to the specified appendable.
        Specified by:
        append in interface FastqWriter
        Type Parameters:
        T - extends Appendable
        Parameters:
        appendable - appendable to append the specified FASTQ formatted sequences to, must not be null
        fastq - variable number of FASTQ formatted sequences to append, must not be null
        Returns:
        the specified appendable with the specified FASTQ formatted sequences appended
        Throws:
        IOException - if an I/O error occurs
      • append

        public final <T extends Appendable> T append​(T appendable,
                                                     Iterable<Fastq> fastq)
                                              throws IOException
        Description copied from interface: FastqWriter
        Append the specified FASTQ formatted sequences to the specified appendable.
        Specified by:
        append in interface FastqWriter
        Type Parameters:
        T - extends Appendable
        Parameters:
        appendable - appendable to append the specified FASTQ formatted sequences to, must not be null
        fastq - zero or more FASTQ formatted sequences to append, must not be null
        Returns:
        the specified appendable with the specified FASTQ formatted sequences appended
        Throws:
        IOException - if an I/O error occurs
      • write

        public final void write​(File file,
                                Fastq... fastq)
                         throws IOException
        Description copied from interface: FastqWriter
        Write the specified FASTQ formatted sequences to the specified file.
        Specified by:
        write in interface FastqWriter
        Parameters:
        file - file to write to, must not be null
        fastq - variable number of FASTQ formatted sequences to write, must not be null
        Throws:
        IOException - if an I/O error occurs
      • write

        public final void write​(File file,
                                Iterable<Fastq> fastq)
                         throws IOException
        Description copied from interface: FastqWriter
        Write the specified FASTQ formatted sequences to the specified file.
        Specified by:
        write in interface FastqWriter
        Parameters:
        file - file to write to, must not be null
        fastq - zero or more FASTQ formatted sequences to write, must not be null
        Throws:
        IOException - if an I/O error occurs
      • write

        public final void write​(OutputStream outputStream,
                                Fastq... fastq)
                         throws IOException
        Description copied from interface: FastqWriter
        Write the specified FASTQ formatted sequences to the specified output stream.
        Specified by:
        write in interface FastqWriter
        Parameters:
        outputStream - output stream to write to, must not be null
        fastq - variable number of FASTQ formatted sequences to write, must not be null
        Throws:
        IOException - if an I/O error occurs
      • write

        public final void write​(OutputStream outputStream,
                                Iterable<Fastq> fastq)
                         throws IOException
        Description copied from interface: FastqWriter
        Write the specified FASTQ formatted sequences to the specified output stream.
        Specified by:
        write in interface FastqWriter
        Parameters:
        outputStream - output stream to write to, must not be null
        fastq - zero or more FASTQ formatted sequences to write, must not be null
        Throws:
        IOException - if an I/O error occurs