Package org.biojava.nbio.genome.io.fastq

Class IlluminaFastqReader

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      protected FastqVariant getVariant()
      Return the FASTQ sequence format variant for this reader.
      void parse​(java.lang.Readable readable, ParseListener listener)
      Parse the specified readable.
      java.lang.Iterable<Fastq> read​(java.io.File file)
      Read zero or more FASTQ formatted sequences from the specified file.
      java.lang.Iterable<Fastq> read​(java.io.InputStream inputStream)
      Read zero or more FASTQ formatted sequences from the specified input stream.
      java.lang.Iterable<Fastq> read​(java.net.URL url)
      Read zero or more FASTQ formatted sequences from the specified url.
      void stream​(java.lang.Readable readable, StreamListener listener)
      Stream the specified readable.

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • IlluminaFastqReader

        public 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​(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