Package org.biojava.nbio.sequencing.io.fastq

Class IlluminaFastqReader

java.lang.Object
org.biojava.nbio.sequencing.io.fastq.IlluminaFastqReader
All Implemented Interfaces:
FastqReader
public final class IlluminaFastqReader extends Object
Reader for FastqVariant.FASTQ_ILLUMINA formatted sequences.
Since:
3.0.3

  • Constructor Details

    • IlluminaFastqReader

      public IlluminaFastqReader()

  • Method Details

    • 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