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

Interface FastqReader

All Known Implementing Classes:
IlluminaFastqReader, SangerFastqReader, SolexaFastqReader
public interface FastqReader
Reader for FASTQ formatted sequences.
Since:
3.0.3

  • Method Details

    • parse

      void parse(Readable readable, ParseListener listener) throws IOException
      Parse the specified readable.
      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

      void stream(Readable readable, StreamListener listener) throws IOException
      Stream the specified readable.
      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

      Iterable<Fastq> read(File file) throws IOException
      Read zero or more FASTQ formatted sequences from the specified file.
      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

      Iterable<Fastq> read(URL url) throws IOException
      Read zero or more FASTQ formatted sequences from the specified url.
      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

      Iterable<Fastq> read(InputStream inputStream) throws IOException
      Read zero or more FASTQ formatted sequences from the specified input stream.
      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