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.
      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.
      protected void validateDescription​(FastqBuilder builder, java.lang.String description, int lineNumber)
      Validate the specified description.
      protected void validateQuality​(FastqBuilder builder, java.lang.String quality, int lineNumber)
      Validate the specified quality scores.
      protected void validateRepeatDescription​(FastqBuilder builder, java.lang.String repeatDescription, int lineNumber)
      Validate the specified repeat description.
      protected void validateSequence​(FastqBuilder builder, java.lang.String sequence, int lineNumber)
      Validate the specified sequence.
      • 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
      • validateDescription

        protected void validateDescription​(FastqBuilder builder,
                                           java.lang.String description,
                                           int lineNumber)
                                    throws java.io.IOException
        Validate the specified description.
        Parameters:
        builder - FASTQ formatted sequence builder, will not be null
        description - description to validate, will not be null
        lineNumber - current line number in input stream
        Throws:
        java.io.IOException - if the specified description is not valid
      • validateSequence

        protected void validateSequence​(FastqBuilder builder,
                                        java.lang.String sequence,
                                        int lineNumber)
                                 throws java.io.IOException
        Validate the specified sequence.
        Parameters:
        builder - FASTQ formatted sequence builder, will not be null
        sequence - sequence to validate, will not be null
        lineNumber - current line number in input stream
        Throws:
        java.io.IOException - if the specified sequence is not valid
      • validateRepeatDescription

        protected void validateRepeatDescription​(FastqBuilder builder,
                                                 java.lang.String repeatDescription,
                                                 int lineNumber)
                                          throws java.io.IOException
        Validate the specified repeat description.
        Parameters:
        builder - FASTQ formatted sequence builder, will not be null
        repeatDescription - repeat description to validate, will not be null
        lineNumber - current line number in input stream
        Throws:
        java.io.IOException - if the specified repeat description is not valid
      • validateQuality

        protected void validateQuality​(FastqBuilder builder,
                                       java.lang.String quality,
                                       int lineNumber)
                                throws java.io.IOException
        Validate the specified quality scores.
        Parameters:
        builder - FASTQ formatted sequence builder, will not be null
        quality - quality scores to validate, will not be null
        lineNumber - current line number in input stream
        Throws:
        java.io.IOException - if the specified quality scores are not valid
      • read

        public final java.lang.Iterable<Fastq> read​(java.io.File file)
                                             throws java.io.IOException
        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 IO error occurs
      • read

        public final java.lang.Iterable<Fastq> read​(java.net.URL url)
                                             throws java.io.IOException
        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 IO error occurs
      • read

        public final java.lang.Iterable<Fastq> read​(java.io.InputStream inputStream)
                                             throws java.io.IOException
        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 IO error occurs