code: public static int[] qualityScores(final Fastq fastq, final int[] qualityScores)
  	{
  		if (fastq == null)
  		{
  			throw new IllegalArgumentException("fastq must not be null");
  		}
  		if (qualityScores == null)
  		{
  			throw new IllegalArgumentException("qualityScores must not be null");
  		}
  		int size = fastq.getQuality().length();
  		if (qualityScores.length != size)
  		{
  			throw new IllegalArgumentException("qualityScores must be the same length as the FASTQ formatted sequence quality");
  		}
  		FastqVariant variant = fastq.getVariant();
  		for (int i = 0; i < size; i++)
  		{
  			char c = fastq.getQuality().charAt(i);
  			qualityScores[i] = variant.qualityScore(c);
  		}
  		return qualityScores;
  	}
docs: Copy the quality scores from the specified FASTQ formatted sequence into the specified int array.
  
  @param fastq FASTQ formatted sequence, must not be null
  @param qualityScores int array of quality scores, must not be null and must be the same
  length as the FASTQ formatted sequence quality
  @return the specified int array of quality scores