/**
* Return the quality scores from the specified FASTQ formatted sequence.
*
* @param fastq FASTQ formatted sequence, must not be null
* @return the quality scores from the specified FASTQ formatted sequence
*/
public static Iterable<Number> qualityScores(final Fastq fastq) {
if (fastq == null) {
throw new IllegalArgumentException("fastq must not be null");
}
int size = fastq.getQuality().length();
List<Number> qualityScores = Lists.newArrayListWithExpectedSize(size);
FastqVariant variant = fastq.getVariant();
for (int i = 0; i < size; i++) {
char c = fastq.getQuality().charAt(i);
qualityScores.add(variant.qualityScore(c));
}
return ImmutableList.copyOf(qualityScores);
}
/**
* 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
*/
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;
}
