/**
* Return the error probabilities from the specified FASTQ formatted sequence.
*
* @param fastq FASTQ formatted sequence, must not be null
* @return the error probabilities from the specified FASTQ formatted sequence
*/
public static Iterable<Number> errorProbabilities(final Fastq fastq) {
if (fastq == null) {
throw new IllegalArgumentException("fastq must not be null");
}
int size = fastq.getQuality().length();
List<Number> errorProbabilities = Lists.newArrayListWithExpectedSize(size);
FastqVariant variant = fastq.getVariant();
for (int i = 0; i < size; i++) {
char c = fastq.getQuality().charAt(i);
errorProbabilities.add(variant.errorProbability(c));
}
return ImmutableList.copyOf(errorProbabilities);
}
/**
* Copy the error probabilities from the specified FASTQ formatted sequence into the specified
* double array.
*
* @param fastq FASTQ formatted sequence, must not be null
* @param errorProbabilities double array of error probabilities, must not be null and must be the
* same length as the FASTQ formatted sequence quality
* @return the specified double array of error probabilities
*/
public static double[] errorProbabilities(final Fastq fastq, final double[] errorProbabilities) {
if (fastq == null) {
throw new IllegalArgumentException("fastq must not be null");
}
if (errorProbabilities == null) {
throw new IllegalArgumentException("errorProbabilities must not be null");
}
int size = fastq.getQuality().length();
if (errorProbabilities.length != size) {
throw new IllegalArgumentException(
"errorProbabilities 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);
errorProbabilities[i] = variant.errorProbability(c);
}
return errorProbabilities;
}
