/**
* Returns the base qualities for the read as a string.
*
* @param read read whose base qualities should be returned
* @return Base qualities string as printable ASCII values (encoded as a FASTQ string).
*/
public static String getBaseQualityString(final GATKRead read) {
Utils.nonNull(read);
if (Arrays.equals(SAMRecord.NULL_QUALS, read.getBaseQualities())) {
return SAMRecord.NULL_QUALS_STRING;
}
return SAMUtils.phredToFastq(read.getBaseQualities());
}
public static byte[] getBaseQualities(final GATKRead read, final EventType errorModel) {
switch (errorModel) {
case BASE_SUBSTITUTION:
return read.getBaseQualities();
case BASE_INSERTION:
return getBaseInsertionQualities(read);
case BASE_DELETION:
return getBaseDeletionQualities(read);
default:
throw new GATKException("Unrecognized Base Recalibration type: " + errorModel);
}
}
/**
* Default utility to query the base deletion quality of a read. If the read doesn't have one, it
* creates an array of default qualities (currently Q45) and assigns it to the read.
*
* @return the base deletion quality array
*/
public static byte[] getBaseDeletionQualities(final GATKRead read) {
byte[] quals = getExistingBaseDeletionQualities(read);
if (quals == null) {
quals = new byte[read.getBaseQualities().length];
Arrays.fill(
quals,
DEFAULT_INSERTION_DELETION_QUAL); // Some day in the future when base insertion and base
// deletion quals exist the samtools API will
// be updated and the original quals will be pulled here, but for now we assume the original
// quality is a flat Q45
}
return quals;
}