/** Setters and Accessors for base insertion and base deletion quality scores */
public void setBaseQualities(final byte[] quals, final EventType errorModel) {
switch (errorModel) {
case BASE_SUBSTITUTION:
setBaseQualities(quals);
break;
case BASE_INSERTION:
setAttribute(
GATKSAMRecord.BQSR_BASE_INSERTION_QUALITIES,
quals == null ? null : SAMUtils.phredToFastq(quals));
break;
case BASE_DELETION:
setAttribute(
GATKSAMRecord.BQSR_BASE_DELETION_QUALITIES,
quals == null ? null : SAMUtils.phredToFastq(quals));
break;
default:
throw new ReviewedGATKException("Unrecognized Base Recalibration type: " + errorModel);
}
}
/** @return the base deletion quality or null if read doesn't have one */
public byte[] getExistingBaseDeletionQualities() {
return SAMUtils.fastqToPhred(getStringAttribute(BQSR_BASE_DELETION_QUALITIES));
}