/**
* Retrieve the original base qualities of the given read, if present, as stored in the OQ
* attribute.
*
* @param read read to check
* @return original base qualities as stored in the OQ attribute, or null if the OQ attribute is
* not present
*/
public static byte[] getOriginalBaseQualities(final GATKRead read) {
if (!read.hasAttribute(ORIGINAL_BASE_QUALITIES_TAG)) {
return null;
}
final String oqString = read.getAttributeAsString(ORIGINAL_BASE_QUALITIES_TAG);
return oqString.length() > 0 ? SAMUtils.fastqToPhred(oqString) : null;
}
/** @return the base deletion quality or null if read doesn't have one */
public static byte[] getExistingBaseDeletionQualities(final GATKRead read) {
return SAMUtils.fastqToPhred(read.getAttributeAsString(BQSR_BASE_DELETION_QUALITIES));
}