/**
* 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());
}
/** 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);
}
}
public static void setDeletionBaseQualities(final GATKRead read, final byte[] quals) {
read.setAttribute(
BQSR_BASE_DELETION_QUALITIES, quals == null ? null : SAMUtils.phredToFastq(quals));
}
