}
// If we've made it this far spit the records into the output!
for (final SAMRecord rec : recs) {
// The only valid quality score encoding scheme is standard; if it's not standard, change it.
final FastqQualityFormat recordFormat = readGroupToFormat.get(rec.getReadGroup());
if (!recordFormat.equals(FastqQualityFormat.Standard)) {
final byte quals[] = rec.getBaseQualities();
for (int i = 0; i < quals.length; i++) {
quals[i] -= SolexaQualityConverter.ILLUMINA_TO_PHRED_SUBTRAHEND;
}
rec.setBaseQualities(quals);