normalizer.normalize(cramRecords, true, refs, container.alignmentStart,
container.h.substitutionMatrix, container.h.AP_seriesDelta);
long time2 = System.nanoTime();
Cram2BamRecordFactory c2sFactory = new Cram2BamRecordFactory(
cramHeader.samFileHeader);
long c2sTime = 0;
for (CramRecord r : cramRecords) {
long time = System.nanoTime();
SAMRecord s = c2sFactory.create(r);
c2sTime += System.nanoTime() - time;
if (!r.segmentUnmapped)
Utils.calculateMdAndNmTags(s, refs, restoreMDTag, restoreNMTag);
s.setValidationStringency(validationStringency);