.getLength() : 0;
refPos += ce.getOperator().consumesReferenceBases() ? ce
.getLength() : 0;
}
preservation.addQualityScores(samRecord, cramRecord, tracks);
}
// mating:
Map<String, CramRecord> mateMap = new TreeMap<String, CramRecord>();
for (CramRecord r : cramRecords) {