/** * Does this Slice contain reads placed on a single reference (whether their unmapped flags are set or not)? * @return true if all reads in the Slice are placed on a single reference */ public boolean isMappedSingleRef() { return ! isUnmapped() && ! isMultiref(); }
if (slice.isUnmapped() && record.isPlaced()) { slice.sequenceId = MULTI_REFERENCE;