final Long ribosomalBasesInitialValue = RIBOSOMAL_INTERVALS != null ? 0L : null;
final OverlapDetector<Interval> ribosomalSequenceOverlapDetector = RnaSeqMetricsCollector.makeOverlapDetector(samFile, header, RIBOSOMAL_INTERVALS);
final HashSet<Integer> ignoredSequenceIndices = RnaSeqMetricsCollector.makeIgnoredSequenceIndicesSet(header, IGNORE_SEQUENCE);
collector = new RnaSeqMetricsCollector(METRIC_ACCUMULATION_LEVEL, header.getReadGroups(), ribosomalBasesInitialValue,
geneOverlapDetector, ribosomalSequenceOverlapDetector, ignoredSequenceIndices, MINIMUM_LENGTH, STRAND_SPECIFICITY, RRNA_FRAGMENT_PERCENTAGE,
true);
// If we're working with a single library, assign that library's name as a suffix to the plot title
final List<SAMReadGroupRecord> readGroups = header.getReadGroups();