Examples of RnaSeqMetricsCollector


Examples of picard.analysis.directed.RnaSeqMetricsCollector

        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();
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