Package org.broadinstitute.gatk.utils.sam

Examples of org.broadinstitute.gatk.utils.sam.AlignmentStartComparator


            // If we triggered the downsampler, we need to sort the reads before returning them,
            // since the ReservoirDownsampler is not guaranteed to preserve relative ordering of items.
            // After consuming the downsampled items in this call to popCurrentReads(), we switch back
            // to using the undownsampledCache until we fill up again.
            poppedReads = downsampler.consumeFinalizedItems()// avoid making a copy here
            Collections.sort(poppedReads, new AlignmentStartComparator());
            downsampler = null;
        }

        initializeUndownsampledCache();
        return poppedReads;
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