// modify the base qualities.
wrappedIterator = new ReadFormattingIterator(wrappedIterator, useOriginalBaseQualities, defaultBaseQualities);
// Read Filters: these are applied BEFORE downsampling, so that we downsample within the set of reads
// that actually survive filtering. Otherwise we could get much less coverage than requested.
wrappedIterator = GATKSAMIteratorAdapter.adapt(new CountingFilteringIterator(readMetrics,wrappedIterator,supplementalFilters));
// Downsampling:
// For locus traversals where we're downsampling to coverage by sample, assume that the downsamplers
// will be invoked downstream from us in LocusIteratorByState. This improves performance by avoiding