// Read transformers: these are applied last, so that we don't bother transforming reads that get discarded
// by the read filters or downsampler.
for ( final ReadTransformer readTransformer : readTransformers ) {
if ( readTransformer.enabled() && readTransformer.getApplicationTime() == ReadTransformer.ApplicationTime.ON_INPUT )
wrappedIterator = new ReadTransformingIterator(wrappedIterator, readTransformer);
}
return wrappedIterator;
}