@Override public Long map( final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) { GenomeLoc refLocus = ref.getLocus(); // process and remove any intervals in the map that are don't overlap the current locus anymore // and add all new intervals that may overlap this reference locus addNewOverlappingIntervals(refLocus); outputFinishedIntervals(refLocus, ref.getBase()); // at this point, all intervals in intervalMap overlap with this locus, so update all of them for (IntervalStratification intervalStratification : intervalMap.values()) intervalStratification.addLocus(context, ref); return 1L; }