code: public static <S extends Sequence<S>> Alignment<S> shiftIndelsAtHomopolymers(Alignment<S> alignment) {
          return new Alignment<>(alignment.sequence1,
                  MutationsUtil.shiftIndelsAtHomopolymers(alignment.sequence1, alignment.sequence1Range.getFrom(), alignment.mutations),
                  alignment.sequence1Range, alignment.sequence2Range, alignment.score);
      }
docs: Shifts indels to the left at homopolymer regions