public static <S extends Sequence<S>> Mutations<S> shiftIndelsAtHomopolymers(S seq1, int seq1From, Mutations<S> mutations) {
        int[] muts = mutations.mutations.clone();
        shiftIndelsAtHomopolymers(seq1, seq1From, muts);
        return new Mutations<>(mutations.alphabet, muts);
    }
public static < S extends Sequence < S > > Mutations < S > shiftIndelsAtHomopolymers ( S seq1 , int seq1From , Mutations < S > mutations ) { int [ ] muts = mutations . mutations . clone ( ) ; shiftIndelsAtHomopolymers ( seq1 , seq1From , muts ) ; return new Mutations < > ( mutations . alphabet , muts ) ; }
This one shifts indels to the left at homopolymer regions Applicable to KAligner data, which normally put indels
randomly along such regions Required for filterMutations algorithm to work correctly Works inplace

@param seq1      reference sequence for the mutations
@param seq1From  seq1 from
@param mutations array of mutations