Table 1 Algorithm for clustering indels into candidate redundant indel groups

Algorithm 1:

Clustering indels into candidate redundant indel groups Algorithm

Input:

An indel List: List (I) ordered by indel positions on the reference genome, each indel I has position P, threshold value D of distance between adjacent indels

Output:

Candidate redundant indel groups List List (G _k )

1

Candidate-Group-Generation (indel list: List(I), threshold-value: D)

2

Set List (G _k ) empty: Ø;

3

Set k =0;

4

Set current indel I _current = I ₀ , the first element in the List (I);

5

for each indel i = 2 to n in indel list List (I)

6

if next adjacent indel I _i ’s position P _i - P _current < = D then

7

Add the next indel into the current candidate group G (k);

8

Set current indel I _current = I _i ;

9

else

10

Append G(k) to candidate group list List (G _k );

11

k = k + 1;

12

end

13

return candidate redundant group list List (G _k );