Table 2.

Algorithm for indel pair redundancy check by applying sliding window on reference genome

Algorithm 2:	Indel pair redundancy check Algorithm
Input:	Two candidate redundant indels A and B’s information
	same type T (either insertion or deletion), T A = T B,, same length L A = L B,
	allele information S A, S B, position information P A, P B, where P A < = P B,
	reference genome sequence S.
Output:	A pair indels A, B are redundant or not: Redundancy
1	Set Redundancy = False;
2	Phase 1: template substring formation
3	Form template substring for insertion type S I or for deletion type S D separately
4	S I = Substring in reference genome with P B - P A;
5	S D = Substring in reference genome with P B - P A + L A;
6	Phase 2: variant substring formation for insertion type
7	if T A = T B = Insertion then
8	Insert S A in front of template substring S I to form variant substring V A for indel A;
9	Append S B at the end of template substring S I to form variant substring V B for indel B;
10	if V A = V B then
11	Redundancy found: Redundancy = True;
12	else
13	No Redundancy
14	Phase 3: variant substring formation for deletion type
15	if T A = T B = Deletion then
16	Cut S A in front of template string S D, form variant substring V A for indel A;
17	Cut S B at the end of template string S D, form variant substring V B for indel B;
18	if V A = V B then
19	Redundancy found: Redundancy = True;
20	else
21	No Redundancy
22	return Redundancy