Potential indexing issue?

[TransGirlCodes]

On this line:

SimpleSmithWatermanCPP/SmithWaterman.cpp

Line 93 in c8e11a1

traceback[0] = matrix[i-1][j-1]+similarityScore(seqA[i-1],seqB[j-1]);

There is the possibility of indexing into a matrix or string with a j of -1 when the loop does its first iteration, as j is initialized as 0 for the start of the inner loop, should j be set to one to start the inner loop?

[jianshu93]

On this line:

SimpleSmithWatermanCPP/SmithWaterman.cpp

Line 93 in c8e11a1

traceback[0] = matrix[i-1][j-1]+similarityScore(seqA[i-1],seqB[j-1]);

There is the possibility of indexing into a matrix or string with a j of -1 when the loop does its first iteration, as j is initialized as 0 for the start of the inner loop, should j be set to one to start the inner loop?

I agree and I try the sequences "CAGTATCGCA" and "AAGTTAGCAG", manually local alignment returns a score of 5 (I believe it is correct) but this script returns 4, I think It is due to the index problem you mentioned.