Closed ArtPoon closed 7 years ago
I've double-checked the R
, P
and Q
matrices and they look ok. The problem seems to be in the bit matrix. Here is the matrix prior to edge assignment:
0 16 16 16
64 84 50 18
64 73 84 18
64 73 73 20
64 65 65 4
and here it is after
0 16 16 7
64 84 55 18
64 79 84 18
71 73 73 23
7 65 7 4
Note that the lower right cell was initialized to 4, i.e., 100
setting the c
-bit to True.
Ugh. I was up too late when I wrote this issue. Traceback is fine.
Working through some test cases, I've come across the following error. For sequences
ACGT
andACT
, match/mismatch scores of-5/+4
and gap open/extend penalties+5,+1
, we get the following cost matrix:results in the following traceback:
But the best path should be V, D, D, D (-9, -6, -10, -5, 0). no it's not