Wrong protein alignment but correct score #61
Description
I tried to align two sequences query WSAPSVLLNAS and target WHSSPSILLNS using the following command.
ssw_test -c -p target.fas query.fas
The resulting score is 56 according to ssw.
optimal_alignment_score: 56 strand: + target_begin: 1 target_end: 11 query_begin: 1 query_end: 11
Target: 1 WHSSPSILL-N 10
|******|* *
Query: 1 WSAPSVLLNAS 11
However if I try to rescore the alignment than I end up with a score of 11
WW HS SA SP PS SV IL LL LN - NS
15 + -1 + 1 + -1 + -1 + -2 + 2 + 5 + -4 + -3 + 1 = 12
The correct alignment should look like this
optimal_alignment_score: 56 strand: + target_begin: 1 target_end: 11 query_begin: 1 query_end: 11
Target: 1 WHSSPSILLN-S 11
| |*||*||| |
Query: 1 W-SAPSVLLNAS 11
The error occurs if there is a single match followed by a deletion at the beginning of the alignment.
The banded_sw function produces the error.