Wrong protein alignment but correct score

[martin-steinegger]

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.

[martin-steinegger]

The fix is to change line

Complete-Striped-Smith-Waterman-Library/src/ssw.c

Line 677 in cabdab1

while (LIKELY(i > 0)) {

to while (LIKELY(i > 0) || LIKELY(j > 0))