Segmentation fault for certain gap open / gap extension configuration

[michal-kierzynka]

Hi,

Below example that is causing segfault:

./opal_aligner -o 1 -e 1 -x 2 -a NW -p test_query.fasta test_db.fasta -f test.mat

test_query.fasta:

>test query
AABB

test_db.fasta:

>test target
AABBC

test.mat:

 A  B  C  D
 1 -1 -1 -1
-1  1 -1 -1
-1 -1  1 -1
-1 -1 -1  1

Looks to me like the underflow is occurring in matrix E, which is initialized incorrectly. It might have to do with issue #28, however extended to a wider set of scenarios than those described there.