Fixed an issue with the computation of the alignment array.
Fixed an issue with the computation of the alignment array.

RJFreund/OpenDSA,hosamshahin/OpenDSA,RJFreund/OpenDSA,hosamshahin/OpenDSA,hosamshahin/OpenDSA,RJFreund/OpenDSA,hosamshahin/OpenDSA,RJFreund/OpenDSA,hosamshahin/OpenDSA,hosamshahin/OpenDSA,RJFreund/OpenDSA,hosamshahin/OpenDSA,hosamshahin/OpenDSA,RJFreund/OpenDSA,RJFreund/OpenDSA,RJFreund/OpenDSA,hosamshahin/OpenDSA