make command line parameters compatible to blast/swipe

[tolot27]

Why introducing another set of command line parameters and not using those of Blast which are also used by swipe?

There is also a tiny bug regarding to the gap open penalty. The help says that -g should be used but only -o works.

[tolot27]

Long commands of blast+ should be implemented as well.

[Martinsos]

@tolot27 Thank you for suggestions, you are right I should adapt the flags! Since main motivation for SWIMD was to create a library, I did not have time to polish aligner completely, its main purpose was to serve as an example of usage of library.