Add windows command line support to aligner

[randrick]

You can get aligner to work on windows command line by inserting the following lines into aligner.ccp
after line 8: #include <queue>

#ifdef _WIN32
#include "getopt.h"
#endif

#include "edlib.h"

Then adding getopt.h file. The one I used is here: https://raw.githubusercontent.com/skandhurkat/Getopt-for-Visual-Studio/master/getopt.h although that's likely not the origin of the file.

[Martinsos]

@randrick Thank you for suggestion! I was looking at it as a possible solution, but I did not like the idea of adding external getopt.h file. However, it does sound like a good solution now.

Would you be up for creating a PR for this? I don't use Windows for development so it would be great if you could also test it a little bit.

There is already an issue for this: #56, I will close it in favor of this one. As mentioned there, we should also add aligner tests to appveyor.

[randrick]

I can create a PR, although I am not really a windows developer either. I really should have said, this change was to make the aligner compile using Visual Studio. It will compile on windows just fine with minGW compiler.

[Martinsos]

Yes that is completely fine, we want for people to be able to use edlib from visual studio also.
Please do create a PR then when you have time :)!