Better Alignment Algorithm

[travisgoodspeed]

The current alignment algorithm, RomAlignerNew works great when there's a little tilt to the image and overlap between rows is limited to a few bits in a row when sorted by the X axis. Images with no tilt at all, and images with more overlap, require that a threshold be set to calculate the appropriate number of bits that might arrive out of order in determining the first column.

Close this issue when we have a new alignment algorithm that does not require such fine tuning and works on all existing samples.

[travisgoodspeed]

Fixed for real in #88.