Remove unused code
Move alignment function into a class.

Instead of globalalign_locate, Aligner.locate is provided.
This makes the code a bit clearer, but also gives a very slight runtime
improvement (1%) since the memory for the DP matrix entries is only allocated
once when the Aligner class is initialized.
Optimize alignment algorithm for the case that STOP_WITHIN_SEQ2 is not true.

This does not occur within cutadapt since all of the adapter types allow the
adapter to end within the read (SEQ2 corresponds to the read). This is only
for other tools that use the same alignment routine.
Start changing terminology: s1 -> ref; s2 -> query
Remove unnecessary assignments.