feat: POA semi-global, local, and custom alignment #569
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Adds support for semi-global, local, and custom-defined clip penalty alignment. Test cases and code are implemented similarly to pairwise alignment functions. Banded POA does not support clipping for now (mentioned in #568).
Also, fixes the following issue.
The last update of memory efficient poa didn't retrieve and set the end of matrix rows correctly, causing poa to crash.
Fixes #549.