Windowed POA #335
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Windowed POA #335
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(Stacks on #334)
abPOA requires memory quadratic in sequence length, so the current version only usable up to a few tens of kb.
this PR splits the MSA problem into windows (default size =10kb) left-to-right on the input sequences, and runs abPOA on each window. What it doesn't do (yet), is try to be clever about window boundaries.
(the whole poa workflow remains experimental and undocumented pending further testing, but we hope it will help with human pangenome graphs where the usual progressive decomposition doesn't apply)