Feature/compute vectorised score for global alignment

[rrahn]

Fixes #1351

Implements the initial version of vectorised alignments.
🎉🎉🎉🎉🎉🎉🎉🎉🎉🎉🎉🎉

Depends on PR #1378 and issue #1375

Accordingly, only the last 9 commits are relevant.

On macos (catalina) the CI breaks because of the allocator bug. This should be fixed once #1362 is merged.

[codecov]

Codecov Report

Merging #1379 into master will increase coverage by 0.01%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master    #1379      +/-   ##
==========================================
+ Coverage   97.56%   97.58%   +0.01%     
==========================================
  Files         231      232       +1     
  Lines        8755     8822      +67     
==========================================
+ Hits         8542     8609      +67     
  Misses        213      213

Impacted Files	Coverage Δ
.../alignment/pairwise/policy/find_optimum_policy.hpp	100% <ø> (ø)	⬆️
...e/seqan3/alignment/pairwise/detail/type_traits.hpp	100% <ø> (ø)	⬆️
...e/seqan3/alignment/scoring/scoring_scheme_base.hpp	100% <ø> (ø)	⬆️
...clude/seqan3/alignment/pairwise/align_pairwise.hpp	100% <100%> (ø)	⬆️
.../pairwise/execution/alignment_executor_two_way.hpp	98.33% <100%> (ø)	⬆️
...ignment/pairwise/policy/simd_affine_gap_policy.hpp	100% <100%> (ø)
...ignment/pairwise/policy/affine_gap_init_policy.hpp	100% <100%> (ø)	⬆️
.../seqan3/alignment/pairwise/alignment_algorithm.hpp	100% <100%> (ø)	⬆️
...qan3/alignment/pairwise/alignment_configurator.hpp	100% <100%> (ø)	⬆️
...lignment/pairwise/policy/scoring_scheme_policy.hpp	100% <100%> (ø)
... and 5 more

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[joergi-w]

We wanted to keep PRs small... I hope this is not an urgent one, I'll need 2-3 days.

[rrahn]

We wanted to keep PRs small...

I tried to make the commits as small as possible. The biggest commit however could not be reduced without introducing compile errors or failing tests. I did not want to open PRs for one-line commits and then manage all the PRs with several rebases. That is not bearable either. I removed larger components already. Also note that only last 9 commits are relevant. In total it was a 500 line change or something. I hope that is ok.

[joergi-w]

Reviewed commits 11-14

[joergi-w]

This is the review for the remaining commits 15-20. As discussed I went through my comments afterwards and applied the suggestion feature where possible.

[rrahn]

not sure why suddenly the osx builds fail. But maybe this is related to catalina issue with the aligned allocator. Waiting for #1362 to test if the error still occurs.

[joergi-w]

Thank you! Looks good now.

[rrahn]

@smehringer I cleaned the commits now. Only the very first commit is not necessary anymore.

[rrahn]

On mac os build failure is probably related to #1362

[smehringer]

I forgot: please fix the commit history.
And what about a note in the Changelog?

[rrahn]

And what about a note in the Changelog?

Well I wanted to add this when the stuff is complete with the various configurations.

[rrahn]

@smehringer polite ping

[smehringer]

I guess it cannot be merged yet since it still depends on another PR

[rrahn]

yes. right. I forgot about that as well. Too long ago