BlockAligner-based Smith-Waterman update #1010
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git-subtree-dir: lib/corrosion git-subtree-split: b1fab721655c5c4b1b08a083d3cd29f163af75d0
git-subtree-dir: lib/block-aligner git-subtree-split: 3f69b35adc596aa453a68a1fbcc681e8b58a552e
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c5ce8f942 Pick consistent query start position among equal maximum scores e16c2b16a Add no_simd fallback b52e2360b Fix pretty call git-subtree-dir: lib/block-aligner git-subtree-split: c5ce8f94264710bd5dda1664ae1422a5467c9e0d
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This PR updates the Smith-Waterman alignment module to use BlockAligner for both seq-seq and profile-seq alignment.
Refactored and cleaned up unused alignment types, such as profile-profile.
Commented out the int32_t alignment (code remains for reference).
Although alignment mode 2 can still be used, BlockAligner supports backtracing. A future update can make use of this to support precise sequence identity for mode 2 as well.