Refactor selection of Myers' bitparallel edit distance algorithm. #3254
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This scheme is alphabet agnostic and used to trigger the myers' bitparallel algorithm to compute the edit distance. It is a special case of the DP alignment algorithm where the score for a substitution is 0 if the characters are equal and -1 otherwise.
…eme which is implementation detail and actually not required by the scoring scheme concept.
…ure Myers' bitparallel edit distance computation. Now the edit distance is selected internally if the hamming scheme was used explicitly and if the gap scheme gives -1 for extending and 0 for opening a gap. The edit distance can now be used independent of the alphabet type and is not bound to seqans nucleotide scoring schemes. Since the recommended way to enable the fast bitparallel algorithm is to use the `align_cfg::edit_scheme` configuration element, the majority of user code should work without noticing the internal changes made to the configuration.
…rithm. It makes more sense to skip the runtime checks if the compiler already knows that no Myers' bitparallel edit distance cannot be used.
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… algorithm. During configruation we check if the gap scheme is set and if not use the default gap scheme with `gap open = 0` and `gap extension = -1`. But this default gap scheme is ignored and was later set to -10 and -1 in the alignment gap policy. This commit fixes this, to keep the defaults consistent.
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Co-authored-by: Enrico Seiler <[email protected]>
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May 31, 2024
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This PR fixes #3253 by:
Due to these changes, users can select the Myers' bitparallel edit distance alignment computation independent of their alphabet types and thus are not forced to work with the nucelotide scoring scheme anymore, which did not allow to customize the alphabet type.
Since the bitparallel edit distance algorithm doesn't even read the values from the given scoring schemes, it makes only sense to enable it without specifying a dedicate scoring scheme anyway.
However, due to the existing configuration modes, too much API breakage would have been introduced if wanted to solve this by moving the bitparallel edit distance computation into its own configuration element.
With this solution the user won't see any difference to the old version, when sticking to the tuorials where we explicitly teach to use the dedicated
align_cfg::edit_schemeshortcut.