Gap-penalty-fixes #8
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Half the time, the first value for traceback was undefined, resulting in a supposed match. This was causing matches at the end of alignments, where generally gaps are more favored.
Previous code was getting the value for del from the del array, but it's possible that this value has been updated by the computation of the optimal delete transition in the same loop. Instead, we create an intermediary variable to store the original value and use it to compute the score for the transition from del to match.
It should only apply to gap opening on the last column, not to gap closing.
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Fixes