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Refactor align_against_collection(), streamlined handling of "reverse" positions

Mathieu Giraud requested to merge feature-a/refactor-align-against-collection into dev

There was code handling conversion to "reverse" positions in several places in dynprog.cpp, segment.cpp, and vdj_assign.cpp, with at least one pair of back-and-forth conversions. Now all these operations are removed and replaced by a unique AlignBox::reverse() call in align_against_collection(). This function is also refactored.

Edited by Mathieu Giraud

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