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WIP: preprocess sequences with MUMmer to detect inversions

Afif Elghraoui requested to merge 1-in-place-inversions-are-not-properly-accounted-for into master

So far, the code is in place to find inversions and write a partial VCF record for it. Still to do is to write a complete VCF record and reverse the inversion before letting it run through diff.

Closes #1

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