inversionfix.py now uses blastn to refine position of inversions
This did not make the output worse, though it did not improve the accuracy as I had hoped. The start and end positions of the inversions are still often off by 1 bp. This may be an off-by-one error somewhere in my code, though it is applied inconsistently. Dnadiff is definatly off by 1 bp in its inversion detection. I created two reference querry fasta file pairs (one based on lambda-phage, one based on H37Rv) with 2 inversions in the same 2 locations, and ran dnadiff on both. Their positions are off from eachother for the end position of the first inversion, and the start and end of the 2nd inversion.
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