Fix bugs preventing tool from working on short reference sequences #16
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… of a chromosome
Note that a few lines above, in the case of a circular chromosome, the code gets this right. Specifically, this check uses <= correctly:
if length + ref_pos <= genome_len:
It's only this spot where the logic was wrong and consequently reads that end on the last base of the chromosome weren't allowed.
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(See #9, and the commit messages of the commits here, for explanation.)