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…rror out when running
…e, which is what broke the sequencing error modeling task
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We found a line that was removed in a previous edit that should not have been. Restored that line (which tabulates scores by position, in order to come up with per-position predictions), and discovered a previous fix in the last commit was actually obscuring the bug and should have been an error instead, so we updated that. We also added a quick way to scan the document and count the number of lines that seems to work very quickly, though it will need to be monitored to ensure it doesn't cause an unwanted slowdown on larger files.