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In the current implementation the default for --min-length is 0 instead of 25000.
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So, I'm not sure if 0 is the correct thing to say for the --min-length default. I guess it would equate to a default of 8,970 as it is 0.3 max ambiguity? I thought about just removing this flag completely, but didn't want to in case it breaks pipelines to remove it! |
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In the current implementation the default for --min-length is 0 instead of 25000, i.e. running pangolin without --min-length and with
--min-length 25000(which evaluates to a maximum ambiguity of 0.164) is not equivalent.