Additional minimap2 parameters that are useful for HiFi data #29
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fedarko
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Closes #23 -- the user can now specify the exact preset themselves. Closes #17 -- piping is now handled by the shell, rather than Python, which should remove the Python-specific piping memory problems. We could add explicit -o at every step if desired, but I think it should be fine. Partial work on #21: it would still be nice to add an "early warning system" for massive FASTA files. Parital work on #29: users can now add these extra parameters themselves if desired. It might be worth adding new default parameters, but that's a less urgent question.
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The set that flye uses may be a good reference. In particular,
-Land-Qare both no-brainers that would be good to add in.https://github.com/fenderglass/Flye/blob/192de706210a96768eb69eed778fe1b81e887165/flye/polishing/alignment.py#L246-L267
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