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R Interfaces to Phylogenetic Software
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[request] mafft function #2

Open Andreas-Bio opened 7 years ago

Andreas-Bio commented 7 years ago

Are you still maintaining the CRAN version?

Can you please add the option to mafft to add options freely? I really need the --unalignlevel --allowshift --keeplength options, but I have to fix() it every time.

FranzKrah commented 6 years ago

If you already coded the solution, please just mail to us, then we can include. Cheers, Franz

Andreas-Bio commented 6 years ago

I just removed this part from the function: 

else {
    options <- match.arg(options, c("--adjustdirection", 
                                    "--adjustdirectionaccurately"))
    options <- paste(options, collapse = " ")
}

Which enables me to pass options via the option parameter of the function like this: options= "--thread 4 --adjustdirection --nwildcard"

This may be less user friendly because it will not catch spelling errors in, for example --adjustdirectionaccurately, however it will give more experienced users more flexibility. Then again it's not that bad, because if mafft is supplied with a mispelled parameter it crashes instantly.

This is just my personal opinion.