consider using new versions of vcftools?

[TomaszSuchan]

Hi Jon, did you consider updating vcftools commands, so dDocent could use new versions of vcftools? So far, I found these changes in vcftools flags to be made:

--geno to --max-missing
--missing to --missing-indv

Am I missing something? I could make these changes if you want.

[jpuritz]

Hi Tomasz,

This has been on the todo list for a little while. It’s a simple update to dDocent, but also requires updating a tutorial and several other scripts. I’ve also tried to avoid, as much as possible, to keep changing version and installation requirements. I’d probably go ahead and add a version check with an if statement to provide the right command for the given version. If you want to take a stab at this, please feel free to do so and submit a pull request.

Thanks,

Jon

-- Jon Puritz, PhD Postdoctoral Research Associate Northeastern University Marine Science Center 430 Nahant Rd, Nahant, MA 01908

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Email: jpuritz@gmail.com

Cell: 401-338-8739

"The most valuable of all talents is that of never using two words when one will do." -Thomas Jefferson

On November 30, 2016 at 2:19:22 PM, Tomasz Suchan (notifications@github.com) wrote:

Hi Jon, did you consider updating vcftools commands, so dDocent could use new versions of vcftools? So far, I found these changes in vcftools flags to be made:

--geno to --max-missing --missing to --missing-indv

Am I missing something? I could make these changes if you want.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/jpuritz/dDocent/issues/28, or mute the thread https://github.com/notifications/unsubscribe-auth/AEnRR8Z7kTfJ4zaUhkZKMjJqL8smT-fjks5rDcw6gaJpZM4LAkx1 .

[TomaszSuchan]

Hi Jon, OK, I'll do this. I think the best way to deal with changing versions it is to keep the flag as a variable that changes the value according to the vcftools version. Cheers, Tomasz