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petrelharp / context

Context-dependent mutation rate inference machinery.
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test json-tree-cpg #36

Open matsen opened 9 years ago

matsen commented 9 years ago

And, I'll take you up on your previous offer: I would like to test json-tree-cpg in a similar way to json-cpg; could you add that in? I would, but it isn't as straightforward as adding another file to nestly/models/, as some of the calls and options are different: fit-tree-model.R rather than fit-model.R, and make-genmat takes no -o flag, as the location of the genmats is specified in the config file.

matsen commented 9 years ago

Hello Peter--

It seems to me that this is the first instance of a path being specified in a config file. It seems to me good to keep it that way unless there is a solid reason to change this and the CLI of all of the tools to accomodate several genmats. What if I changed things to save the several genmats into one .RData file, such that we could keep things as they are?

Thanks!

petrelharp commented 9 years ago

Hm, so: changing make-genmat.R to store in a single file everything needed for the tree? That sounds like a good idea. Perhaps it should also do the setup done by peel.transmat, since that is shared in common by anything with the same tree as well; then the thing that is being stored is still a single object.

-p

On Sat, Feb 7, 2015 at 11:54 AM, Erick Matsen notifications@github.com wrote:

Hello Peter--

It seems to me that this is the first instance of a path being specified in a config file. It seems to me good to keep it that way unless there is a solid reason to change this and the CLI of all of the tools to accomodate several genmats. What if I changed things to save the several genmats into one .RData file, such that we could keep things as they are?

Thanks!

— Reply to this email directly or view it on GitHub https://github.com/petrelharp/context/issues/36#issuecomment-73380019.