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petrelharp / ftprime_ms

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more of peter's edits #17

Closed petrelharp closed 6 years ago

petrelharp commented 6 years ago

So far I have changed the title and added an unchecked version of the simplify algorithm to the (new) methods. More edits to follow.

petrelharp commented 6 years ago

OK - I think I'm done going through this round. I'll merge this soon.

jeromekelleher commented 6 years ago

All looks good to me @petrelharp, ping me if you want specific input somewhere.

petrelharp commented 6 years ago

done

On Thu, Nov 16, 2017 at 11:36 AM, Jerome Kelleher notifications@github.com wrote:

@jeromekelleher commented on this pull request.

In forwards_paper.tex https://github.com/petrelharp/ftprime_ms/pull/17#discussion_r151516206:

The \msprime\ API provides a method to compute $\pi$ among arbitrary subsets of the -samples in a tree sequence, and calculating $\pi$ over all 500K samples -in the example above required about 1.2 seconds. -\jk{I haven't checked the analysis of computing $\pi$ here and not thought about -it too deeply. I guess we should also compare this with something else in order to

Yep, looks good to me. Would you mind dropping this into the sims/msprime-examples.py file so it doesn't get lost? I'll run it when I get a chance.

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petrelharp commented 6 years ago

Nit-picking here: we haven't provided a C API, just a Python one. C API is planned.

—

Whoops, right. I'll let you rephrase this on your next go-round. The C is at least well-tested.

petrelharp commented 6 years ago

OK, I will merge this now. @molpopgen and @ashander - feel free to discuss here further.