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petrelharp / ftprime_ms

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New simplify algorithm #61

Closed jeromekelleher closed 6 years ago

jeromekelleher commented 6 years ago

OK, this is as simple as simplify is going to get.

The algorithm is actually pretty nice and concise now (and literally implemented in the Python code (see simplify-alg.py), so we could actually consider putting it back into the main text. The rest of you should make this call though; it's probably still a pretty obscure thing.

The description could do with another pass through from someone else, and a lookover to make sure I haven't made any mistakes.

I'll follow up with a few more commits and annotate my changes a bit later.

molpopgen commented 6 years ago

I quite like the idea of providing a Python implementation with the paper. There are going to be folks who will prefer to code it up themselves rather than try to make the bridge to Python. (In fact, I have an idea that may require doing so myself...)

jeromekelleher commented 6 years ago

I quite like the idea of providing a Python implementation with the paper. There are going to be folks who will prefer to code it up themselves rather than try to make the bridge to Python. (In fact, I have an idea that may require doing so myself...)

I'm perfectly happy to include Python as SI. It's a good way of archiving something that definitely works...

molpopgen commented 6 years ago

I'm perfectly happy to include Python as SI. It's a good way of archiving something that definitely works...

It is also a good way of making the algorithm notation concrete. Some folks will just prefer to look at code.

petrelharp commented 6 years ago

looks good; merging to make minor fixes