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popgenmethods / smcpp

SMC++ infers population history from whole-genome sequence data.
GNU General Public License v3.0
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--tK option : no effect !? #74

Open PaulYJay opened 6 years ago

PaulYJay commented 6 years ago

Hi,

Running different estimate analyses, I encounter (with the latest version) that the --tK option seems to have absolutely no effect. I try to use a lot of different value, from negative to huge positive, and I can't see what it changes. I can even use tK value inferior that t1, without any error output. I try to combine it with different value of t1. In this case, only t1 value are taken into account.

So, is it a bug or do I missed something ?

I seem that the limit t1 and Tk depend of the data analyzed. How default tK is calculated ?

Thank you very much,

Best regards,

Paul

terhorst commented 6 years ago

The algorithm tries to guess values of t1 and tK such that it actually has power to infer size history over that interval. Not sure why tK is not working, I'll look into it.