modify inference code to include vertical shift and take mean of x->y and y->x hitting times

petrelharp / tortoisescape

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modify inference code to include vertical shift and take mean of x->y and y->x hitting times #11

Closed petrelharp closed 9 years ago

petrelharp commented 9 years ago

Currently, the writeup and code try to make H[x,y] fit D[x,y]; but D is symmetric and H is not; instead, make (H[x,y]+H[y,x])/2 fit D[x,y]. Also, should add a vertical shift to D to account for sequencing error and within-pop divergence.

petrelharp commented 9 years ago

vertical shift added in 72e41b616c6d9d55fc9a597d78f9610b0f5476ed to trust optimization code

petrelharp commented 9 years ago

symmetrization added in f994bf8e2a7dcecfbf937b418fc27a06bb815550