Benjamin Redelings

Hi @shajoezhu, thanks for the advice! I will try adding a reference panel. I wasn't sure it would help because it seems that rho/theta is pretty high in vivax, so...

OK, I had a few ideas about fixing mixing problems. It looks like you have transition kernels to update (w|h) and transition kernels to update (h|w), where h is the...

Another idea was to allow adding and removing haplotypes instead of fixing the number at five and setting the prior so that some have very low frequencies. This probably makes...

Any thoughts? It also looks like the `doc` branch has disappeared... do you know where it went?

Sorry, I just saw this because the e-mails went into my spam folder. Yeah, finding some time to talk would be great. I am also really interested in your ideas...

I have some patches I wanted to submit to illustrate some of what I was talking about and clarify about the dynamic programming. Is there a good branch for me...

BTW, it looks like there _might_ be some double-counting in this line of `UpdateSingleHap::calcFwdProbs()`: ``` C++ fwdTmp[i] = emission_[j][panel_->content_[hapIndex][i]] * (fwdProbs_.back()[i] * pNoRec + massFromRec); ``` It looks like the...