Murillo F. Rodrigues
Murillo F. Rodrigues
I'm interested in this, so might have a go at it soon.
I ran the same example (with a msprime tree sequence) and didn't run into issues.  Then I ran a minimal example with three `sim_mutation` calls to one of my...
I would volunteer to implement this, except I can't think of a clever way to do this in numpy. I've run across this exact problem many times and always end...
It would be nice to be able to define a RateMap with left and right intervals so that it automatically converts to the breakpoints representation. Or is this sth we...
Still hoping to see a reversal to the old behavior for no-calls!
never mind about the generation, this has to do with having to adjust the times if the two simulations were run for different amount of times. we could decide to...
No, this seemed really hard to do with matplotlib...
I think a lot of downstream code that handles VCFs will assume it's 1-based. Should I at least add a warning to the docs with this potential workaround?
I'm going to echo @bhaller's opinion. I agree it is confusing to have the positions in the VCF be off by one when compared to positions in the tree sequence,...
Wait, so if we have a tree sequence with `sequence_length=100` it is allowed to have sites at positions 0 and 100?