Nick Harding
Nick Harding
Seems to be the same issue as described here: https://github.com/cggh/scikit-allel/issues/376 Workaround: https://github.com/cggh/scikit-allel/issues/376#issuecomment-1132116452
Hi- I don't think this is a missing library issue. The error is because the python `str` method `.strip()` is trying to operate on a `None`, rather than the expected...
To me, the package looks like it has installed correctly. How are you calling it from the command line? It looks like you are not providing an input filename?
Yes. Missing genotypes should be encoded as `-1`, following the convention of `VCF`.
Leaving this open as a note to document this more fully. Generally I want to encourage users to give `VCF` or `zarr` as inputs though.
Currently- this is not possible as things stand. This functionality could certainly be added- but unsure when I can dedicate some time to it. PRs are welcome. In the meantime-...
Hmm- what seems to be happening is that a likelihood is below 0 before the `np.log` is applied. This might be an edge case- where the area under the curve...
Thanks. In the `RunTime Warning` output- do any rows have a `Nan` value for the `xpclr` column? If so, can you share those rows?
I think that's a slightly different issue. Where there are no SNPs, your likelihoods should be 0, which when you log is `-Inf`. Which gives a distinct warning. The warning...
Sorry I must have missed the first question- apologies. I suspect the use of genomic positions is to blame- the implementation should give similar results, excluding some minor differences in...