Tim Millar

@jeromekelleher I'll close this via #1030 (just VCF representation). Do you want to open another issue for "pretty" formatting?

FWIW I also prefer lowercase. But then what about parameter strings? `method="Hamilton-Kerr"` or `method="hamilton-kerr"`? Maybe case insensitive languages are a good idea...

Hi @fouerghi, yes we currently only support dense arrays. From memory, we decided to avoid sparse arrays until there is more standardized support in our dependencies (Xarray and Zarr). An...

> P.S: I have a lot of unrelated pairs of individuals in the trees and I am only interested in ones that are above a certain threshold. Could that help?...

> Could you elaborate more on the chunking part? It's a strategy to compute large arrays/matrices in parts which can avoid needing to hold the entire matrix in memory at...

Hi @fouerghi, sorry for my slow response. I'm afraid we don't have an equivalent function in the current 0.7 release. Hopefully the next release won't be too far away.

Possibly a similar bug with a FORMAT field which is length `R`. Getting some random crashes which may be due to out of bounds memory access in Numba code.

With an updated dataset (slightly larger), including the length `R` FORMAT field resulted in `ValueError: Codec does not support buffers of > 2147483647 bytes`. This led me to https://github.com/zarr-developers/zarr-python/issues/487 and...

Possibly related to #869? Do you get segfaults if you disable numba caching?

I have opened https://github.com/numba/numba/issues/9452 related to this. Note that the root cause seems to be a discrepancy between behavior when the jit is/isn't disabled. The caching seems to be hiding...