Ben Jeffery
Ben Jeffery
Our current newick parsing relies on the `newick` python library, which for trees we've tested is ~120x slower than parsing with a common (C extension) `R` library. My initial rough...
Summary with click to expand for details.
Once we have a citation for tskit we should add some small unobtrusive hint to cite tskit to the notebook representations.
As discussed in #1899 30% of the time required to load a 1G tree sequence is spent checking its integrity. We could bypass this by recording when check integrity has...
As `struct` doesn't support properties that are not specified in the schema it errors out with a `KeyError` if `properties` is not present in the schema dict, for example `tskit.MetadataSchema({'codec':'struct'})`....
Looks like all other dep updates are good, but stdpopsim is failing: `AttributeError: 'DemographicModel' object has no attribute 'population_configurations'`
This arose in the context of https://github.com/pystatgen/sgkit-publication/issues/35#issuecomment-1840492652 where dask workers being rotated due to slow memory leaks caused work to be redone and the VCF parse to never complete. This...
@tnguyengel has hit the following error while running `vcf_to_zarr` with the default arguments: ``` File "/home/tnguyen/conda/sgkit_main/lib/python3.10/site-packages/zarr/core.py", line 2168, in _process_for_setitem chunk = value.astype(self._dtype, order=self._order, copy=False) ValueError: could not convert string...
#1043 shows that we should test with a processed-based dask cluster. I've tried this by adding `client = dask.distributed.Client(n_workers=1, threads_per_worker=1)` to `conftest.py` but I get segfaults in workers. Attaching GDB...
I have a 56GB VCF which contains the variants for part of chr20, however the header of the VCF lists over _2000_ contigs! This confuses `partition_into_regions` which returns a region...