Jeff Hammerbacher
Jeff Hammerbacher
When the investigation resolves, would you mind documenting how you instrumented sgkit to log memory allocations in the VCF reader? I’d like to do the same for PLINK.
Ah I filed the sample metadata part of this already https://github.com/pystatgen/sgkit/issues/1151
Just noting that merging separate contigs could be easy with `ds = xr.concat([ds1, ds2], dim='variants')` but we also need to update `ds.variant_contig`, and I think `contig_id` needs to have its...
Okay I think this should do it for merging 2 datasets with no overlapping contigs, which I think will be the most common case. If we wanted to do this...
Issue opened upstream at https://github.com/fastlmm/bed-reader/issues/22
Here's an example that took me way too long to figure out. I wanted to add one column of sample metadata to my dataset. The [file](https://ftp.ebi.ac.uk/biostudies/fire/S-BSST/936/S-BSST936/Files/example/synthetic_small_v1_chr-10.sample) with the new column...
cc @ravwojdyla and @eric-czech in case they have thoughts
What permissions do I need to change?
https://github.com/pystatgen/sgkit/issues/347 may be related
This would be great @sanjaynagi! Linking to some prior discussion on the topic: https://github.com/pystatgen/sgkit/discussions/711