Christopher Vittal

This simplifies the code and means that region bookeeping for the prune queue is unnecessary.

This will allow expert users to import these functions directly and use them in, for example, grouped aggregators. ```python3 from hail.vds.sample_qc import vmt_sample_qc, vmt_sample_qc_variant_annotations vmt = vds.variant_data vmt = vmt.annotate_entries(GT=hl.vds.lgt_to_gt(vmt.LGT,...

[hailctl] script generated for hailctl batch submit attempts to change working directory to nonexistent directory

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### What happened? `hailctl batch submit ` See: https://batch.hail.is/batches/8122929/jobs/1 This `cd` was introduced in #13812 ### Version main ### Relevant log output _No response_

Add hailctl fs as a cloud agnostic filesystem utility, along with two commands `ls` and `du`. Output is rudimentary at this point and is subject to change. du: ``` Usage:...

[query] Zip length mismatch error on join

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from: https://discuss.hail.is/t/zip-length-mismatch-error/3548 ``` > > 2023-08-09 15:56:05.872 Hail: INFO: wrote table with 104 rows in 104 partitions to gs://gnomad-tmp-4day/__iruid_845-wg8w0gBbPsilRDfRegbVW3 INFO (constraint_pipeline 463): Copying log to logging bucket... 2023-08-09 15:56:33.276 Hail:...

This catches a few things missed in https://github.com/hail-is/hail/pull/14521 and adds `PCanonicalArrayBackedContainer` as an extension trait to `PArrayBackedContainer`, ensuring that types implementing this trait are specifically backed by `PCanonicalArray`.

Right now, we perform a full scan in `to_dense_mt`, we have information to do less work and densify in a single pass. - Expose partitioning in python - For each...