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Cloud-native genomic dataframes and batch computing
[HDF5](https://www.hdfgroup.org/solutions/hdf5/) could be a natural file format for matrix tables, esp. block partitioned and/or higher-dimensional generalizations. More near term, HDF5 is used for large single cell data, and adding import...
### What happened? Here is a reproducer, though I would like to find a simpler one: ```python mt = hl.balding_nichols_model(1, 10, 10) mt = mt.annotate_rows(foo=hl.agg.count_where(hl.is_defined(mt['GT'])) - hl.sum(hl.agg.call_stats(mt.GT, mt.alleles).homozygote_count)) ht =...
### What happened? ``` mt = hl.utils.range_matrix_table(10, 10) ht = mt.entries() ht = ht.sample(0.5) ht._force_count() ``` throws a `is.hail.utils.HailException: expected non-missing` from inside generated code. ### Version 0.2.127 ### Relevant...
### What happened? Public access buckets typically grant ```yaml - members: - allUsers role: roles/storage.objectViewer ``` which permits ``` resourcemanager.projects.get resourcemanager.projects.list storage.managedFolders.get storage.managedFolders.list storage.objects.get storage.objects.list ``` Notably excluding ``` storage.buckets.get...
This will hopefully make it harder to accidentally build in debug mode when doing performance testing.
### What happened? This code block should work: ```python import hailtop.fs as hfs with hfs.open('gs://foo/bar.txt') as f: f.seek(2) print(f.read()) ``` But this fails with an `OSError` because the `ReadableStream`s that...
### What happened? Hana Snow is the engineer for SEQR. Previously, SEQR used elastic search as its datastore. Unfortunately, elastic search was very expensive because, to get reasonable performance, SEQR...
### What happened? gnomAD team asks: > We would like to get these same sample stats broken down by different variant stratifications, so essentially, this is like what we do...