Patrick Schultz

[compiler] make readers support uid generation

1

High level changes: * `TableRead` and `MatrixRead` text representation change: where before the requested type could be `None`, it can now also be `DropRowUIDs`, or for `MatrixRead` `DropColUIDs` or `DropRowColUIDs`....

[query] add local whitening method

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~Stacked on #11045~ Implements a method to orthogonalize each row of (an entry field of) a matrixtable against all previous rows within a specified window size. The method has time...

[query] Consider adding import/export support for HDF5

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[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 =...

[query] error when sampling an entries table

1

### 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...

This will hopefully make it harder to accidentally build in debug mode when doing performance testing.

scalafix wasn't running in CI.