Update annotate_freq and qual_hists, add split_vds and compute_freq_by_strata #571
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jkgoodrich
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Aug 3, 2023
gnomad/utils/annotations.py
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| Compute call statistics and, when passed, entry aggregation function(s) by strata. | ||
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| The computed call statistics are AC, AF, AN, and homozygote_count. Downsamplings are | ||
| added to the strata when downsamplings when passed. The entry aggregation functions |
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| added to the strata when downsamplings when passed. The entry aggregation functions | |
| added to the strata when `downsamplings` is passed. The entry aggregation functions |
jkgoodrich
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Aug 4, 2023
jkgoodrich
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Aug 4, 2023
Co-authored-by: jkgoodrich <33063077+jkgoodrich@users.noreply.github.com>
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This updates annotate_freq to use the added array aggregation functionality in hail, originally added by Tim in #537, adds the ability to add entry aggregation annotations, and generally cleans up the function by splitting the existing annotate_freq into two functions: annotate_freq which calls compute_freq_by_strata.
This also adds split_vds_by_strata which returns a lists of VDSs with as many VDSs as there are unique values for the passed expression.
We also add the ability to return a single struct of qual histograms, containing separate structs of raw and adj qual histograms.