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Improve performance of variant_stats #1119

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Oct 3, 2023
Merged

Improve performance of variant_stats #1119

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74d2f2b
Improve performance of variant_stats #1116
timothymillar Aug 29, 2023
798da78
Fixup getting_started docs to handle dask array
timothymillar Aug 29, 2023
9e8bd1e
Use gufunc in sample_stats
timothymillar Sep 4, 2023
69f9293
Faster count_variant_alleles in Tajimas_D
timothymillar Sep 4, 2023
ee0d07c
:Update changelog
timothymillar Sep 5, 2023
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9 changes: 7 additions & 2 deletions docs/changelog.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -19,15 +19,20 @@ New Features
(:user:`timothymillar`, :pr:`1100`, :issue:`1062`)
- Add :func:`display_pedigree` function.
(:user:`timothymillar`, :pr:`1104`, :issue:`1097`)
- Add option to count variant alleles directly from call genotypes in function :func:`count_variant_alleles`.
(:user:`timothymillar`, :pr:`1119`, :issue:`1116`)

.. Breaking changes
.. ~~~~~~~~~~~~~~~~

.. Deprecations
.. ~~~~~~~~~~~~

.. Improvements
.. ~~~~~~~~~~~~
Improvements
~~~~~~~~~~~~

- Improve performance of :func:`variant_stats` and :func:`sample_stats` functions.
(:user:`timothymillar`, :pr:`1119`, :issue:`1116`)

.. Bug fixes
.. ~~~~~~~~~
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6 changes: 3 additions & 3 deletions docs/getting_started.rst
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Expand Up @@ -203,7 +203,7 @@ shows how it can be used in the context of doing something simple like counting

# Now the result is correct -- only the third sample is heterozygous so the count should be 1.
# This how many sgkit functions handle missing data internally:
sg.variant_stats(ds).variant_n_het.item(0)
sg.variant_stats(ds).variant_n_het.values.item(0)

Windowing
---------
Expand Down Expand Up @@ -320,8 +320,8 @@ Xarray and Pandas operations in a single pipeline:
# for windows of size 20 variants
(
ds
# Add call rate and other statistics
.pipe(sg.variant_stats)
# Add and compute call rate and other statistics
.pipe(sg.variant_stats).compute()
# Apply filter to include variants present across > 80% of samples
.pipe(lambda ds: ds.sel(variants=ds.variant_call_rate > .8))
# Create windows of size 20 variants
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