Add documentation for Hail interoperation #310
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Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
Codecov Report
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…l-interop-docs
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@henrydavidge Ready for review on this one; I'm not sure why the tests are failing though. |
Signed-off-by: Karen Feng <[email protected]>
build.sbt
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| .settings( | ||
| pythonSettings, | ||
| test in Test := { | ||
| hailtest.toTask(" --doctest-modules python/glow/hail/").value | ||
| hailtest.toTask(" --doctest-modules python/glow/hail/ docs/source/etl/hail.rst").value |
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nit: make this into a variable hailPaths in case we have more hail related docs in the future
python/glow/hail/functions.py
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| @@ -156,6 +154,8 @@ def from_matrix_table(mt: MatrixTable, include_sample_ids: bool = True) -> DataF | |||
| """ | |||
| Converts a Hail MatrixTable to a Glow DataFrame. | |||
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| Requires that the MatrixTable rows contain locus and alleles fields. | |||
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| Args: | |||
| mt : The Hail MatrixTable to convert | |||
| include_sample_ids : If true, include sample IDs in the Glow DataFrame | |||
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nit: could you document why you might want this to be false?
python/glow/hail/functions.py
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| @@ -156,6 +154,8 @@ def from_matrix_table(mt: MatrixTable, include_sample_ids: bool = True) -> DataF | |||
| """ | |||
| Converts a Hail MatrixTable to a Glow DataFrame. | |||
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Could you describe what the schema will look like? How is it translated from the Hail schema?
Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
Signed-off-by: Karen Feng <[email protected]>
What changes are proposed in this pull request?
Add docs for the Hail interop function
from_matrix_table, which will be available in 0.7.Also fixes a bug in the aforementioned function; previously, missing names were represented as an empty array; this should be null.
How is this patch tested?
Includes docs-side testing in
hail/test. This is chained to our Python-side testing to leverage the Spark-Hail setup; otherwise, we'd have to copypython/glow/hail/conftest.pyto the docs.