Add merge parameter to variant_stats

Author: tomwhite

sgkit/stats/aggregation.py

@@ -1,5 +1,8 @@
+from typing import Any, Dict, Hashable
+
 import dask.array as da
 import numpy as np
+import xarray as xr
 from numba import guvectorize
 from typing_extensions import Literal
 from xarray import Dataset
@@ -181,7 +184,7 @@ def genotype_count(ds: Dataset, dim: Dimension) -> Dataset:
     n_het = ~(n_hom_alt | n_hom_ref)
     # This would 0 out the `het` case with any missing calls
     agg = lambda x: xr.where(M, False, x).sum(dim=dim)  # type: ignore[no-untyped-call]
-    return xr.Dataset(
+    return Dataset(
         {
             f"{odim}_n_het": agg(n_het),  # type: ignore[no-untyped-call]
             f"{odim}_n_hom_ref": agg(n_hom_ref),  # type: ignore[no-untyped-call]
@@ -192,26 +195,29 @@ def genotype_count(ds: Dataset, dim: Dimension) -> Dataset:
 
 
 def allele_frequency(ds: Dataset) -> Dataset:
-    AC = count_variant_alleles(ds)
+    data_vars: Dict[Hashable, Any] = {}
+    # only compute variant allele count if not already in dataset
+    if "variant_allele_count" in ds:
+        AC = ds["variant_allele_count"]
+    else:
+        AC = count_variant_alleles(ds, merge=False)["variant_allele_count"]
+        data_vars["variant_allele_count"] = AC
 
     M = ds["call_genotype_mask"].stack(calls=("samples", "ploidy"))
     AN = (~M).sum(dim="calls")  # type: ignore
     assert AN.shape == (ds.dims["variants"],)
 
-    return xr.Dataset(
-        {
-            "variant_allele_count": AC,
-            "variant_allele_total": AN,
-            "variant_allele_frequency": AC / AN,
-        }
-    )
+    data_vars["variant_allele_total"] = AN
+    data_vars["variant_allele_frequency"] = AC / AN
+    return Dataset(data_vars)
 
 
-def variant_stats(ds: Dataset) -> Dataset:
-    return xr.merge(
+def variant_stats(ds: Dataset, merge: bool = True) -> Dataset:
+    new_ds = xr.merge(
         [
             call_rate(ds, dim="samples"),
             genotype_count(ds, dim="samples"),
             allele_frequency(ds),
         ]
     )
+    return ds.merge(new_ds) if merge else new_ds

sgkit/tests/test_aggregation.py

@@ -1,10 +1,15 @@
 from typing import Any
 
 import numpy as np
+import pytest
 import xarray as xr
 from xarray import Dataset
 
-from sgkit.stats.aggregation import count_call_alleles, count_variant_alleles, variant_stats
+from sgkit.stats.aggregation import (
+    count_call_alleles,
+    count_variant_alleles,
+    variant_stats,
+)
 from sgkit.testing import simulate_genotype_call_dataset
 from sgkit.typing import ArrayLike
 
@@ -204,10 +209,13 @@ def test_count_call_alleles__chunked():
     xr.testing.assert_equal(ac1, ac2)  # type: ignore[no-untyped-call]
 
 
-def test_variant_stats():
+@pytest.mark.parametrize("precompute_variant_allele_count", [False, True])
+def test_variant_stats(precompute_variant_allele_count):
     ds = get_dataset(
         [[[1, 0], [-1, -1]], [[1, 0], [1, 1]], [[0, 1], [1, 0]], [[-1, -1], [0, 0]]]
     )
+    if precompute_variant_allele_count:
+        ds = count_variant_alleles(ds)
     vs = variant_stats(ds)
 
     np.testing.assert_equal(vs["variant_n_called"], np.array([1, 2, 2, 1]))