Fix/fake sample count het

.gitignore

@@ -27,3 +27,4 @@ docs/source/generated
 # gcloud cli
 google-cloud-cli-*
 google-cloud-sdk
+.venv/

malariagen_data/anopheles.py

@@ -11,6 +11,7 @@
 import plotly.express as px  # type: ignore
 import plotly.graph_objects as go  # type: ignore
 from numpydoc_decorator import doc  # type: ignore
+from .util import parse_single_region
 
 
 from .anoph import (
@@ -553,6 +554,45 @@ def _sample_count_het(
         )
 
         return sample_id, sample_set, windows, counts
+
+    @check_types
+    @doc(
+        summary="Return windowed heterozygosity for a single sample over a genome region.",
+    )
+    def heterozygosity(
+        self,
+        sample: base_params.sample,
+        region: base_params.region,
+        window_size: het_params.window_size = het_params.window_size_default,
+        site_mask: Optional[base_params.site_mask] = base_params.DEFAULT,
+        sample_set: Optional[base_params.sample_set] = None,
+        chunks: base_params.chunks = base_params.native_chunks,
+        inline_array: base_params.inline_array = base_params.inline_array_default,
+    ) -> Tuple[np.ndarray, np.ndarray]:
+        """
+        Returns
+        -------
+        windows : np.ndarray of shape (n_windows, 2)
+            Start and end positions of each window.
+        counts : np.ndarray of shape (n_windows,)
+            Number of heterozygous sites in each window.
+        """
+        # Ensure region object
+        resolved_region: Region = parse_single_region(self, region)
+        del region
+
+        # Delegate to the private helper
+        _, _, windows, counts = self._sample_count_het(
+            sample=sample,
+            region=resolved_region,
+            site_mask=site_mask,
+            window_size=window_size,
+            sample_set=sample_set,
+            chunks=chunks,
+            inline_array=inline_array,
+        )
+
+        return windows, counts
 
     @check_types
     @doc(

tests/anoph/test_heterozygosity.py

@@ -0,0 +1,43 @@
+import numpy as np
+import pytest
+import malariagen_data
+from malariagen_data.anopheles import AnophelesDataResource  
+from malariagen_data.util import Region
+
+@pytest.fixture
+def fake_windows_counts():
+    # pretend we have two windows
+    windows = np.array([[0, 10], [10, 20]])
+    counts  = np.array([3, 7])
+    return windows, counts
+
+def test_heterozygosity_wraps_sample_count_het(monkeypatch, fake_windows_counts):
+    # Define a dummy logger with a debug method
+    class DummyLogger:
+        def debug(self, *args, **kwargs):
+            pass
+
+    # monkey-patch __init__ to set up a dummy _log attribute
+    monkeypatch.setattr(
+        AnophelesDataResource,
+        "__init__",
+        lambda self, *args, **kwargs: setattr(self, "_log", DummyLogger())
+    )
+
+    # monkey-patch the private helper to return (sid, sset, windows, counts)
+    def fake_sample_count_het(self, sample, region, site_mask, window_size, sample_set, chunks, inline_array):
+        return "S1", "setA", fake_windows_counts[0], fake_windows_counts[1]
+
+    monkeypatch.setattr(AnophelesDataResource, "_sample_count_het", fake_sample_count_het)
+
+    resource = AnophelesDataResource()  
+    # call for public method
+    windows, counts = resource.heterozygosity(
+        sample="any_sample",
+        region=Region(contig="2L", start=100, end=200),
+        window_size=10,
+    )
+
+    # assert that we got exactly the arrays the fake helper returned
+    assert np.array_equal(windows, fake_windows_counts[0])
+    assert np.array_equal(counts,  fake_windows_counts[1])