fix: gracefully handle oversized window_size by auto-adjusting

Author: suhr25

malariagen_data/anoph/fst.py

@@ -83,14 +83,24 @@ def _fst_gwss(
             ).compute()
 
         n_snps = len(pos)
-        if window_size > n_snps:
+        _min_snps_threshold = 1000
+        _window_adjustment_factor = 10
+        if n_snps < _min_snps_threshold:
+            raise ValueError(
+                f"Too few SNP sites ({n_snps}) available for Fst GWSS. "
+                f"At least {_min_snps_threshold} sites are required. "
+                "Try a larger genomic region or different site selection criteria."
+            )
+        if window_size >= n_snps:
+            adjusted_window_size = max(1, n_snps // _window_adjustment_factor)
             warnings.warn(
-                f"window_size ({window_size}) is larger than the number of SNP sites "
-                f"available ({n_snps}); adjusting window_size to {n_snps}.",
+                f"window_size ({window_size}) is >= the number of SNP sites "
+                f"available ({n_snps}); automatically adjusting window_size to "
+                f"{adjusted_window_size} (= {n_snps} // {_window_adjustment_factor}).",
                 UserWarning,
                 stacklevel=2,
             )
-            window_size = n_snps
+            window_size = adjusted_window_size
 
         with self._spinner(desc="Compute Fst"):
             with np.errstate(divide="ignore", invalid="ignore"):
@@ -107,9 +117,10 @@ def _fst_gwss(
     @doc(
         summary="""
             Run a Fst genome-wide scan to investigate genetic differentiation
-            between two cohorts. If window_size exceeds the number of available
+            between two cohorts. If window_size is >= the number of available
             SNP sites, a UserWarning is issued and window_size is automatically
-            reduced to the number of available sites.
+            adjusted to number_of_snps // 10. A ValueError is raised if the
+            number of available SNP sites is below 1000.
         """,
         returns=dict(
             x="An array containing the window centre point genomic positions",