refactor: standardise biallelic diplotypes to count ref allele and handle missing calls

Author: Tanisha127

malariagen_data/anoph/snp_data.py

@@ -2040,7 +2040,7 @@ def _biallelic_diplotypes(
         # with missing calls coded as -127.
         gt = allel.GenotypeDaskArray(ds["call_genotype"].data)
         with self._dask_progress(desc="Compute biallelic diplotypes"):
-            gn = gt.to_n_alt().compute()
+            gn = gt.to_n_ref().compute()
         # Code missing calls as -127.
         missing = np.all(ds["call_genotype"].values == -1, axis=2)
         gn[missing] = -127