Add helper function to reencode alleles

python/tests/beagle_numba.py

@@ -36,6 +36,24 @@ def __post_init__(self):
 """ TODO: Implement a class to encapsulate the data for imputation (`ImpData`). """
 
 
+def remap_alleles(a):
+    """
+    Helper function.
+
+    TODO: Move elsewhere.
+    """
+    _ALLELES_ACGT_ = "ACGT"
+    b = np.zeros(len(a), dtype=np.int8) - 1
+    for i in range(len(a)):
+        if a[i] in [None, ""]:
+            continue
+        elif a[i] in _ALLELES_ACGT_:
+            b[i] = _ALLELES_ACGT_.index(a[i])
+        else:
+            raise AssertionError(f"Unrecognised: {a[i]}")
+    return b
+
+
 def convert_to_genetic_map_positions(pos, genetic_map=None):
     """
     Convert physical positions (bp) to genetic map positions (cM).