Fix bug

Author: szhan

python/tests/test_beagle.py

@@ -373,8 +373,8 @@ def run_beagle(ref_h, query_h, pos):
     """
     assert ref_h.shape[0] == len(pos)
     assert query_h.shape[0] == len(pos)
-    genotyped_pos_idx = np.where(query_h != -1)
-    imputed_pos_idx = np.where(query_h == -1)
+    genotyped_pos_idx = np.where(query_h != -1)[0]
+    imputed_pos_idx = np.where(query_h == -1)[0]
     assert len(genotyped_pos_idx) > 0
     assert len(imputed_pos_idx) > 0
     genotyped_pos = pos[genotyped_pos_idx]