Fix errors

Author: szhan

python/tests/test_imputation.py

@@ -226,18 +226,18 @@ def get_test_data(matrix_text, par):
     x = convert_to_numpy(matrix_text)
     if par == "switch":
         # Switch probability, one per site
-        return x[:, 2].reshape((4, 4))[:, 2]
+        return x[:, 2].reshape((4, 4))[:, 0]
     elif par == "mismatch":
-        # Mismatch probability
-        return x[:, 2].reshape((4, 4))[:, 4]
+        # Mismatch probability, one per site
+        return x[:, 4].reshape((4, 4))[:, 0]
     elif par == "ref_hap_allele":
         # Allele in haplotype in reference panel
         # 0 = ref allele, 1 = alt allele
-        return x[:, 2].reshape((4, 4))[:, 6]
+        return x[:, 6].reshape((4, 4))
     elif par == "query_hap_allele":
         # Allele in haplotype in query
         # 0 = ref allele, 1 = alt allele
-        return x[:, 2].reshape((4, 4))[:, 7]
+        return x[:, 7].reshape((4, 4))[:, 0]
     elif par == "shift":
         # Shift factor
         # TODO
@@ -248,6 +248,6 @@ def get_test_data(matrix_text, par):
         pass
     elif par == "sum":
         # Sum of values over haplotypes
-        return x[:, 2].reshape((4, 4))[:, 10]
+        return x[:, 10].reshape((4, 4))[:, 0]
     else:
         raise ValueError(f"Unknown parameter: {par}")