Minor edits to comments

tests/lsbase.py

@@ -77,7 +77,8 @@ def get_examples_diploid(self, ts, include_ancestors):
             raise NotImplementedError
         ref_panel = ts.genotype_matrix()
         num_sites = ref_panel.shape[0]
-        # Queries are unphased genotypes (calculated as allele dosages).
+        # Take some haplotypes as queries from the reference panel.
+        # Note that the queries contain unphased genotypes (calculated as allele dosages).
         query1 = ref_panel[:, 0].reshape(1, num_sites)
         query1 += ref_panel[:, 1].reshape(1, num_sites)
         query2 = ref_panel[:, -2].reshape(1, num_sites)
@@ -90,11 +91,11 @@ def get_examples_diploid(self, ts, include_ancestors):
         query_miss_most = query1.copy()
         query_miss_most[0, 1:] = core.MISSING
         queries = [query1, query2, query_miss_last, query_miss_mid, query_miss_most]
-        # Remove queries from the reference panel.
+        # Exclude the arbitrarily chosen queries from the reference panel.
         ref_panel = ref_panel[:, 2:-2]
-        ref_panel_size = ref_panel.shape[1]
-        # Reference panel contains unphased genotypes.
-        G = np.zeros((num_sites, ref_panel_size, ref_panel_size))
+        num_ref_haps = ref_panel.shape[1]   # Haplotypes, not individuals.
+        # Reference panel contains phased genotypes.
+        G = np.zeros((num_sites, num_ref_haps, num_ref_haps))
         for i in range(num_sites):
             G[i, :, :] = np.add.outer(ref_panel[i, :], ref_panel[i, :])
         return ref_panel, G, queries