From 492a282a6bfb8096b57a77659ab05bcb0974e9df Mon Sep 17 00:00:00 2001
From: Shing Zhan <shing.zhan@gmail.com>
Date: Mon, 19 Jun 2023 16:39:14 +0100
Subject: [PATCH] Reorganise

---
 tests/test_compare_vcfs.py | 34 +++++++++++++++++-----------------
 1 file changed, 17 insertions(+), 17 deletions(-)

diff --git a/tests/test_compare_vcfs.py b/tests/test_compare_vcfs.py
index 6d288ac..dd428f3 100644
--- a/tests/test_compare_vcfs.py
+++ b/tests/test_compare_vcfs.py
@@ -99,20 +99,21 @@ def test_both_biallelic_same_alleles_different_order():
     assert np.array_equal(actual, expected)
 
 
-def test_biallelic_monoallelic():
+def test_both_biallelic_different_alleles():
     ds1 = make_test_case()
     ds2 = ds1.copy(deep=True)
     # At the first site, one allele is shared.
+    ds2.variant_allele[0] = xr.DataArray([b'C', b'G'])
+    ds2.call_genotype[0] = xr.DataArray([[0, 1], [1, 0]])
     # At the second site, no allele is shared.
-    for i in np.arange(ds2.variant_contig.size):
-        ds2.variant_allele[i] = xr.DataArray([b'C', b''])
-        ds2.call_genotype[i] = xr.DataArray(np.zeros_like(ds2.call_genotype[i]))
+    ds2.variant_allele[1] = xr.DataArray([b'A', b'C'])
+    ds2.call_genotype[1] = xr.DataArray([[0, 1], [1, 0]])
     # Subtest 1
     _, actual = compare_vcfs.remap_genotypes(ds1, ds2)
     expected = xr.DataArray(
         [
-            [[1, 1], [1, 1]],
-            [[2, 2], [2, 2]],
+            [[1, 2], [2, 1]],
+            [[2, 3], [3, 2]],
         ],
         dims=["variants", "samples", "ploidy"]
     )
@@ -121,29 +122,28 @@ def test_biallelic_monoallelic():
     _, actual = compare_vcfs.remap_genotypes(ds2, ds1)
     expected = xr.DataArray(
         [
-            [[1, 0], [0, 1]],
-            [[2, 1], [1, 2]],
+            [[2, 0], [0, 2]],
+            [[3, 2], [2, 3]],
         ],
         dims=["variants", "samples", "ploidy"]
     )
     assert np.array_equal(actual, expected)
 
 
-def test_both_biallelic_different_alleles():
+def test_biallelic_monoallelic():
     ds1 = make_test_case()
     ds2 = ds1.copy(deep=True)
     # At the first site, one allele is shared.
-    ds2.variant_allele[0] = xr.DataArray([b'C', b'G'])
-    ds2.call_genotype[0] = xr.DataArray([[0, 1], [1, 0]])
     # At the second site, no allele is shared.
-    ds2.variant_allele[1] = xr.DataArray([b'A', b'C'])
-    ds2.call_genotype[1] = xr.DataArray([[0, 1], [1, 0]])
+    for i in np.arange(ds2.variant_contig.size):
+        ds2.variant_allele[i] = xr.DataArray([b'C', b''])
+        ds2.call_genotype[i] = xr.DataArray(np.zeros_like(ds2.call_genotype[i]))
     # Subtest 1
     _, actual = compare_vcfs.remap_genotypes(ds1, ds2)
     expected = xr.DataArray(
         [
-            [[1, 2], [2, 1]],
-            [[2, 3], [3, 2]],
+            [[1, 1], [1, 1]],
+            [[2, 2], [2, 2]],
         ],
         dims=["variants", "samples", "ploidy"]
     )
@@ -152,8 +152,8 @@ def test_both_biallelic_different_alleles():
     _, actual = compare_vcfs.remap_genotypes(ds2, ds1)
     expected = xr.DataArray(
         [
-            [[2, 0], [0, 2]],
-            [[3, 2], [2, 3]],
+            [[1, 0], [0, 1]],
+            [[2, 1], [1, 2]],
         ],
         dims=["variants", "samples", "ploidy"]
     )