Fix saddle_strength() to compute extent=0

cooltools/api/saddle.py

@@ -784,6 +784,18 @@ def saddle_strength(S, C):
         raise ValueError("`saddledata` should be square.")
 
     ratios = np.zeros(n)
+
+    # extent=0 reduces to a single pair of corner bins on each side
+    intra0_sum = np.nansum(S[0, 0]) + np.nansum(S[-1, -1])
+    intra0_count = np.nansum(C[0, 0]) + np.nansum(C[-1, -1])
+    intra0 = intra0_sum / intra0_count
+
+    inter0_sum = np.nansum(S[0, -1]) + np.nansum(S[-1, 0])
+    inter0_count = np.nansum(C[0, -1]) + np.nansum(C[-1, 0])
+    inter0 = inter0_sum / inter0_count
+
+    ratios[0] = intra0 / inter0
+
     for k in range(1, n):
         intra_sum = np.nansum(S[0:k, 0:k]) + np.nansum(S[n - k : n, n - k : n])
         intra_count = np.nansum(C[0:k, 0:k]) + np.nansum(C[n - k : n, n - k : n])

tests/test_compartments_saddle.py

@@ -419,3 +419,34 @@ def test_saddle(request, tmpdir):
     # TODO: tests after adding input agreement, e.g.
     # asserting saddle.saddle(clr, cis-type-expected, track, "trans")
     # throws an error
+
+
+def test_saddle_strength():
+    # asymmetric bin counts on the diagonal (C[0, 0] != C[-1, -1]) so that
+    # a naive extent=0 default of 0 would be distinguishable from the
+    # correct value
+    S = np.array(
+        [
+            [10.0, 2.0, 1.0],
+            [2.0, 5.0, 2.0],
+            [1.0, 2.0, 8.0],
+        ]
+    )
+    C = np.array(
+        [
+            [4.0, 2.0, 1.0],
+            [2.0, 5.0, 2.0],
+            [1.0, 2.0, 2.0],
+        ]
+    )
+
+    ratios = saddle.saddle_strength(S, C)
+
+    # extent=0: ((S/C)[0, 0] + (S/C)[-1, -1]) / (2 * (S/C)[-1, 0])
+    # hand-computed from S, C above
+    expected = np.array([3.0, 3.0, 1.5])
+
+    assert np.allclose(ratios, expected)
+    # regression check: extent=0 must not be left at its zero-initialized
+    # default (see https://github.com/open2c/cooltools/issues/565)
+    assert ratios[0] != 0