fix coverage with custom cols1 (#170)

* fix coverage with custom cols1 * add requested test for custom column names in coverage * updates from main (#177)
open2c · Dec 22, 2023 · 6ffeb6d · 6ffeb6d
1 parent 5affbc6
commit 6ffeb6d
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Showing 2 changed files with 14 additions and 1 deletion.
diff --git a/bioframe/ops.py b/bioframe/ops.py
@@ -884,7 +884,7 @@ def coverage(
         cols2=cols2,
     )
 
-    df_overlap["overlap"] = df_overlap["overlap_end"] - df_overlap["overlap_start"]
+    df_overlap["overlap"] = df_overlap[f"overlap_{ek1}"] - df_overlap[f"overlap_{sk1}"]
 
     out_df = (
         pd.DataFrame(

diff --git a/tests/test_ops.py b/tests/test_ops.py
@@ -1073,6 +1073,19 @@ def test_coverage():
     df = pd.read_csv(StringIO(d), sep=r"\s+")
     pd.testing.assert_frame_equal(df, bioframe.coverage(df1, df2))
 
+    ### with custom column names
+    cols1 = ["chromosome", "begin", "stop"]
+    cols2 = ["chr", "cluster_start", "cluster_end"]
+    df1 = pd.DataFrame([["chr1", 3, 8]], columns=cols1)
+    df2 = pd.DataFrame([["chr1", 3, 8]], columns=cols2)
+    d = """chromosome    begin   stop coverage
+         0  chr1     3       8     5"""
+    df = pd.read_csv(StringIO(d), sep=r"\s+")
+    pd.testing.assert_frame_equal(
+        df,
+        bioframe.coverage(df1, df2, cols1=cols1, cols2=cols2)
+    )
+
     ### coverage of NA interval returns zero for coverage
     df1 = pd.DataFrame(
         [