Update

tests/parsers/test_score_parser.py

@@ -103,7 +103,7 @@ def test_add_score_parser_with_invalid_src():
     add_score_parser(subparsers)  # Add the `score` subcommand to the parser
 
     # Simulate command-line input
-    args = parser.parse_args(
+    args1 = parser.parse_args(
         [
             "score",
             "--vcf",
@@ -143,6 +143,48 @@ def test_add_score_parser_with_invalid_src():
         ]
     )
 
+    args2 = parser.parse_args(
+        [
+            "score",
+            "--vcf",
+            "tests/data/example.vcf",
+            "--chr-name",
+            "chr1",
+            "--ref",
+            "tests/data/example.ref.ind.list",
+            "--tgt",
+            "tests/data/example.tgt.ind.list",
+            "--src",
+            "tests/data/example.src.ind.list",
+            "--win-len",
+            "50000",
+            "--win-step",
+            "10000",
+            "--num-src",
+            "2",  # Expecting 2 populations
+            "--anc-alleles",
+            "tests/data/test.anc.allele.bed",
+            "--ploidy",
+            "2",
+            "--phased",
+            "--w",
+            "0.3",
+            "--x",
+            "0.5",
+            "--y",
+            "0.1",
+            "--output",
+            "output/results.tsv",
+            "--q",
+            "0.95",
+            "--workers",
+            "4",
+        ]
+    )
+
     # Trigger _run_score to validate the arguments and raise ValueError
     with pytest.raises(ValueError, match=r"The number of populations in the file .* does not match .*"):
-        _run_score(args)
+        _run_score(args1)
+
+    with pytest.raises(ValueError, match=r"The length of y .* does not match .*"):
+        _run_score(args2)