Remove sample subsetting temporarily.

It has a number of problems and better not to try and fix them in a hurry pre shipping. See sgkit-dev#121 and sgkit-dev#122
jeromekelleher · Jan 14, 2025 · cb846c0 · cb846c0
1 parent 229cc29
commit cb846c0
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Showing 3 changed files with 65 additions and 59 deletions.
diff --git a/tests/test_bcftools_validation.py b/tests/test_bcftools_validation.py
@@ -54,19 +54,21 @@ def run_vcztools(args: str) -> str:
                 "view --no-version -G",
                 "sample.vcf.gz"
         ),
-        (
-                "view --no-update --no-version --samples-file "
-                "tests/data/txt/samples.txt",
-                "sample.vcf.gz"),
-        ("view -I --no-version -S tests/data/txt/samples.txt", "sample.vcf.gz"),
-        ("view --no-version -s NA00001", "sample.vcf.gz"),
-        ("view --no-version -s NA00001,NA00003", "sample.vcf.gz"),
-        ("view --no-version -s HG00096", "1kg_2020_chrM.vcf.gz"),
-        ("view --no-version -s '' --force-samples", "sample.vcf.gz"),
-        ("view --no-version -s ^NA00001", "sample.vcf.gz"),
-        ("view --no-version -s ^NA00003,NA00002", "sample.vcf.gz"),
-        ("view --no-version -s ^NA00003,NA00002,NA00003", "sample.vcf.gz"),
-        ("view --no-version -S ^tests/data/txt/samples.txt", "sample.vcf.gz"),
+        # Temporarily removing until sample handling fixed:
+        # https://github.com/sgkit-dev/vcztools/issues/121
+        # (
+        #         "view --no-update --no-version --samples-file "
+        #         "tests/data/txt/samples.txt",
+        #         "sample.vcf.gz"),
+        # ("view -I --no-version -S tests/data/txt/samples.txt", "sample.vcf.gz"),
+        # ("view --no-version -s NA00001", "sample.vcf.gz"),
+        # ("view --no-version -s NA00001,NA00003", "sample.vcf.gz"),
+        # ("view --no-version -s HG00096", "1kg_2020_chrM.vcf.gz"),
+        # ("view --no-version -s '' --force-samples", "sample.vcf.gz"),
+        # ("view --no-version -s ^NA00001", "sample.vcf.gz"),
+        # ("view --no-version -s ^NA00003,NA00002", "sample.vcf.gz"),
+        # ("view --no-version -s ^NA00003,NA00002,NA00003", "sample.vcf.gz"),
+        # ("view --no-version -S ^tests/data/txt/samples.txt", "sample.vcf.gz"),
     ]
 )
 # fmt: on

diff --git a/tests/test_cli.py b/tests/test_cli.py
@@ -76,14 +76,16 @@ def test_view_write_pipe(self, tmp_path, vcz_path):
         assert "Is a directory" in result.stderr
 
 
-def test_excluding_and_including_samples(vcz_path):
-    samples_file_path = pathlib.Path("tests/data/txt/samples.txt")
-    error_message = re.escape("vcztools does not support combining -s and -S")
-
-    with pytest.raises(AssertionError, match=error_message):
-        run_vcztools(f"view {vcz_path} -s NA00001 -S ^{samples_file_path}")
-    with pytest.raises(AssertionError, match=error_message):
-        run_vcztools(f"view {vcz_path} -s ^NA00001 -S {samples_file_path}")
+# Removing until we reimplement sample handling:
+# https://github.com/sgkit-dev/vcztools/issues/121
+# def test_excluding_and_including_samples(vcz_path):
+#     samples_file_path = pathlib.Path("tests/data/txt/samples.txt")
+#     error_message = re.escape("vcztools does not support combining -s and -S")
+
+#     with pytest.raises(AssertionError, match=error_message):
+#         run_vcztools(f"view {vcz_path} -s NA00001 -S ^{samples_file_path}")
+#     with pytest.raises(AssertionError, match=error_message):
+#         run_vcztools(f"view {vcz_path} -s ^NA00001 -S {samples_file_path}")
 
 
 @mock.patch("sys.exit")

diff --git a/vcztools/cli.py b/vcztools/cli.py
@@ -138,29 +138,29 @@ def query(path, output, list_samples, format, include, exclude):
     default=None,
     help="Regions to include.",
 )
-@click.option(
-    "--force-samples", is_flag=True, help="Only warn about unknown sample subsets."
-)
-@click.option(
-    "-I",
-    "--no-update",
-    is_flag=True,
-    help="Do not recalculate INFO fields for the sample subset.",
-)
-@click.option(
-    "-s",
-    "--samples",
-    type=str,
-    default=None,
-    help="Samples to include.",
-)
-@click.option(
-    "-S",
-    "--samples-file",
-    type=str,
-    default=None,
-    help="File of sample names to include.",
-)
+# @click.option(
+#     "--force-samples", is_flag=True, help="Only warn about unknown sample subsets."
+# )
+# @click.option(
+#     "-I",
+#     "--no-update",
+#     is_flag=True,
+#     help="Do not recalculate INFO fields for the sample subset.",
+# )
+# @click.option(
+#     "-s",
+#     "--samples",
+#     type=str,
+#     default=None,
+#     help="Samples to include.",
+# )
+# @click.option(
+#     "-S",
+#     "--samples-file",
+#     type=str,
+#     default=None,
+#     help="File of sample names to include.",
+# )
 @click.option(
     "-G",
     "--drop-genotypes",
@@ -185,10 +185,10 @@ def view(
     no_version,
     regions,
     targets,
-    force_samples,
-    no_update,
-    samples,
-    samples_file,
+    # force_samples,
+    # no_update,
+    # samples,
+    # samples_file,
     drop_genotypes,
     include,
     exclude,
@@ -201,17 +201,19 @@ def view(
             f"Only uncompressed VCF output supported, suffix .{suffix} not allowed"
         )
 
-    if samples_file:
-        assert not samples, "vcztools does not support combining -s and -S"
+    # Dropping implementation here until it's reimplemented after initial release:
+    # https://github.com/sgkit-dev/vcztools/issues/121
+    # if samples_file:
+    #     assert not samples, "vcztools does not support combining -s and -S"
 
-        samples = ""
-        exclude_samples_file = samples_file.startswith("^")
-        samples_file = samples_file.lstrip("^")
+    #     samples = ""
+    #     exclude_samples_file = samples_file.startswith("^")
+    #     samples_file = samples_file.lstrip("^")
 
-        with open(samples_file) as file:
-            if exclude_samples_file:
-                samples = "^" + samples
-            samples += ",".join(line.strip() for line in file.readlines())
+    #     with open(samples_file) as file:
+    #         if exclude_samples_file:
+    #             samples = "^" + samples
+    #         samples += ",".join(line.strip() for line in file.readlines())
 
     with handle_broken_pipe(output):
         vcf_writer.write_vcf(
@@ -222,8 +224,8 @@ def view(
             no_version=no_version,
             variant_regions=regions,
             variant_targets=targets,
-            no_update=no_update,
-            samples=samples,
+            # no_update=no_update,
+            # samples=samples,
             drop_genotypes=drop_genotypes,
             include=include,
             exclude=exclude,