Support empty sample subset semantics

tests/test_bcftools_validation.py

@@ -56,6 +56,7 @@ def run_vcztools(args: str) -> str:
         ("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")
     ]
 )
 # fmt: on

tests/test_query.py

@@ -82,8 +82,8 @@ def root(self):
                 "19:111\n19:112\n20:14370\n20:17330\n20:1110696\n20:1230237\n20:1234567\n20:1235237\nX:10\n",
             ),
             (r"%INFO/DP\n", ".\n.\n14\n11\n10\n13\n9\n.\n.\n"),
-            (r"%AC\n", ".\n.\n.\n.\n.\n.\n3,1\n.\n.\n"),
-            (r"%AC{0}\n", ".\n.\n.\n.\n.\n.\n3\n.\n.\n"),
+            (r"%AC\n", ".\n.\n.\n.\n.\n.\n1,1\n.\n.\n"),
+            (r"%AC{0}\n", ".\n.\n.\n.\n.\n.\n1\n.\n.\n"),
         ],
     )
     def test(self, root, query_format, expected_result):

vcztools/cli.py

@@ -85,6 +85,9 @@ def query(path, list_samples, format):
     default=None,
     help="Regions to include.",
 )
+@click.option(
+    "--force-samples", is_flag=True, help="Only warn about unknown sample subsets."
+)
 @click.option(
     "-s",
     "--samples",
@@ -120,6 +123,7 @@ def view(
     no_version,
     regions,
     targets,
+    force_samples,
     samples,
     drop_genotypes,
     include,

vcztools/vcf_writer.py

@@ -153,6 +153,8 @@ def write_vcf(
         else:
             all_samples = root["sample_id"][:]
             sample_ids = np.array(samples.split(","))
+            if np.all(sample_ids == np.array("")):
+                sample_ids = np.empty((0,))
             samples_selection = search(all_samples, sample_ids)
 
         if not no_header and vcf_header is None:
@@ -347,6 +349,7 @@ def c_chunk_to_vcf(
         else:
             gt = get_vchunk_array(array, v_chunk, v_mask_chunk)
 
+        # Recompute INFO/AC and INFO/AN
         if samples_selection is not None:
             flatter_gt = gt.reshape((gt.shape[0], gt.shape[1] * gt.shape[2]))
 
@@ -363,7 +366,10 @@ def filter_and_bincount(values: np.ndarray):
             computed_AN = np.count_nonzero(computed_AN + 1, axis=1).astype(np.int8)
             info_fields["AC"] = computed_AC
             info_fields["AN"] = computed_AN
-        if "call_genotype_phased" in root and not drop_genotypes:
+
+        if num_samples == 0:
+            gt = None
+        if "call_genotype_phased" in root and not drop_genotypes and num_samples > 0:
             array = root["call_genotype_phased"]
             gt_phased = get_vchunk_array(
                 array, v_chunk, v_mask_chunk, samples_selection
@@ -397,13 +403,13 @@ def filter_and_bincount(values: np.ndarray):
             array = array.reshape((num_variants, 1))
         encoder.add_info_field(name, array)
 
-    for name, array in format_fields.items():
-        assert num_samples > 0
-        if array.dtype.kind in ("O", "U"):
-            array = array.astype("S")
-        if len(array.shape) == 2:
-            array = array.reshape((num_variants, num_samples, 1))
-        encoder.add_format_field(name, array)
+    if num_samples != 0:
+        for name, array in format_fields.items():
+            if array.dtype.kind in ("O", "U"):
+                array = array.astype("S")
+            if len(array.shape) == 2:
+                array = array.reshape((num_variants, num_samples, 1))
+            encoder.add_format_field(name, array)
     # TODO: (1) make a guess at this based on number of fields and samples,
     # and (2) log a DEBUG message when we have to double.
     buflen = 1024