rebase

vcztools/cli.py

@@ -77,6 +77,13 @@ def query(path, list_samples):
     default=None,
     help="Samples to include.",
 )
+@click.option(
+    "-G",
+    "--drop_genotypes",
+    type=bool,
+    is_flag=True,
+    help="Drop genotypes.",
+)
 @click.option(
     "-t",
     "--targets",
@@ -98,6 +105,7 @@ def view(
     regions,
     targets,
     samples,
+    drop_genotypes,
     include,
     exclude,
 ):
@@ -109,6 +117,7 @@ def view(
         variant_regions=regions,
         variant_targets=targets,
         samples=samples,
+        drop_genotypes=drop_genotypes,
         include=include,
         exclude=exclude,
     )

vcztools/vcf_writer.py

@@ -86,6 +86,7 @@ def write_vcf(
     variant_regions=None,
     variant_targets=None,
     samples=None,
+    drop_genotypes: bool = False,
     include: Optional[str] = None,
     exclude: Optional[str] = None,
 ) -> None:
@@ -139,7 +140,14 @@ def write_vcf(
     root = zarr.open(vcz, mode="r")
 
     with open_file_like(output) as output:
-        if samples is None:
+        if samples and drop_genotypes:
+            raise ValueError(
+                "Cannot select samples and drop genotypes."
+            )
+        elif drop_genotypes:
+            sample_ids = []
+            samples_selection = np.array([])
+        elif samples is None:
             sample_ids = root["sample_id"][:]
             samples_selection = None
         else:
@@ -302,19 +310,20 @@ def c_chunk_to_vcf(
     num_samples = len(samples_selection) if samples_selection is not None else None
     for name, array in root.items():
         if name.startswith("call_") and not name.startswith("call_genotype"):
-            vcf_name = name[len("call_") :]
-            format_fields[vcf_name] = get_vchunk_array(
-                array, v_chunk, v_mask_chunk, samples_selection
-            )
-            if num_samples is None:
-                num_samples = array.shape[1]
+            if num_samples != 0:
+                vcf_name = name[len("call_") :]
+                format_fields[vcf_name] = get_vchunk_array(
+                    array, v_chunk, v_mask_chunk, samples_selection
+                )
+                if num_samples is None:
+                    num_samples = array.shape[1]
         elif name.startswith("variant_") and name not in RESERVED_VARIABLE_NAMES:
             vcf_name = name[len("variant_") :]
             info_fields[vcf_name] = get_vchunk_array(array, v_chunk, v_mask_chunk)
 
     gt = None
     gt_phased = None
-    if "call_genotype" in root:
+    if "call_genotype" in root and num_samples != 0:
         array = root["call_genotype"]
         gt = get_vchunk_array(array, v_chunk, v_mask_chunk, samples_selection)
         if "call_genotype_phased" in root:
@@ -352,7 +361,7 @@ def c_chunk_to_vcf(
         encoder.add_info_field(name, array)
 
     for name, array in format_fields.items():
-        assert num_samples > 0
+        #assert num_samples > 0
         if array.dtype.kind in ("O", "U"):
             array = array.astype("S")
         if len(array.shape) == 2: