Rename plink command

Closes #157

Author: jeromekelleher

tests/test_plink_validation.py

@@ -44,7 +44,7 @@ def test_conversion_identical(tmp_path, args, vcf_file):
     result = subprocess.run(cmd, shell=True, cwd=plink_workdir, capture_output=True)
     assert result.returncode == 0
 
-    cmd = f"plink1.9-vcf {vcz.absolute()} {args}"
+    cmd = f"view-plink1 {vcz.absolute()} {args}"
     runner = ct.CliRunner(mix_stderr=False)
     with runner.isolated_filesystem(tmp_path) as working_dir:
         vcz_workdir = pathlib.Path(working_dir)

vcztools/cli.py

@@ -254,12 +254,15 @@ def view(
         )
 
 
-@click.command(name="plink1.9-vcf")
+@click.command
 @click.argument("path", type=click.Path())
 @click.option("--out", default="plink")
-def plink1_9_vcf(path, out):
+def view_plink1(path, out):
     """
-    Convert VCZ to plink, compatible with plink1.9 --vcf.
+    Generate a plink1 binary fileset compatible with plink1.9 --vcf.
+    This command is equivalent to running ``vcztools view [filtering options]
+    -o intermediate.vcf && plink 1.9 --vcf intermediate.vcf [plink options]``
+    without generating the intermediate VCF.
     """
     out_prefix = pathlib.Path(out)
     writer = plink.Writer(
@@ -279,4 +282,4 @@ def vcztools_main():
 vcztools_main.add_command(index)
 vcztools_main.add_command(query)
 vcztools_main.add_command(view)
-vcztools_main.add_command(plink1_9_vcf)
+vcztools_main.add_command(view_plink1)