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Add output option to vcztools view #66

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merged 2 commits into from
Aug 30, 2024
Merged

Add output option to vcztools view #66

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22166f5
Add output option to vcztools view
Will-Tyler Aug 26, 2024
db67740
Change CLI test to validation test
Will-Tyler Aug 29, 2024
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14 changes: 14 additions & 0 deletions tests/test_cli.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
import os.path
import pathlib

from tests.test_bcftools_validation import run_vcztools
from tests.utils import vcz_path_cache


def test_view_output(tmp_path):
vcf_path = pathlib.Path("tests/data/vcf/sample.vcf.gz")
vcz_path = vcz_path_cache(vcf_path)
output = tmp_path / "output.vcf"

run_vcztools(f"view {vcz_path} --output {output}")
assert os.path.exists(output)
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Can you call assert_vcfs_close to check the output is correct?

Also, perhaps this should belong in test_bcftools_validation as you are using run_vcztools from there anyway?

6 changes: 5 additions & 1 deletion vcztools/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,9 @@ def query(path, list_samples):

@click.command
@click.argument("path", type=click.Path())
@click.option(
"-o", "--output", type=str, default=None, help="File path to write output to."
)
@click.option(
"-h",
"--header-only",
Expand Down Expand Up @@ -92,6 +95,7 @@ def query(path, list_samples):
)
def view(
path,
output,
header_only,
no_header,
no_version,
Expand All @@ -103,7 +107,7 @@ def view(
):
vcf_writer.write_vcf(
path,
sys.stdout,
output,
header_only=header_only,
no_header=no_header,
variant_regions=regions,
Expand Down