From 22166f5328a566043f6bc67f3ee8767a093ad63f Mon Sep 17 00:00:00 2001
From: willtyler <will.tyler11@gmail.com>
Date: Mon, 26 Aug 2024 23:42:22 +0000
Subject: [PATCH 1/2] Add output option to vcztools view

---
 tests/test_cli.py | 14 ++++++++++++++
 vcztools/cli.py   |  6 +++++-
 2 files changed, 19 insertions(+), 1 deletion(-)
 create mode 100644 tests/test_cli.py

diff --git a/tests/test_cli.py b/tests/test_cli.py
new file mode 100644
index 0000000..a11aa0e
--- /dev/null
+++ b/tests/test_cli.py
@@ -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)
diff --git a/vcztools/cli.py b/vcztools/cli.py
index 873880a..de32c83 100644
--- a/vcztools/cli.py
+++ b/vcztools/cli.py
@@ -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",
@@ -92,6 +95,7 @@ def query(path, list_samples):
 )
 def view(
     path,
+    output,
     header_only,
     no_header,
     no_version,
@@ -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,

From db67740823afa7090e38f735a9bde58d949a8545 Mon Sep 17 00:00:00 2001
From: willtyler <will.tyler11@gmail.com>
Date: Thu, 29 Aug 2024 17:40:29 +0000
Subject: [PATCH 2/2] Change CLI test to validation test

---
 tests/test_bcftools_validation.py | 21 +++++++++++++++++++++
 tests/test_cli.py                 | 14 --------------
 2 files changed, 21 insertions(+), 14 deletions(-)
 delete mode 100644 tests/test_cli.py

diff --git a/tests/test_bcftools_validation.py b/tests/test_bcftools_validation.py
index 3a5cb88..65cf775 100644
--- a/tests/test_bcftools_validation.py
+++ b/tests/test_bcftools_validation.py
@@ -68,6 +68,27 @@ def test_vcf_output(tmp_path, args, vcf_file):
 
     assert_vcfs_close(bcftools_out_file, vcztools_out_file)
 
+@pytest.mark.parametrize(
+    ("args", "vcf_file"),
+    [
+        ("view --no-version", "sample.vcf.gz")
+    ],
+)
+def test_vcf_output_with_output_option(tmp_path, args, vcf_file):
+    vcf_path = pathlib.Path("tests/data/vcf") / vcf_file
+    vcz_path = vcz_path_cache(vcf_path)
+
+    bcftools_out_file = tmp_path.joinpath("bcftools_out.vcf")
+    vcztools_out_file = tmp_path.joinpath("vcztools_out.vcf")
+
+    bcftools_args = f"{args} -o {bcftools_out_file}"
+    vcztools_args = f"{args} -o {vcztools_out_file}"
+
+    run_bcftools(f"{bcftools_args} {vcf_path}")
+    run_vcztools(f"{vcztools_args} {vcz_path}")
+
+    assert_vcfs_close(bcftools_out_file, vcztools_out_file)
+
 
 @pytest.mark.parametrize(
     ("args", "vcf_name"),
diff --git a/tests/test_cli.py b/tests/test_cli.py
deleted file mode 100644
index a11aa0e..0000000
--- a/tests/test_cli.py
+++ /dev/null
@@ -1,14 +0,0 @@
-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)