From a0c131bb119ade97eb0946988222f9d15aff2015 Mon Sep 17 00:00:00 2001
From: willtyler <will.tyler11@gmail.com>
Date: Tue, 3 Sep 2024 16:25:47 +0000
Subject: [PATCH] Add samples file option to view CLI

---
 tests/data/txt/samples.txt        |  2 ++
 tests/test_bcftools_validation.py |  5 +++++
 vcztools/cli.py                   | 22 ++++++++++++++++++++++
 3 files changed, 29 insertions(+)
 create mode 100644 tests/data/txt/samples.txt

diff --git a/tests/data/txt/samples.txt b/tests/data/txt/samples.txt
new file mode 100644
index 0000000..7e4784c
--- /dev/null
+++ b/tests/data/txt/samples.txt
@@ -0,0 +1,2 @@
+NA00001
+NA00003
diff --git a/tests/test_bcftools_validation.py b/tests/test_bcftools_validation.py
index 9d79763..757d40f 100644
--- a/tests/test_bcftools_validation.py
+++ b/tests/test_bcftools_validation.py
@@ -53,6 +53,11 @@ def run_vcztools(args: str) -> str:
                 "view --no-version -G",
                 "sample.vcf.gz"
         ),
+        (
+                "view --no-update --no-version --samples-file "
+                "tests/data/txt/samples.txt",
+                "sample.vcf.gz"),
+        ("view -I --no-version -S tests/data/txt/samples.txt", "sample.vcf.gz"),
     ]
 )
 # fmt: on
diff --git a/vcztools/cli.py b/vcztools/cli.py
index fe82bf1..3f61dcb 100644
--- a/vcztools/cli.py
+++ b/vcztools/cli.py
@@ -85,6 +85,12 @@ def query(path, list_samples, format):
     default=None,
     help="Regions to include.",
 )
+@click.option(
+    "-I",
+    "--no-update",
+    is_flag=True,
+    help="Do not recalculate INFO fields for the sample subset.",
+)
 @click.option(
     "-s",
     "--samples",
@@ -92,6 +98,13 @@ def query(path, list_samples, format):
     default=None,
     help="Samples to include.",
 )
+@click.option(
+    "-S",
+    "--samples-file",
+    type=str,
+    default=None,
+    help="File of sample names to include.",
+)
 @click.option(
     "-G",
     "--drop-genotypes",
@@ -120,7 +133,9 @@ def view(
     no_version,
     regions,
     targets,
+    no_update,
     samples,
+    samples_file,
     drop_genotypes,
     include,
     exclude,
@@ -129,6 +144,13 @@ def view(
         split = output.split(".")
         raise ValueError(f"Output file extension must be .vcf, got: .{split[-1]}")
 
+    if samples_file:
+        with open(samples_file) as file:
+            samples = samples or ""
+            samples += ",".join(line.strip() for line in file.readlines())
+
+    # TODO: use no_update when fixing https://github.com/sgkit-dev/vcztools/issues/75
+
     vcf_writer.write_vcf(
         path,
         output,