Merge pull request #71 from Clinical-Genomics/add_test_for_trgt_dot_mcs

Add test for when TRGT `FORMAT.MC` is `.`

CHANGELOG.md

@@ -5,7 +5,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 ## [unreleased]
 ### Fixed
 - Use codecov badge and fix scout link on README page
-
+- Added a test for TRGT MCs set to `.`
 
 ## [0.9.1]
 ### Added

stranger/cli.py

@@ -19,7 +19,6 @@
     parse_repeat_file,
     update_decomposed_variant_format_fields,
 )
-from stranger.vcf_utils import print_headers
 
 LOG = logging.getLogger(__name__)
 LOG_LEVELS = ["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]

tests/cli/test_cli.py

@@ -19,3 +19,9 @@ def test_stranger_cli_zipped(vcf_zipped_path):
     runner = CliRunner()
     result = runner.invoke(cli, [vcf_zipped_path])
     assert result.exit_code == 0
+
+
+def test_stranger_trgt_dot_mc(vcf_trgt_path_dot_mc):
+    runner = CliRunner()
+    result = runner.invoke(cli, ["--trgt", vcf_trgt_path_dot_mc])
+    assert result.exit_code == 0

tests/conftest.py

@@ -1,5 +1,3 @@
-import os
-
 import pytest
 
 from stranger.resources import repeats_path
@@ -15,6 +13,11 @@ def vcf_zipped_path():
     return "tests/fixtures/643594.clinical.str.vcf.gz"
 
 
+@pytest.fixture()
+def vcf_trgt_path_dot_mc():
+    return "tests/fixtures/HG002_Revio.sort.vcf.gz"
+
+
 @pytest.fixture()
 def repeats_file_handle():
     return open(repeats_path, "r")

tests/test_utils.py

@@ -1,6 +1,6 @@
 import pytest
 
-from stranger.utils import get_repeat_info, parse_repeat_file
+from stranger.utils import parse_repeat_file
 
 
 def test_parse_repeat_file(repeats_file_handle):