From 5c35542ab9e03e0b4c0ee66f2529655addf32ae4 Mon Sep 17 00:00:00 2001
From: Ivan Blagoev Topolsky <ivan.topolsky@sib.swiss>
Date: Wed, 27 Nov 2024 12:02:36 +0100
Subject: [PATCH] end-to-end test the new features

- tabmut: --add-mutations
- coocmutbamscan: --fix-subsets
---
 tests/test_integration.py | 24 +++++++++++++++++++++++-
 1 file changed, 23 insertions(+), 1 deletion(-)

diff --git a/tests/test_integration.py b/tests/test_integration.py
index ca0c77a..1edc22f 100644
--- a/tests/test_integration.py
+++ b/tests/test_integration.py
@@ -94,6 +94,19 @@ def test_workflow():
             "amplicons.v3.yaml",
         ]
     )
+    subprocess.check_call(
+        [
+            "cojac",
+            "cooc-mutbamscan",
+            "-b",
+            "nCoV-2019.insert.V3.bed",
+            "-m",
+            "voc/",
+            "--fs",
+            "-A",
+            "amplicons.v3.fixedsub.yaml",
+        ]
+    )
     subprocess.check_call(
         [
             "cojac",
@@ -141,7 +154,16 @@ def test_workflow():
         ]
     )
     subprocess.check_call(
-        ["cojac", "cooc-tabmut", "-j", "cooc-test.json", "-o", "cooc-export.csv"]
+        [
+            "cojac",
+            "cooc-tabmut",
+            "-j",
+            "cooc-test.json",
+            "--am",
+            "amplicons.v3.yaml",
+            "-o",
+            "cooc-export.csv",
+        ]
     )
 
     # primers affected by mutations