fix according to test

Clinical-Genomics · Jul 1, 2024 · 258a106 · 258a106
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commit 258a106
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/.github/workflows/tests_and_cov.yml b/.github/workflows/tests_and_cov.yml
@@ -48,7 +48,7 @@ jobs:
           key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}
 
       - name: Install pytest
-        run: pip install pytest
+        run: pip install pytest pytest-cov
 
       - name: Run pytest
         run: pytest --cov --rootdir=/home/runner/work/stranger

diff --git a/stranger/cli.py b/stranger/cli.py
@@ -189,9 +189,10 @@ def cli(context, vcf, family_id, repeats_file, loglevel, trgt):
             if len(variant_info["alts"]) > 1:
                 variant_infos = decompose_var(variant_info)
 
-        for variant_info in variant_infos:
-            update_decomposed_variant_format_fields(variant_info, header_info, individual_index)
+            for variant_info in variant_infos:
+                update_decomposed_variant_format_fields(variant_info, header_info, individual_index)
 
+        for variant_info in variant_infos:
             repeat_data = get_repeat_info(variant_info, repeat_information)
 
             if repeat_data: