Updated reporting of *13 tandem arrangements

Illumina · May 3, 2021 · 28b53f4 · 28b53f4
1 parent 0031eeb
commit 28b53f4
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Showing 2 changed files with 18 additions and 4 deletions.
diff --git a/caller/match_star_allele.py b/caller/match_star_allele.py
@@ -227,10 +227,14 @@ def get_final_call_clean(final_call, cnvcall, spacer_cn):
             return "*13/" + split_call[0]
         return None
     if cnvcall == "dup_star13intron1":
-        if split_call.count("*2") >= 2:
-            split_call.remove("*2")
-            split_call.remove("*2")
-            return "*13+*2/" + split_call[0]
+        unique_stars = list(set(split_call))
+        if len(unique_stars) == 2:
+            if split_call.count(unique_stars[0]) == 2:
+                return "*13+" + unique_stars[0] + "/" + unique_stars[1]
+            elif split_call.count(unique_stars[1]) == 2:
+                return "*13+" + unique_stars[1] + "/" + unique_stars[0]
+        elif len(unique_stars) == 1:
+            return "*13+" + unique_stars[0] + "/" + unique_stars[0]
         return None
     if cnvcall == "dup_star13":
         if spacer_cn is not None and spacer_cn == 1:

diff --git a/caller/tests/test_match_star.py b/caller/tests/test_match_star.py
@@ -130,6 +130,16 @@ def test_clean_call(self):
         clean_call = get_final_call_clean(final_call, cnvcall, spacer_cn)
         assert clean_call == "*13+*2/*1"
 
+        cnvcall = "dup_star13intron1"
+        final_call = ["*9_*4_*4"]
+        clean_call = get_final_call_clean(final_call, cnvcall, spacer_cn)
+        assert clean_call == "*13+*4/*9"
+
+        cnvcall = "dup_star13intron1"
+        final_call = ["*4_*4_*4"]
+        clean_call = get_final_call_clean(final_call, cnvcall, spacer_cn)
+        assert clean_call == "*13+*4/*4"
+
         cnvcall = "dup_star13"
         final_call = ["*1_*2"]
         spacer_cn = None