handle recombinant assignments that dont pass both parents- dont acce…

…pt best constellation update if mrca lineage is an empty string
cov-lineages · Apr 14, 2022 · 9b6e2fc · 9b6e2fc
1 parent 2ae9e99
commit 9b6e2fc
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Showing 2 changed files with 8 additions and 7 deletions.
diff --git a/scorpio/__init__.py b/scorpio/__init__.py
@@ -1,2 +1,2 @@
 _program = "scorpio"
-__version__ = "0.3.16"
+__version__ = "0.3.17"
diff --git a/scorpio/scripts/type_constellations.py b/scorpio/scripts/type_constellations.py
@@ -1051,12 +1051,13 @@ def classify_constellations(in_fasta, list_constellation_files, constellation_na
                         or (counts['support'] == best_support and counts['conflict'] < best_conflict)\
                         or (counts['support'] == best_support and counts['conflict'] == best_conflict and counts['rules'] > best_counts["rules"])\
                         or (best_constellation in parents):
-                        best_constellation = constellation
-                        logging.debug("Set best constellation %s" %best_constellation)
-                        best_support = counts['support']
-                        best_conflict = counts['conflict']
-                        best_counts = counts
-                        best_call = call
+                        if mrca_lineage_dict[constellation]:
+                            best_constellation = constellation
+                            logging.debug("Set best constellation %s" %best_constellation)
+                            best_support = counts['support']
+                            best_conflict = counts['conflict']
+                            best_counts = counts
+                            best_call = call
 
                 if interspersion:
                     if counts["alt"] > 1: