Add explanation for max search depth

bacpop · Nov 6, 2024 · 6d32dcc · 6d32dcc
1 parent e8f28d6
commit 6d32dcc
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/PopPUNK/models.py b/PopPUNK/models.py
@@ -1124,7 +1124,9 @@ def __init__(self, outPrefix, ranks, max_search_depth, reciprocal_only, count_un
         ClusterFit.__init__(self, outPrefix)
         self.type = 'lineage'
         self.preprocess = False
-        self.max_search_depth = max_search_depth+5
+        self.max_search_depth = max_search_depth+5 # Set to highest rank by default in main; need to store additional distances
+                                                   # when there is redundancy (e.g. reciprocal matching, unique distance counting)
+                                                   # or other sequences may be pruned out of the database
         self.nn_dists = None # stores the unprocessed kNN at the maximum search depth
         self.ranks = []
         for rank in sorted(ranks):