From 552a04ffaca0c2abc83fca0312b9fb55cf2096fa Mon Sep 17 00:00:00 2001
From: Jody Phelan <jody.phelan@lshtm.ac.uk>
Date: Wed, 27 Nov 2024 17:57:29 +0000
Subject: [PATCH] bugfix

---
 pathogenprofiler/barcode.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/pathogenprofiler/barcode.py b/pathogenprofiler/barcode.py
index aa5e388..239a29d 100644
--- a/pathogenprofiler/barcode.py
+++ b/pathogenprofiler/barcode.py
@@ -58,6 +58,8 @@ def get_barcoding_mutations(mutations: dict, barcode_bed: str) -> tuple[dict, Li
 
 
 def barcode(mutations,barcode_bed: str,snps_file=None,stdev_cutoff=0.15) -> List[BarcodeResult]:
+    if stdev_cutoff is None:
+        stdev_cutoff = 0.15
     bed_num_col = len(open(barcode_bed).readline().rstrip().split("\t"))
     # bed = []
     lineage_info = {}