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 = {}