From 5d27787e3b15ae1e191771371b42404973c833ab Mon Sep 17 00:00:00 2001 From: rhysnewell Date: Wed, 13 Sep 2023 22:11:39 +0000 Subject: [PATCH] fix #143 removes checking for non-existent arguments when running in configure --- aviary/modules/processor.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/aviary/modules/processor.py b/aviary/modules/processor.py index 006713c9..17bf4fa5 100644 --- a/aviary/modules/processor.py +++ b/aviary/modules/processor.py @@ -151,10 +151,10 @@ def __init__(self, except AttributeError: self.reference_filter = 'none' self.gold_standard = 'none' - self.min_read_size = args.min_read_size - self.min_mean_q = args.min_mean_q - self.keep_percent = args.keep_percent - self.skip_qc = args.skip_qc + self.min_read_size = 0 + self.min_mean_q = 0 + self.keep_percent = 100 + self.skip_qc = False try: self.gsa_mappings = args.gsa_mappings