From 62dc32da291665f2b0470a381936cc253d198fc6 Mon Sep 17 00:00:00 2001 From: ViralVerity Date: Tue, 24 Sep 2024 12:56:23 -0400 Subject: [PATCH] fix in summary script for single reference run --- denv_pipeline/scripts/make_summary_files.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/denv_pipeline/scripts/make_summary_files.py b/denv_pipeline/scripts/make_summary_files.py index 493f924..6d3b09b 100644 --- a/denv_pipeline/scripts/make_summary_files.py +++ b/denv_pipeline/scripts/make_summary_files.py @@ -203,7 +203,7 @@ def pull_low_coverage_seqs(config, all_coverage, high_coverage): lst.append(cov) in_order = sorted(lst, reverse=True) - if len(in_order) > 1: #I'm not sure when it would ever be less than 6, but leaving for now just in case + if len(in_order) > 1: if in_order[0] > (in_order[1] + 5): top = [i for i in cov_dict if cov_dict[i]==in_order[0]][0] else: @@ -219,7 +219,7 @@ def pull_low_coverage_seqs(config, all_coverage, high_coverage): top = "NA" elif len(in_order) == 1: - top = in_order[0] + top = [i for i in cov_dict if cov_dict[i]==in_order[0]][0] else: top = "NA"