From f12db4c2f4962d99c5afa2660c1b6284c8a58db2 Mon Sep 17 00:00:00 2001 From: aineniamh Date: Wed, 5 May 2021 12:51:17 +0100 Subject: [PATCH] updating default min length to 25K bases --- pangolin/command.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pangolin/command.py b/pangolin/command.py index c5b9596..557a08a 100644 --- a/pangolin/command.py +++ b/pangolin/command.py @@ -49,7 +49,7 @@ def main(sysargs = sys.argv[1:]): parser.add_argument("--no-temp",action="store_true",help="Output all intermediate files, for dev purposes.") parser.add_argument('--decompress-model',action="store_true",dest="decompress",help="Permanently decompress the model file to save time running pangolin.") parser.add_argument('--max-ambig', action="store", default=0.5, type=float,help="Maximum proportion of Ns allowed for pangolin to attempt assignment. Default: 0.5",dest="maxambig") - parser.add_argument('--min-length', action="store", default=10000, type=int,help="Minimum query length allowed for pangolin to attempt assignment. Default: 10000",dest="minlen") + parser.add_argument('--min-length', action="store", default=25000, type=int,help="Minimum query length allowed for pangolin to attempt assignment. Default: 25000",dest="minlen") parser.add_argument('--panGUIlin', action='store_true',help="Run web-app version of pangolin",dest="panGUIlin") parser.add_argument("--verbose",action="store_true",help="Print lots of stuff to screen") parser.add_argument("-t","--threads",action="store",help="Number of threads")