From ce0834c476abc9ee99785fa930608218b7d78990 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 18 Nov 2021 22:49:07 +0100 Subject: [PATCH] doc(tree.py): make explicit in help string that exclude sites are second column in tsv --- augur/tree.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/augur/tree.py b/augur/tree.py index f4f50dca1..062284e12 100644 --- a/augur/tree.py +++ b/augur/tree.py @@ -345,7 +345,7 @@ def register_arguments(parser): parser.add_argument('--nthreads', type=nthreads_value, default=1, help="number of threads to use; specifying the value 'auto' will cause the number of available CPU cores on your system, if determinable, to be used") parser.add_argument('--vcf-reference', type=str, help='fasta file of the sequence the VCF was mapped to') - parser.add_argument('--exclude-sites', type=str, help='file name of one-based sites to exclude for raw tree building (BED format in .bed files, DRM format in tab-delimited files, or one position per line)') + parser.add_argument('--exclude-sites', type=str, help='file name of one-based sites to exclude for raw tree building (BED format in .bed files, second column in tab-delimited files, or one position per line)') parser.add_argument('--tree-builder-args', type=str, default='', help='extra arguments to be passed directly to the executable of the requested tree method (e.g., --tree-builder-args="-czb")')