From aab713ccf6962ba511006be9043c77f1b3d7f697 Mon Sep 17 00:00:00 2001 From: Trevor Bedford Date: Tue, 11 Feb 2020 21:34:31 -0800 Subject: [PATCH] Default to --infer-ambiguous This keeps default augur behavior unchanged despite the TreeTime upgrade. By adding the --keep-ambiguous flag, new behavior can be requested. This seemed safer in terms of not causing unexpected behavior for users. --- augur/ancestral.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/augur/ancestral.py b/augur/ancestral.py index c5fa0856c..ddc80c626 100644 --- a/augur/ancestral.py +++ b/augur/ancestral.py @@ -106,9 +106,9 @@ def register_arguments(parser): parser.add_argument('--vcf-reference', type=str, help='fasta file of the sequence the VCF was mapped to') parser.add_argument('--output-vcf', type=str, help='name of output VCF file which will include ancestral seqs') ambiguous = parser.add_mutually_exclusive_group() - ambiguous.add_argument('--keep-ambiguous', action="store_false", dest='infer-ambiguous', + ambiguous.add_argument('--keep-ambiguous', action="store_false", default=False, dest='infer-ambiguous', help='do not infer nucleotides at ambiguous (N) sites on tip sequences (leave as N).') - ambiguous.add_argument('--infer-ambiguous', action="store_true", default=False, + ambiguous.add_argument('--infer-ambiguous', action="store_true", help='infer nucleotides at ambiguous (N,W,R,..) sites on tip sequences and replace with most likely state.') parser.add_argument('--keep-overhangs', action="store_true", default=False, help='do not infer nucleotides for gaps (-) on either side of the alignment')