From f07aef19cc0722e7ac17e76cb73b63a732fe4bb7 Mon Sep 17 00:00:00 2001 From: Nick Croucher Date: Tue, 23 Apr 2024 11:58:17 +0100 Subject: [PATCH] Update gubbins arguments --- src/main.c | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/src/main.c b/src/main.c index fd184037..421b1a25 100644 --- a/src/main.c +++ b/src/main.c @@ -32,7 +32,7 @@ const char* program_name; // Assumptions: // The sequences in the multi fasta alignment file are the same length -// Your only interested in SNPs, INDELS are ignored +// You are only interested in SNPs, INDELS are ignored // The first sequence is chosen as the reference sequence // If there is an indel in the reference sequence, the first normal base found in another strain is used. @@ -46,9 +46,10 @@ void print_usage(FILE* stream, int exit_code) " -t Newick tree file\n" " -v VCF file\n" " -f Original Multifasta file\n" + " -n Number of threads to use for recombination detection\n" " -m Min SNPs for identifying a recombination block\n" - " -a Min window size\n" - " -b Max window size\n" + " -a Min window size\n" + " -b Max window size\n" " -p p value for detecting recombinations\n" " -i p value ratio for trimming recombinations\n" " -h Display this usage information.\n\n" @@ -110,7 +111,7 @@ int main (int argc, char ** argv) }; /* getopt_long stores the option index here. */ int option_index = 0; - c = getopt_long (argc, argv, "hrxv:f:t:m:a:b:p:i:", + c = getopt_long (argc, argv, "hrxv:f:t:m:a:b:p:i:n:", long_options, &option_index); /* Detect the end of the options. */ if (c == -1)