From f09c3067eb5dd9fea6f764ecfef65aed58665e8f Mon Sep 17 00:00:00 2001 From: gkarthik Date: Wed, 2 Sep 2020 11:38:21 -0700 Subject: [PATCH] Added input option to prompt --- src/ivar.cpp | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/ivar.cpp b/src/ivar.cpp index 6b4034fa..58ac524b 100644 --- a/src/ivar.cpp +++ b/src/ivar.cpp @@ -117,7 +117,8 @@ void print_consensus_usage(){ " -k If '-k' flag is added, regions with depth less than minimum depth will not be added to the consensus sequence. Using '-k' will override any option specified using -n \n" " -n (N/-) Character to print in regions with less than minimum coverage(Default: N)\n\n" "Output Options Description\n" - " -p (Required) Prefix for the output fasta file and quality file\n"; + " -p (Required) Prefix for the output fasta file and quality file\n" + " -i (Optional) Name of fasta header. By default, the prefix is used to create the fasta header in the following format, Consensus__threshold__quality_\n"; } void print_removereads_usage(){ @@ -326,8 +327,8 @@ int main(int argc, char* argv[]){ g_args.min_threshold = atof(optarg); break; case 'i': - g_args.seq_id = optarg; - break; + g_args.seq_id = optarg; + break; case 'p': g_args.prefix = optarg; break;