From ac0f55c3f6ca8acdfb3727ab6b2fc3dab398852d Mon Sep 17 00:00:00 2001 From: Jana Ebler Date: Tue, 22 Aug 2023 10:44:51 +0200 Subject: [PATCH] added a message in case PanGenie is run in the old way --- src/pangenie-genotype.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/pangenie-genotype.cpp b/src/pangenie-genotype.cpp index f595eb2..8d777e5 100644 --- a/src/pangenie-genotype.cpp +++ b/src/pangenie-genotype.cpp @@ -119,6 +119,8 @@ int main(int argc, char* argv[]) { kmersize = stoi(argument_parser.get_argument('k')); bool add_reference = true; + cerr << endl << "NOTE: by running PanGenie-index first to pre-process data, you can reduce memory usage and speed up PanGenie. This is helpful especially when genotyping the same variants across multiple samples." << endl << endl; + int exit_code = run_single_command(outname, readfile, reffile, vcffile, kmersize, outname, sample_name, nr_jellyfish_threads, nr_core_threads, only_genotyping, only_phasing, effective_N, regularization, count_only_graph, ignore_imputed, add_reference, sampling_size, hash_size); getrusage(RUSAGE_SELF, &rss_total);