Commit 24de1340 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: inverse flag 'multi_germline_one_unique_index'

This is the opposite than the previous 'multi_germline_one_index_per_germline'.
CLI11.hpp, by default, works with postive flags.
See #2732.
parent d971892b
......@@ -266,7 +266,7 @@ int main (int argc, char **argv)
vector <string> multi_germlines ;
bool multi_germline = false;
bool multi_germline_mark = false;
bool multi_germline_one_index_per_germline = true;
bool multi_germline_one_unique_index = false;
bool multi_germline_unexpected_recombinations_12 = false;
bool multi_germline_unexpected_recombinations_1U = false;
......@@ -667,10 +667,10 @@ int main (int argc, char **argv)
if (command == CMD_GERMLINES)
{
multi_germline = true ;
multi_germline_one_index_per_germline = false ;
multi_germline_one_unique_index = true ;
}
MultiGermline *multigermline = new MultiGermline(indexType, multi_germline_one_index_per_germline);
MultiGermline *multigermline = new MultiGermline(indexType, !multi_germline_one_unique_index);
{
cout << "Load germlines and build Kmer indexes" << endl ;
......@@ -705,7 +705,7 @@ int main (int argc, char **argv)
cout << endl ;
if (!multi_germline_one_index_per_germline) {
if (multi_germline_one_unique_index) {
multigermline->build_with_one_index(seed, true);
}
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment