clarify fasta input usage

waveygang · Nov 1, 2024 · 1f9d9b2 · 1f9d9b2
1 parent 9e86feb
commit 1f9d9b2
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/src/interface/parse_args.hpp b/src/interface/parse_args.hpp
@@ -67,8 +67,8 @@ void parse_args(int argc,
     parser.helpParams.eachgroupindent = 2;
 
     args::Group options_group(parser, "");
-    args::Positional<std::string> target_sequence_file(options_group, "target.fa", "target sequences (required)");
-    args::Positional<std::string> query_sequence_file(options_group, "query.fa", "query sequences (optional, defaults to target)");
+    args::Positional<std::string> target_sequence_file(options_group, "target.fa", "target sequences (required, default: self-map)");
+    args::Positional<std::string> query_sequence_file(options_group, "query.fa", "query sequences (optional)");
     args::Group indexing_opts(options_group, "Indexing:");
     args::ValueFlag<std::string> write_index(indexing_opts, "FILE", "build and save index to FILE", {'W', "write-index"});
     args::ValueFlag<std::string> mashmap_index(indexing_opts, "FILE", "use pre-built index from FILE", {'i', "index"});