refactor: Update overlap threshold description and default value

waveygang · Nov 14, 2024 · 09e4c08 · 09e4c08
1 parent f4b929d
commit 09e4c08
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/src/interface/parse_args.hpp b/src/interface/parse_args.hpp
@@ -93,7 +93,7 @@ void parse_args(int argc,
     args::Flag no_split(mapping_opts, "no-split", "map each sequence in one piece", {'N',"no-split"});
     args::ValueFlag<std::string> chain_gap(mapping_opts, "INT", "chain gap: max distance to chain mappings [2k]", {'c', "chain-gap"});
     args::ValueFlag<std::string> max_mapping_length(mapping_opts, "INT", "target mapping length [50k]", {'P', "max-length"});
-    args::ValueFlag<double> overlap_threshold(mapping_opts, "FLOAT", "maximum mapping overlap fraction [0.5]", {'O', "overlap"});
+    args::ValueFlag<double> overlap_threshold(mapping_opts, "FLOAT", "maximum overlap with better mappings (1.0=keep all) [1.0]", {'O', "overlap"});
     args::Flag no_filter(mapping_opts, "", "disable mapping filtering", {'f', "no-filter"});
     args::Flag no_merge(mapping_opts, "", "disable merging of consecutive mappings", {'M', "no-merge"});
     args::ValueFlag<double> kmer_complexity(mapping_opts, "FLOAT", "minimum k-mer complexity threshold", {'J', "kmer-cmplx"});