diff --git a/src/interface/parse_args.hpp b/src/interface/parse_args.hpp index b96a23f7..b0752655 100644 --- 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 chain_gap(mapping_opts, "INT", "chain gap: max distance to chain mappings [2k]", {'c', "chain-gap"}); args::ValueFlag max_mapping_length(mapping_opts, "INT", "target mapping length [50k]", {'P', "max-length"}); - args::ValueFlag overlap_threshold(mapping_opts, "FLOAT", "maximum mapping overlap fraction [0.5]", {'O', "overlap"}); + args::ValueFlag 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 kmer_complexity(mapping_opts, "FLOAT", "minimum k-mer complexity threshold", {'J', "kmer-cmplx"});