diff --git a/src/interface/parse_args.hpp b/src/interface/parse_args.hpp index 986189c9..432896f6 100644 --- a/src/interface/parse_args.hpp +++ b/src/interface/parse_args.hpp @@ -86,7 +86,7 @@ void parse_args(int argc, args::Flag drop_low_map_pct_identity(mapping_opts, "K", "drop mappings with estimated identity below --map-pct-id=%", {'K', "drop-low-map-id"}); args::Flag no_filter(mapping_opts, "MODE", "disable mapping filtering", {'f', "no-filter"}); args::ValueFlag map_sparsification(mapping_opts, "FACTOR", "keep this fraction of mappings", {'x', "sparsify-mappings"}); - args::Flag keep_ties(mapping_opts, "", "keep all mappings with equal score even if it results in more than n mappings", {'D', "keep-ties"}); + //ToFix: args::Flag keep_ties(mapping_opts, "", "keep all mappings with equal score even if it results in more than n mappings", {'D', "keep-ties"}); args::ValueFlag sketch_size(mapping_opts, "N", "sketch size for sketching.", {'w', "sketch-size"}); args::ValueFlag kmer_complexity(mapping_opts, "F", "Drop segments w/ predicted kmer complexity below this cutoff. Kmer complexity defined as #kmers / (s - k + 1)", {'J', "kmer-complexity"}); args::Flag no_hg_filter(mapping_opts, "", "Don't use the hypergeometric filtering and instead use the MashMap2 first pass filtering.", {'1', "no-hg-filter"}); @@ -352,7 +352,7 @@ void parse_args(int argc, align_parameters.sam_format = args::get(sam_format); align_parameters.no_seq_in_sam = args::get(no_seq_in_sam); map_parameters.split = !args::get(no_split); - map_parameters.dropRand = !args::get(keep_ties); + map_parameters.dropRand = false;//ToFix: !args::get(keep_ties); align_parameters.split = !args::get(no_split); map_parameters.mergeMappings = !args::get(no_merge);