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Clarify help string for -n #206

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Nov 9, 2023
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Clarify help string for -n #206

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4 changes: 2 additions & 2 deletions src/interface/parse_args.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -71,8 +71,8 @@ void parse_args(int argc,
args::ValueFlag<float> map_pct_identity(mapping_opts, "%", "percent identity in the mashmap step [default: 90]", {'p', "map-pct-id"});
args::ValueFlag<std::string> segment_length(mapping_opts, "N", "segment seed length for mapping [default: 5k]", {'s', "segment-length"});
args::ValueFlag<std::string> block_length(mapping_opts, "N", "keep merged mappings supported by homologies of this total length [default: 5*segment-length]", {'l', "block-length"});
args::ValueFlag<uint32_t> num_mappings_for_segments(mapping_opts, "N", "number of mappings to retain for each segment [default: 1]", {'n', "num-mappings-for-segment"});
args::ValueFlag<uint32_t> num_mappings_for_short_seq(mapping_opts, "N", "number of mappings to retain for each sequence shorter than segment length [default: 1]", {'S', "num-mappings-for-short-seq"});
args::ValueFlag<uint32_t> num_mappings_for_segments(mapping_opts, "N", "number of mappings to retain for each query/reference pair [default: 1]", {'n', "num-mappings-for-segment"});
args::ValueFlag<uint32_t> num_mappings_for_short_seq(mapping_opts, "N", "number of mappings to retain for each query/reference pair where the query sequence is shorter than segment length [default: 1]", {'S', "num-mappings-for-short-seq"});
args::ValueFlag<int> kmer_size(mapping_opts, "N", "kmer size [default: 19]", {'k', "kmer"});
args::ValueFlag<float> kmer_pct_threshold(mapping_opts, "%", "ignore the top % most-frequent kmers [default: 0.001]", {'H', "kmer-threshold"});
args::Flag lower_triangular(mapping_opts, "", "only map shorter sequences against longer", {'L', "lower-triangular"});
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