Merge pull request #206 from bkille/clarify-n-help

Clarify help string for -n

src/interface/parse_args.hpp

@@ -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"});