removed useless option -n

README.md

@@ -91,7 +91,7 @@ where the code was compiled (see the section [Compiling the Code](#compiling-the
 
 to show the usage of the driver program (reported below for convenience).
 
-	Usage: ./build [-h,--help] input_filename k m [-s seed] [-n max_num_kmers] [-l l] [-c c] [--canonical-parsing] [-o output_filename] [--check] [--bench] [--verbose]
+	Usage: ./build [-h,--help] input_filename k m [-s seed] [-l l] [-c c] [--canonical-parsing] [-o output_filename] [--check] [--bench] [--verbose]
 
 	 input_filename
 		Must be a FASTA file (.fa/fasta extension) compressed with gzip (.gz) or not:
@@ -108,9 +108,6 @@ to show the usage of the driver program (reported below for convenience).
 	 [-s seed]
 		Seed for construction (default is 1).
 
-	 [-n max_num_kmers]
-		Build the dictionary from at most this number of k-mers.
-
 	 [-l l]
 		A (integer) constant that controls the space/time trade-off of the dictionary. A reasonable values lies between 2 and 12 (default is 6).
 

include/builder/build.cpp

@@ -27,7 +27,6 @@ void parse_file(std::istream& is, parse_data& data, build_configuration const& b
     uint64_t k = build_config.k;
     uint64_t m = build_config.m;
     uint64_t seed = build_config.seed;
-    uint64_t max_num_kmers = build_config.max_num_kmers;
     uint64_t max_num_kmers_in_string = k - m + 1;
     uint64_t block_size = 2 * k - m;  // max_num_kmers_in_string + k - 1
 
@@ -82,7 +81,7 @@ void parse_file(std::istream& is, parse_data& data, build_configuration const& b
         return true;
     };
 
-    while (!is.eof() and data.num_kmers != max_num_kmers) {
+    while (!is.eof()) {
         std::getline(is, line);  // skip header line
         std::getline(is, line);
 
@@ -120,7 +119,6 @@ void parse_file(std::istream& is, parse_data& data, build_configuration const& b
             }
 
             ++data.num_kmers;
-            if (data.num_kmers == max_num_kmers) break;
 
             ++end;
         }

include/util.hpp

@@ -60,7 +60,6 @@ struct build_configuration {
         : k(31)
         , m(17)
         , seed(constants::seed)
-        , max_num_kmers(-1)
 
         , l(constants::min_l)
         , c(constants::c)
@@ -71,7 +70,6 @@ struct build_configuration {
     uint64_t k;  // kmer size
     uint64_t m;  // minimizer size
     uint64_t seed;
-    uint64_t max_num_kmers;
 
     uint64_t l;  // drive dictionary trade-off
     double c;    // drive PTHash trade-off

src/build.cpp

@@ -24,8 +24,6 @@ int main(int argc, char** argv) {
     parser.add("seed",
                "Seed for construction (default is " + std::to_string(constants::seed) + ").", "-s",
                false);
-    parser.add("max_num_kmers", "Build the dictionary from at most this number of k-mers.", "-n",
-               false);
     parser.add("l",
                "A (integer) constant that controls the space/time trade-off of the dictionary. "
                "A reasonable values lies between 2 and 12 (default is " +
@@ -60,9 +58,6 @@ int main(int argc, char** argv) {
     build_config.m = m;
 
     if (parser.parsed("seed")) build_config.seed = parser.get<uint64_t>("seed");
-    if (parser.parsed("max_num_kmers")) {
-        build_config.max_num_kmers = parser.get<uint64_t>("max_num_kmers");
-    }
     if (parser.parsed("l")) build_config.l = parser.get<double>("l");
     if (parser.parsed("c")) build_config.c = parser.get<double>("c");
     build_config.canonical_parsing = parser.get<bool>("canonical_parsing");