Freq filter yes

src/interface/parse_args.hpp

@@ -98,7 +98,7 @@ void parse_args(int argc,
     args::ValueFlag<double> kmer_complexity(mapping_opts, "FLOAT", "minimum k-mer complexity threshold", {'J', "kmer-cmplx"});
     args::ValueFlag<std::string> hg_filter(mapping_opts, "numer,ani-Δ,conf", "hypergeometric filter params [1.0,0.0,99.9]", {"hg-filter"});
     args::ValueFlag<int> min_hits(mapping_opts, "INT", "minimum number of hits for L1 filtering [auto]", {'H', "l1-hits"});
-    args::ValueFlag<uint64_t> max_kmer_freq(mapping_opts, "INT", "maximum allowed k-mer frequency [unlimited]", {'F', "max-kmer-freq"});
+    args::ValueFlag<double> max_kmer_freq(mapping_opts, "FLOAT", "filter out top FLOAT fraction of repetitive minimizers [0.0002]", {'F', "filter-freq"});
 
     args::Group alignment_opts(options_group, "Alignment:");
     args::ValueFlag<std::string> input_mapping(alignment_opts, "FILE", "input PAF file for alignment", {'i', "align-paf"});
@@ -557,7 +557,7 @@ void parse_args(int argc,
     if (max_kmer_freq) {
         map_parameters.max_kmer_freq = args::get(max_kmer_freq);
     } else {
-        map_parameters.max_kmer_freq = std::numeric_limits<uint64_t>::max(); // unlimited
+        map_parameters.max_kmer_freq = 0.0002; // default filter fraction
     }
 
     //if (window_minimizers) {

src/map/include/map_parameters.hpp

@@ -87,7 +87,7 @@ struct Parameters
     //std::unordered_set<std::string> high_freq_kmers;  //
     int64_t index_by_size = std::numeric_limits<int64_t>::max();  // Target total size of sequences for each index subset
     int minimum_hits = -1;  // Minimum number of hits required for L1 filtering (-1 means auto)
-    uint64_t max_kmer_freq = std::numeric_limits<uint64_t>::max();  // Maximum allowed k-mer frequency
+    double max_kmer_freq = 0.0002;  // Maximum allowed k-mer frequency fraction (0-1) or count (>1)
 };
 
 

src/map/include/winSketch.hpp

@@ -256,7 +256,15 @@ namespace skch
                       continue;  // Should never happen
                   }
 
-                  if (freq_it->second > param.max_kmer_freq) {
+                  uint64_t freq_cutoff;
+                  if (param.max_kmer_freq <= 1.0) {
+                      // Calculate cutoff based on fraction of total windows
+                      freq_cutoff = std::max(1UL, (uint64_t)(total_windows * param.max_kmer_freq));
+                  } else {
+                      // Use direct count cutoff
+                      freq_cutoff = (uint64_t)param.max_kmer_freq;
+                  }
+                  if (freq_it->second > freq_cutoff) {
                       filtered_kmers++;
                       continue;
                   }
@@ -282,12 +290,24 @@ namespace skch
           // Finish second progress meter
           index_progress.finish();
 
-          double filtered_pct = (filtered_kmers * 100.0) / total_kmers;
+          uint64_t freq_cutoff;
+          if (param.max_kmer_freq <= 1.0) {
+              freq_cutoff = std::max(1UL, (uint64_t)(total_windows * param.max_kmer_freq));
+          } else {
+              freq_cutoff = (uint64_t)param.max_kmer_freq;
+          }
           std::cerr << "[wfmash::mashmap] Processed " << totalSeqProcessed << " sequences (" << totalSeqSkipped << " skipped, " << total_seq_length << " total bp), " 
                     << minmerPosLookupIndex.size() << " unique hashes, " << minmerIndex.size() << " windows" << std::endl
                     << "[wfmash::mashmap] Filtered " << filtered_kmers << "/" << total_kmers 
-                    << " k-mers (" << std::fixed << std::setprecision(2) << filtered_pct << "%) exceeding frequency threshold of " 
-                    << param.max_kmer_freq << std::endl;
+                    << " k-mers occurring > " << freq_cutoff << " times"
+                    << " (target: " << (param.max_kmer_freq <= 1.0 ? 
+                                      ([&]() { 
+                                          std::stringstream ss;
+                                          ss << std::fixed << std::setprecision(2) << (param.max_kmer_freq * 100);
+                                          return ss.str();
+                                      })() + "%" :
+                                      ">" + std::to_string((int)param.max_kmer_freq) + " occurrences") 
+                    << ")" << std::endl;
         }
 
         std::chrono::duration<double> timeRefSketch = skch::Time::now() - t0;