From b6eb193f6040137b068f2f642d0437c0037753d1 Mon Sep 17 00:00:00 2001
From: "Erik Garrison (aider)" <erik.garrison@gmail.com>
Date: Sat, 19 Oct 2024 18:54:59 -0500
Subject: [PATCH] feat: allow hgNumerator parameter to be a double

---
 src/interface/parse_args.hpp       | 12 ++++++------
 src/map/include/map_parameters.hpp |  2 +-
 src/map/include/winSketch.hpp      |  2 +-
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/interface/parse_args.hpp b/src/interface/parse_args.hpp
index 44478219..a59f824e 100644
--- a/src/interface/parse_args.hpp
+++ b/src/interface/parse_args.hpp
@@ -92,9 +92,9 @@ void parse_args(int argc,
     args::ValueFlag<double> map_sparsification(mapping_opts, "FACTOR", "keep this fraction of mappings", {'x', "sparsify-mappings"});
     //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<int64_t> sketch_size(mapping_opts, "N", "sketch size for sketching.", {'w', "sketch-size"});
-    args::ValueFlag<int> hg_numerator(mapping_opts, "N", 
+    args::ValueFlag<double> hg_numerator(mapping_opts, "N", 
         "Set the numerator for the hypergeometric filter's Jaccard similarity calculation. "
-        "Higher values increase speed at the cost of sensitivity. [default: 1]", 
+        "Higher values increase speed at the cost of sensitivity. [default: 1.0]", 
         {"hg-numerator"});
     args::ValueFlag<double> 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.", {"no-hg-filter"});
@@ -611,14 +611,14 @@ void parse_args(int argc,
     }
 
     if (hg_numerator) {
-        int value = args::get(hg_numerator);
-        if (value < 1) {
-            std::cerr << "[wfmash] ERROR: hg-numerator must be >= 1." << std::endl;
+        double value = args::get(hg_numerator);
+        if (value < 1.0) {
+            std::cerr << "[wfmash] ERROR: hg-numerator must be >= 1.0." << std::endl;
             exit(1);
         }
         map_parameters.hgNumerator = value;
     } else {
-        map_parameters.hgNumerator = 1;  // Default value
+        map_parameters.hgNumerator = 1.0;  // Default value
     }
 
     // Set the total reference size
diff --git a/src/map/include/map_parameters.hpp b/src/map/include/map_parameters.hpp
index b9248ee8..7aa2eb2c 100644
--- a/src/map/include/map_parameters.hpp
+++ b/src/map/include/map_parameters.hpp
@@ -72,7 +72,7 @@ struct Parameters
     std::vector<std::string> query_prefix;            // prefix for query sequences to use
 
     int sketchSize;
-    int hgNumerator = 1;                              // Numerator for the hypergeometric filter's Jaccard similarity calculation
+    double hgNumerator = 1.0;                         // Numerator for the hypergeometric filter's Jaccard similarity calculation
     uint64_t totalReferenceSize = 0;                  // Total size of all reference sequences
     uint64_t estimatedUniqueKmers = 0;                // Estimate of total unique k-mers
     bool use_spaced_seeds;                            //
diff --git a/src/map/include/winSketch.hpp b/src/map/include/winSketch.hpp
index 9eb51a7b..eff4efb5 100644
--- a/src/map/include/winSketch.hpp
+++ b/src/map/include/winSketch.hpp
@@ -103,7 +103,7 @@ namespace skch
       input_queue_t input_queue;
       output_queue_t output_queue;
 
-      int hgNumerator;
+      double hgNumerator;
 
       private: