Fix count module FPR adjustment

Author: parham-k

src/modules/count/args.hpp

@@ -12,7 +12,7 @@ class ProgramArguments
   std::vector<uint64_t> histogram;
   std::string out_path;
   size_t out_size;
-  float target_fpr;
+  float target_err;
   unsigned kmer_length;
   unsigned num_threads;
   bool long_mode;
@@ -24,8 +24,8 @@ class ProgramArguments
     parser.add_argument("-s").help("path to spaced seeds file (one per line, if -k not specified)");
     parser.add_argument("-f").help("path to k-mer spectrum file (from ntCard)").required();
     parser.add_argument("-e")
-      .help("target output false positive rate")
-      .default_value(0.01F)
+      .help("target output count error rate")
+      .default_value(0.001F)
       .scan<'g', float>();
     parser.add_argument("-b").help("output CBF size (bytes)").scan<'u', size_t>();
     parser.add_argument("--long")
@@ -43,7 +43,7 @@ class ProgramArguments
     reads_paths = parser.get<std::vector<std::string>>("reads");
     out_path = parser.get("-o");
     out_size = parser.is_used("-b") ? parser.get<size_t>("-b") : 0;
-    target_fpr = parser.get<float>("-e");
+    target_err = parser.get<float>("-e");
     num_threads = parser.get<unsigned>("-t");
     long_mode = parser.get<bool>("--long");
 
@@ -83,7 +83,7 @@ class ProgramArguments
       }
     }
     ss << "[-t] thread limit: " << num_threads << std::endl;
-    ss << "[-e] target output false-positive rate: " << target_fpr << std::endl;
+    ss << "[-e] target output false-positive rate: " << target_err << std::endl;
     return ss.str();
   }
 

src/modules/count/main.cpp

@@ -29,13 +29,12 @@ run(std::vector<std::string> argv)
   size_t out_size;
   unsigned num_hashes;
   bool out_size_known = args.get()->out_size != 0;
-  const auto cascade_fpr = 1 - std::cbrt(1 - args.get()->target_fpr);
   if (out_size_known) {
     out_size = args.get()->out_size;
     num_hashes = num_elements * log(2) / out_size;
   } else {
     num_hashes = 3;
-    out_size = get_bf_size(num_elements, cascade_fpr, num_hashes);
+    out_size = get_bf_size(num_elements, args.get()->target_err / 0.3, num_hashes);
   }
 
   std::cout << "number of hash functions: " << num_hashes << std::endl;

tests/test_count.py

@@ -51,10 +51,15 @@ def test_counts(self):
         self.logger.info(f"cbf size (bytes) = {counts_cbf.get_bytes()}")
         self.logger.info(f"counts fpr = {counts_cbf.get_fpr()}")
         self.logger.info(f"depths fpr = {depths_cbf.get_fpr()}")
-        self.assertLessEqual(counts_cbf.get_fpr(), 1e-3)
-        self.assertLessEqual(depths_cbf.get_fpr(), 1e-3)
+        self.assertLess(counts_cbf.get_fpr(), 0.04)
+        self.assertLess(depths_cbf.get_fpr(), 0.04)
+        num_err = 0
         for kmer, count, depth in zip(kmers, counts, depths):
-            self.assertEqual(counts_cbf.contains(kmer), min(count, 255))
-            self.assertEqual(depths_cbf.contains(kmer), min(depth, 255))
+            count_err = counts_cbf.contains(kmer) != min(count, 255)
+            depth_err = depths_cbf.contains(kmer) != min(depth, 255)
+            num_err += 1 if count_err or depth_err else 0
+        err_rate = num_err / len(kmers)
+        self.logger.info(f"{num_err} errors ({err_rate})")
+        self.assertLess(err_rate, 0.002)
         # remove temporary files
         out_dir.cleanup()