Merge remote-tracking branch 'upstream/master'

include/info.impl

@@ -16,22 +16,13 @@ static double bits_per_kmer_formula(uint64_t k, /* kmer length */
     assert(k > 0);
     assert(k >= m);
 
-    const uint64_t N = n + M * (k - 1);  // num. symbols in SPSS
+    const uint64_t N = n + M * (k - 1);  // num. characters in SPSS
 
-    // double num_minimizers = (2.0 * n) / (k - m + 2);  // not distinct, hence num. of super-kmers
-    // std::cout << "num_minimizers = " << num_minimizers << std::endl;
-    // std::cout << "minimizers: " << (3.0 * num_minimizers) / n << " [bits/kmer]" << std::endl;
-    // std::cout << "pieces: " << (M * (2.0 + std::ceil(std::log2(static_cast<double>(N) / M)))) / n
-    //           << " [bits/kmer]" << std::endl;
-    // std::cout << "num_super_kmers_before_bucket: " << (2.0 * num_minimizers) / n << " [bits/kmer]
-    // "
-    //           << std::endl;
-    // std::cout << "offsets: " << (std::ceil(std::log2(N)) * num_minimizers) / n << " [bits/kmer]"
-    //           << std::endl;
-    // std::cout << "strings: " << (2.0 * N) / n << " [bits/kmer]" << std::endl;
+    /* summing (M-1) provides an upper bound to the num. of super-kmers */
+    double Z = (2.0 * n) / (k - m + 2) + (M - 1);
 
-    double num_bits = 2 * n * (1.0 + (5.0 + std::ceil(std::log2(N))) / (k - m + 2)) +
-                      M * (2 * k + std::ceil(std::log2(static_cast<double>(n) / M + k - 1)));
+    double num_bits = 2 * N + Z * (5.0 + std::ceil(std::log2(N))) +
+                      M * (2.0 + std::ceil(std::log2(static_cast<double>(N) / M)));
 
     return num_bits / n;
 }