Merge pull request #26 from camel-cdr/knucleotide

k-nucleotide benchmark

src/benchmarks/knucleotide.cpp

@@ -0,0 +1,128 @@
+// This code is adapted from Jeremy Zerfas [0] submission to the
+// "The Computer Language Benchmarks Game" [1], the appropriate license is at
+// the bottom of the file.
+//
+// [0] https://benchmarksgame-team.pages.debian.net/benchmarksgame/program/knucleotide-clang-1.html
+// [1] https://salsa.debian.org/benchmarksgame-team/benchmarksgame/
+
+
+#include <vector>
+#include <cstdint>
+
+#include "Map.h"
+#include "bench.h"
+
+
+// Macro to convert a nucleotide character to a code. Note that upper and lower
+// case ASCII letters only differ in the fifth bit from the right and we only
+// need the three least significant bits to differentiate the letters 'A', 'C',
+// 'G', and 'T'. Spaces in this array/string will never be used as long as
+// characters other than 'A', 'C', 'G', and 'T' aren't used.
+#define CODE_FOR_NUCLEOTIDE(nucleotide) (" \0 \1\3  \2"[nucleotide & 0x7])
+
+
+static size_t count(const std::vector<char> &poly, const std::string &oligo) {
+
+    using M = Map<uint64_t, uint32_t>;
+#ifdef USE_POOL_ALLOCATOR
+    Resource<uint64_t, uint32_t> resource;
+    M map{0, M::hasher{}, M::key_equal{}, &resource};
+#else
+    M map;
+#endif
+
+    uint64_t key = 0;
+    const uint64_t mask = ((uint64_t)1 << 2 * oligo.size()) - 1;
+
+    // For the first several nucleotides we only need to append them to key in
+    // preparation for the insertion of complete oligonucleotides to map.
+    for (size_t i = 0; i < oligo.size() - 1; ++i)
+        key = (key << 2 & mask) | poly[i];
+
+    // Add all the complete oligonucleotides of oligo.size() to
+    // map and update the count for each oligonucleotide.
+    for (size_t i = oligo.size() - 1; i < poly.size(); ++i){
+        key= (key << 2 & mask) | poly[i];
+        ++map[key];
+    }
+
+    // Generate the key for oligonucleotide.
+    key = 0;
+    for (size_t i = 0; i < oligo.size(); ++i) {
+        key = (key << 2) | CODE_FOR_NUCLEOTIDE(oligo[i]);
+    }
+
+    // Output the count for oligonucleotide to output.
+    return map.find(key)->second;
+}
+
+static inline int fasta_next() {
+    static constexpr int IM = 139968, IA = 3877, IC = 29573;
+    static int state = 42;
+
+    state = (state * IA + IC) % IM;
+    float p = state * (1.0f / IM);
+    return (p >= 0.3029549426680f) + (p >= 0.5009432431601f) + (p >= 0.6984905497992f);
+}
+
+
+BENCHMARK(knucleotide) {
+    constexpr size_t n = 25000000;
+
+    for (size_t i = 0; i < n * 3; ++i)
+        (void)fasta_next();
+
+    std::vector<char> poly(n * 5);
+    for (size_t i = 0; i < poly.size(); ++i) {
+        poly[i] = fasta_next();
+    }
+
+    bench.beginMeasure("Count GGTATTTTAATTTATAGT");
+    bench.endMeasure(893, count(poly, "GGTATTTTAATTTATAGT"));
+
+    bench.beginMeasure("Count GGTATTTTAATT");
+    bench.endMeasure(893, count(poly, "GGTATTTTAATT"));
+
+    bench.beginMeasure("Count GGTATT");
+    bench.endMeasure(47336, count(poly, "GGTATT"));
+
+    bench.beginMeasure("Count GGTA");
+    bench.endMeasure(446535, count(poly, "GGTA"));
+
+    bench.beginMeasure("Count GGT");
+    bench.endMeasure(1471758, count(poly, "GGT"));
+}
+
+
+// Copyright © 2004-2008 Brent Fulgham, 2005-2023 Isaac Gouy All rights
+// reserved. Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are met:
+//
+//
+// Redistributions of source code must retain the above copyright notice, this
+// list of conditions and the following disclaimer.
+//
+//
+// Redistributions in binary form must reproduce the above copyright notice,
+// this list of conditions and the following disclaimer in the documentation
+// and/or other materials provided with the distribution.
+//
+//
+// Neither the name "The Computer Language Benchmarks Game" nor the name "The
+// Benchmarks Game" nor the name "The Computer Language Shootout Benchmarks"
+// nor the names of its contributors may be used to endorse or promote products
+// derived from this software without specific prior written permission.
+//
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+// ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+// LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+// CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+// SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+// INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+// CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+// ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+// POSSIBILITY OF SUCH DAMAGE.
+