Fix for sanitizer's initialization-order-fiasco

src/basic/basic.cpp

@@ -27,6 +27,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include "statistics.h"
 #include "sequence.h"
 #include "stats/standard_matrix.h"
+#include "stats/matrices/accessors.h"
 #include "util/log_stream.h"
 
 const char* Const::version_string = "2.1.13";
@@ -278,7 +279,7 @@ Reduction::Reduction(const char* definition_string)
 			map_[letter] = i;
 			map8_[letter] = i;
 			map8b_[letter] = i;
-			freq_[i] += Stats::blosum62.background_freqs[letter];
+			freq_[i] += Stats::getBlosum62().background_freqs[letter];
 		}
 	for (double& f : freq_)
 		f = std::log(f);
@@ -298,4 +299,4 @@ std::string Reduction::decode_seed(const uint64_t seed, const size_t len) const
 		c /= size_;
 	}
 	return s;
-}
+}

src/stats/matrices/accessors.h

@@ -0,0 +1,32 @@
+/****
+DIAMOND protein aligner
+Copyright (C) 2020 Max Planck Society for the Advancement of Science e.V.
+
+Code developed by Benjamin Buchfink <benjamin.buchfink@tue.mpg.de>
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+****/
+
+#pragma once
+
+namespace Stats {
+    const StandardMatrix& getBlosum45();
+    const StandardMatrix& getBlosum50();
+    const StandardMatrix& getBlosum62();
+    const StandardMatrix& getBlosum80();
+    const StandardMatrix& getBlosum90();
+    const StandardMatrix& getPam30();
+    const StandardMatrix& getPam70();
+    const StandardMatrix& getPam250();
+}

src/stats/matrices/blosum45.cpp

@@ -22,7 +22,9 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 namespace Stats {
 
-const StandardMatrix blosum45{
+const StandardMatrix& getBlosum45() {
+
+    static const StandardMatrix blosum45_instance {
 
     14, 2,
 
@@ -445,6 +447,8 @@ const StandardMatrix blosum45{
  6.28722660e-01, 7.50000000e-01, 9.41772708e-01, 5.67250003e-01,
  7.50000000e-01, 2.90000000e-01, 7.50000000e-01, 2.36320536e+00} }
 
-};
+    };
+    return blosum45_instance;
+}
 
-}
+}

src/stats/matrices/blosum50.cpp

@@ -22,7 +22,9 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 namespace Stats {
 
-const StandardMatrix blosum50{
+const StandardMatrix& getBlosum50() {
+
+    static const StandardMatrix blosum50_instance {
 
     13, 2,
 
@@ -446,6 +448,8 @@ const StandardMatrix blosum50{
     5.69808181e-01, 7.50000000e-01, 8.45421029e-01, 4.85898712e-01,
     7.50000000e-01, 2.90000000e-01, 7.50000000e-01, 2.55759716e+00} }
 
-};
+    };
+    return blosum50_instance;
+}
 
-}
+}

src/stats/matrices/blosum62.cpp

@@ -22,7 +22,9 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 namespace Stats {
 
-const StandardMatrix blosum62{
+const StandardMatrix& getBlosum62() {
+
+    static const StandardMatrix blosum62_instance {
 
     11, 1, 
 
@@ -442,6 +444,9 @@ const StandardMatrix blosum62{
     5.03239261e-01, 7.50000000e-01, 6.66952325e-01, 3.87839626e-01,
     7.50000000e-01, 2.50000000e-01, 7.50000000e-01, 2.81516607e+00} }
 
-};
 
-}
+    };
+    return blosum62_instance;
+}
+
+}

src/stats/matrices/blosum80.cpp

@@ -22,7 +22,9 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 namespace Stats {
 
-const StandardMatrix blosum80{
+const StandardMatrix& getBlosum80() {
+
+    static const StandardMatrix blosum80_instance {
 
     10, 1, 
 
@@ -440,5 +442,7 @@ const StandardMatrix blosum80{
  7.50000000e-01, 1.40000000e-01, 7.50000000e-01, 3.18242650e+00} }
 
 };
+return blosum80_instance;
 
-}
+}
+}

src/stats/matrices/blosum90.cpp

@@ -22,7 +22,9 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 namespace Stats {
 
-const StandardMatrix blosum90{
+const StandardMatrix& getBlosum90() {
+
+    static const StandardMatrix blosum90_instance {
 
     10, 1,
 
@@ -437,6 +439,8 @@ const StandardMatrix blosum90{
     3.37037347e-01, 7.50000000e-01, 4.96615724e-01, 2.74820979e-01,
     7.50000000e-01, 1.20000000e-01, 7.50000000e-01, 3.47015056e+00} }
 
-};
+    };
+    return blosum90_instance;
+}
 
-}
+}

src/stats/matrices/pam250.cpp

@@ -22,7 +22,9 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 namespace Stats {
 
-const StandardMatrix pam250{
+const StandardMatrix& getPam250() {
+
+    static const StandardMatrix pam250_instance {
 
     14, 2,
 
@@ -445,6 +447,8 @@ const StandardMatrix pam250{
     5.43022417e-01, 7.50000000e-01, 8.10366134e-01, 5.73996058e-01,
     7.50000000e-01, 1.70000000e-01, 7.50000000e-01, 2.91088108e+00} }
 
-};
+    };
+    return pam250_instance;
+}
 
-}
+}

src/stats/matrices/pam30.cpp

@@ -22,7 +22,9 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 namespace Stats {
 
-const StandardMatrix pam30{
+const StandardMatrix& getPam30() {
+
+    static const StandardMatrix pam30_instance {
 
     9, 1,
 
@@ -436,6 +438,7 @@ const StandardMatrix pam30{
     9.17500230e-02, 7.50000000e-01, 1.02140077e-01, 1.07889016e-01,
     7.50000000e-01, 3.00000000e-03, 7.50000000e-01, 6.85288369e+00} }
 
-};
-
-}
+    };
+    return pam30_instance;
+}
+}

src/stats/matrices/pam70.cpp

@@ -22,7 +22,9 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 namespace Stats {
 
-const StandardMatrix pam70{
+const StandardMatrix& getPam70() {
+
+    static const StandardMatrix pam70_instance {
 
     10, 1,
 
@@ -437,5 +439,7 @@ const StandardMatrix pam70{
  7.50000000e-01, 2.00000000e-02, 7.50000000e-01, 5.58422761e+00} }
 
 };
+return pam70_instance;
 
-}
+}
+}

src/stats/score_matrix.cpp

@@ -30,6 +30,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include "score_matrix.h"
 #include "basic/config.h"
 #include "stats/cbs.h"
+#include "stats/matrices/accessors.h"
 
 using std::string;
 using std::vector;
@@ -174,7 +175,7 @@ ScoreMatrix::ScoreMatrix(const string& matrix_file, int gap_open, int gap_extend
 			m[i][j] = score_array_[i * AMINO_ACID_COUNT + j];
 		p[i] = m[i];
 	}
-	const double* bg = Stats::blosum62.background_freqs.data();
+	const double* bg = Stats::getBlosum62().background_freqs.data();
 	try {
 		evaluer.initGapped(N, p, bg, bg, gap_open_, gap_extend_, gap_open_, gap_extend_, false, 0.01, 0.05, 120.0, 1024.0, 1);
 	}
@@ -238,12 +239,12 @@ void ScoreMatrix::init_background_scores()
 	for (size_t i = 0; i < 20; ++i) {
 		background_scores_[i] = 0;
 		for (size_t j = 0; j < 20; ++j)
-			background_scores_[i] += Stats::blosum62.background_freqs[j] * (*this)(i, j);
+			background_scores_[i] += Stats::getBlosum62().background_freqs[j] * (*this)(i, j);
 	}
 }
 
 double ScoreMatrix::bitscore(double raw_score) const
 {
 	const double s = std::round(raw_score / scale_);	// maintain compatibility with BLAST
 	return (lambda() * s - ln_k()) / LN_2;
-}
+}

src/stats/stats.cpp

@@ -21,15 +21,16 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include <algorithm>
 #include <iterator>
 #include "standard_matrix.h"
+#include "matrices/accessors.h"
 
 using std::string;
 using std::max;
 using std::min;
 
 namespace Stats {
 
-const std::map<std::string, const StandardMatrix&> StandardMatrix::matrices = { { "blosum45", blosum45 }, { "blosum62", blosum62 }, { "blosum50", blosum50 }, { "blosum80", blosum80 }, { "blosum90", blosum90 },
-	{ "pam250", pam250 }, { "pam30", pam30 }, { "pam70", pam70 } };
+const std::map<std::string, const StandardMatrix&> StandardMatrix::matrices = { { "blosum45", getBlosum45() }, { "blosum62", getBlosum62() }, { "blosum50", getBlosum50() }, { "blosum80", getBlosum80() }, { "blosum90", getBlosum90() },
+	{ "pam250", getPam250() }, { "pam30", getPam30() }, { "pam70", getPam70() } };
 
 const StandardMatrix& StandardMatrix::get(const std::string& name) {
 	string n;
@@ -59,4 +60,4 @@ double approx_id(Score raw_score, Loc range1, Loc range2) {
 	return min(max((double)raw_score / m * 16.56 + 11.41, 0.0), 100.0);
 }
 
-}
+}

src/tools/benchmark.cpp

@@ -40,6 +40,7 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include "dp/swipe/config.h"
 #include "util/simd/dispatch.h"
 #include "dp/score_vector_int16.h"
+#include "stats/matrices/accessors.h"
 
 void benchmark_io();
 
@@ -447,7 +448,7 @@ void matrix_adjust(const Sequence& s1, const Sequence& s2) {
 	high_resolution_clock::time_point t1 = high_resolution_clock::now();
 	vector<double> mat_final(TRUE_AA * TRUE_AA);
 	int iteration_count;
-	const double* joint_probs = (const double*)(Stats::blosum62.joint_probs);
+	const double* joint_probs = (const double*)(Stats::getBlosum62().joint_probs);
 	auto row_probs = Stats::composition(s1), col_probs = Stats::composition(s2);
 	config.cbs_err_tolerance = 0.0001;