merging martin's master branch

Merge branch 'master' of github.com:martin-steinegger/kraken2 into hll
eladc · May 5, 2020 · 32e97bd · 32e97bd
2 parents 1b49965 + 52519ed
commit 32e97bd
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Showing 13 changed files with 2,670 additions and 27 deletions.
diff --git a/src/Makefile b/src/Makefile
@@ -1,4 +1,3 @@
-CXX = g++
 CXXFLAGS = -fopenmp -Wall -std=c++11 -O3
 CXXFLAGS += -DLINEAR_PROBING
 
@@ -15,6 +14,7 @@ clean:
 	rm -f *.o $(PROGS)
 
 taxonomy.o: taxonomy.cc taxonomy.h mmap_file.h
+hyperloglogplus.o: hyperloglogplus.cc hyperloglogplus.h 
 mmap_file.o: mmap_file.cc mmap_file.h
 compact_hash.o: compact_hash.cc compact_hash.h kv_store.h mmap_file.h
 mmscanner.o: mmscanner.cc mmscanner.h
@@ -26,7 +26,7 @@ utilities.o: utilities.cc utilities.h
 
 build_db: build_db.cc mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o utilities.o
 
-classify: classify.cc reports.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o aa_translate.o utilities.o
+classify: classify.cc reports.o hyperloglogplus.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o aa_translate.o utilities.o
 
 estimate_capacity: estimate_capacity.cc seqreader.o mmscanner.o omp_hack.o utilities.o
 

diff --git a/src/assert_helpers.h b/src/assert_helpers.h
@@ -0,0 +1,284 @@
+/*
+ * Copyright 2011, Ben Langmead <[email protected]>
+ *
+ * This file is part of Bowtie 2.
+ *
+ * Bowtie 2 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.
+ *
+ * Bowtie 2 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 Bowtie 2.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#ifndef ASSERT_HELPERS_H_
+#define ASSERT_HELPERS_H_
+
+#include <stdexcept>
+#include <string>
+#include <cassert>
+#include <iostream>
+
+/**
+ * Assertion for release-enabled assertions
+ */
+class ReleaseAssertException : public std::runtime_error {
+public:
+	ReleaseAssertException(const std::string& msg = "") : std::runtime_error(msg) {}
+};
+
+/**
+ * Macros for release-enabled assertions, and helper macros to make
+ * all assertion error messages more helpful.
+ */
+#ifndef NDEBUG
+#define ASSERT_ONLY(...) __VA_ARGS__
+#else
+#define ASSERT_ONLY(...)
+#endif
+
+#define rt_assert(b)  \
+	if(!(b)) { \
+		std::cerr << "rt_assert at " << __FILE__ << ":" << __LINE__ << std::endl; \
+		throw ReleaseAssertException(); \
+	}
+#define rt_assert_msg(b,msg)  \
+	if(!(b)) { \
+		std::cerr << msg <<  " at " << __FILE__ << ":" << __LINE__ << std::endl; \
+		throw ReleaseAssertException(msg); \
+	}
+
+#define rt_assert_eq(ex,ac)  \
+	if(!((ex) == (ac))) { \
+		std::cerr << "rt_assert_eq: expected (" << (ex) << ", 0x" << std::hex << (ex) << std::dec << ") got (" << (ac) << ", 0x" << std::hex << (ac) << std::dec << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		throw ReleaseAssertException(); \
+	}
+#define rt_assert_eq_msg(ex,ac,msg)  \
+	if(!((ex) == (ac))) { \
+		std::cerr << "rt_assert_eq: " << msg <<  ": (" << (ex) << ", 0x" << std::hex << (ex) << std::dec << ") got (" << (ac) << ", 0x" << std::hex << (ac) << std::dec << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		throw ReleaseAssertException(msg); \
+	}
+
+#ifndef NDEBUG
+#define assert_eq(ex,ac)  \
+	if(!((ex) == (ac))) { \
+		std::cerr << "assert_eq: expected (" << (ex) << ", 0x" << std::hex << (ex) << std::dec << ") got (" << (ac) << ", 0x" << std::hex << (ac) << std::dec << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		assert(0); \
+	}
+#define assert_eq_msg(ex,ac,msg)  \
+	if(!((ex) == (ac))) { \
+		std::cerr << "assert_eq: " << msg <<  ": (" << (ex) << ", 0x" << std::hex << (ex) << std::dec << ") got (" << (ac) << ", 0x" << std::hex << (ac) << std::dec << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		assert(0); \
+	}
+#else
+#define assert_eq(ex,ac)
+#define assert_eq_msg(ex,ac,msg)
+#endif
+
+#define rt_assert_neq(ex,ac)  \
+	if(!((ex) != (ac))) { \
+		std::cerr << "rt_assert_neq: expected not (" << (ex) << ", 0x" << std::hex << (ex) << std::dec << ") got (" << (ac) << ", 0x" << std::hex << (ac) << std::dec << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		throw ReleaseAssertException(); \
+	}
+#define rt_assert_neq_msg(ex,ac,msg)  \
+	if(!((ex) != (ac))) { \
+		std::cerr << "rt_assert_neq: " << msg << ": (" << (ex) << ", 0x" << std::hex << (ex) << std::dec << ") got (" << (ac) << ", 0x" << std::hex << (ac) << std::dec << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		throw ReleaseAssertException(msg); \
+	}
+
+#ifndef NDEBUG
+#define assert_neq(ex,ac)  \
+	if(!((ex) != (ac))) { \
+		std::cerr << "assert_neq: expected not (" << (ex) << ", 0x" << std::hex << (ex) << std::dec << ") got (" << (ac) << ", 0x" << std::hex << (ac) << std::dec << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		assert(0); \
+	}
+#define assert_neq_msg(ex,ac,msg)  \
+	if(!((ex) != (ac))) { \
+		std::cerr << "assert_neq: " << msg << ": (" << (ex) << ", 0x" << std::hex << (ex) << std::dec << ") got (" << (ac) << ", 0x" << std::hex << (ac) << std::dec << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		assert(0); \
+	}
+#else
+#define assert_neq(ex,ac)
+#define assert_neq_msg(ex,ac,msg)
+#endif
+
+#define rt_assert_gt(a,b) \
+	if(!((a) > (b))) { \
+		std::cerr << "rt_assert_gt: expected (" << (a) << ") > (" << (b) << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		throw ReleaseAssertException(); \
+	}
+#define rt_assert_gt_msg(a,b,msg) \
+	if(!((a) > (b))) { \
+		std::cerr << "rt_assert_gt: " << msg << ": (" << (a) << ") > (" << (b) << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		throw ReleaseAssertException(msg); \
+	}
+
+#ifndef NDEBUG
+#define assert_gt(a,b) \
+	if(!((a) > (b))) { \
+		std::cerr << "assert_gt: expected (" << (a) << ") > (" << (b) << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		assert(0); \
+	}
+#define assert_gt_msg(a,b,msg) \
+	if(!((a) > (b))) { \
+		std::cerr << "assert_gt: " << msg << ": (" << (a) << ") > (" << (b) << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		assert(0); \
+	}
+#else
+#define assert_gt(a,b)
+#define assert_gt_msg(a,b,msg)
+#endif
+
+#define rt_assert_geq(a,b) \
+	if(!((a) >= (b))) { \
+		std::cerr << "rt_assert_geq: expected (" << (a) << ") >= (" << (b) << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		throw ReleaseAssertException(); \
+	}
+#define rt_assert_geq_msg(a,b,msg) \
+	if(!((a) >= (b))) { \
+		std::cerr << "rt_assert_geq: " << msg << ": (" << (a) << ") >= (" << (b) << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		throw ReleaseAssertException(msg); \
+	}
+
+#ifndef NDEBUG
+#define assert_geq(a,b) \
+	if(!((a) >= (b))) { \
+		std::cerr << "assert_geq: expected (" << (a) << ") >= (" << (b) << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		assert(0); \
+	}
+#define assert_geq_msg(a,b,msg) \
+	if(!((a) >= (b))) { \
+		std::cerr << "assert_geq: " << msg << ": (" << (a) << ") >= (" << (b) << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		assert(0); \
+	}
+#else
+#define assert_geq(a,b)
+#define assert_geq_msg(a,b,msg)
+#endif
+
+#define rt_assert_lt(a,b) \
+	if(!(a < b)) { \
+		std::cerr << "rt_assert_lt: expected (" << a << ") < (" << b << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		throw ReleaseAssertException(); \
+	}
+#define rt_assert_lt_msg(a,b,msg) \
+	if(!(a < b)) { \
+		std::cerr << "rt_assert_lt: " << msg << ": (" << a << ") < (" << b << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		throw ReleaseAssertException(msg); \
+	}
+
+#ifndef NDEBUG
+#define assert_lt(a,b) \
+	if(!(a < b)) { \
+		std::cerr << "assert_lt: expected (" << a << ") < (" << b << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		assert(0); \
+	}
+#define assert_lt_msg(a,b,msg) \
+	if(!(a < b)) { \
+		std::cerr << "assert_lt: " << msg << ": (" << a << ") < (" << b << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		assert(0); \
+	}
+#else
+#define assert_lt(a,b)
+#define assert_lt_msg(a,b,msg)
+#endif
+
+#define rt_assert_leq(a,b) \
+	if(!((a) <= (b))) { \
+		std::cerr << "rt_assert_leq: expected (" << (a) << ") <= (" << (b) << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		throw ReleaseAssertException(); \
+	}
+#define rt_assert_leq_msg(a,b,msg) \
+	if(!((a) <= (b))) { \
+		std::cerr << "rt_assert_leq: " << msg << ": (" << (a) << ") <= (" << (b) << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		throw ReleaseAssertException(msg); \
+	}
+
+#ifndef NDEBUG
+#define assert_leq(a,b) \
+	if(!((a) <= (b))) { \
+		std::cerr << "assert_leq: expected (" << (a) << ") <= (" << (b) << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		assert(0); \
+	}
+#define assert_leq_msg(a,b,msg) \
+	if(!((a) <= (b))) { \
+		std::cerr << "assert_leq: " << msg << ": (" << (a) << ") <= (" << (b) << ")" << std::endl; \
+		std::cerr << __FILE__ << ":" << __LINE__ << std::endl; \
+		assert(0); \
+	}
+#else
+#define assert_leq(a,b)
+#define assert_leq_msg(a,b,msg)
+#endif
+
+#ifndef NDEBUG
+#define assert_in(c, s) assert_in2(c, s, __FILE__, __LINE__)
+static inline void assert_in2(char c, const char *str, const char *file, int line) {
+	const char *s = str;
+	while(*s != '\0') {
+		if(c == *s) return;
+		s++;
+	}
+	std::cerr << "assert_in: (" << c << ") not in  (" << str << ")" << std::endl;
+	std::cerr << file << ":" << line << std::endl;
+	assert(0);
+}
+#else
+#define assert_in(c, s)
+#endif
+
+#ifndef NDEBUG
+#define assert_range(b, e, v) assert_range_helper(b, e, v, __FILE__, __LINE__)
+template<typename T>
+inline static void assert_range_helper(const T& begin,
+                                       const T& end,
+                                       const T& val,
+                                       const char *file,
+                                       int line)
+{
+	if(val < begin || val > end) {
+		std::cerr << "assert_range: (" << val << ") not in  ["
+		          << begin << ", " << end << "]" << std::endl;
+		std::cerr << file << ":" << line << std::endl;
+		assert(0);
+	}
+}
+#else
+#define assert_range(b, e, v)
+#endif
+
+// define a macro to indicate variables that are only required for asserts
+// used to make production build happy, i.e. disable "warning: variable ‘x’ set but not used [-Wunused-but-set-variable]"
+#define _unused(x) ((void)x)
+
+#endif /*ASSERT_HELPERS_H_*/
+