Fixed last few warnings and enabled -Werror in Linux Travis

.travis.yml

@@ -115,7 +115,9 @@ script:
       docker build --build-arg NAMESPACE=arm64v8/ -t mmseqs . || exit 1; \
     elif [[ "$TRAVIS_OS_NAME" == "linux" ]]; then \
       if [[ -n "$MPI" ]]; then MPI=1; else MPI=0; fi; \
-      mkdir build; cd build; cmake -G Ninja -DHAVE_MPI="$MPI" -DHAVE_SSE4_1=1 .. || exit 1; ninja || exit 1; \
+      mkdir build; cd build; \
+      cmake -G Ninja -DENABLE_WERROR=1 -DHAVE_MPI="$MPI" -DHAVE_SSE4_1=1 .. \
+        || exit 1; ninja || exit 1; \
     elif [[ "$TRAVIS_OS_NAME" == "osx" ]]; then \
       ./util/build_osx.sh . build || exit 1; \
     else \

src/CMakeLists.txt

@@ -5,6 +5,7 @@ set(HAVE_NEON 0 CACHE BOOL "Have NEON")
 set(HAVE_TESTS 1 CACHE BOOL "Have Tests")
 set(HAVE_SHELLCHECK 1 CACHE BOOL "Have ShellCheck")
 set(HAVE_GPROF 0 CACHE BOOL "Have GPROF Profiler")
+set(ENABLE_WERROR 0 CACHE BOOL "Enable Warnings as Errors")
 
 include(AppendTargetProperty)
 
@@ -66,6 +67,11 @@ endif ()
 append_target_property(mmseqs-framework COMPILE_FLAGS ${MMSEQS_CXX_FLAGS} -fno-exceptions -pedantic -Wall -Wextra -Wdisabled-optimization)
 append_target_property(mmseqs-framework LINK_FLAGS ${MMSEQS_CXX_FLAGS} -fno-exceptions -pedantic -Wall -Wextra -Wdisabled-optimization)
 
+if (${ENABLE_WERROR})
+    append_target_property(mmseqs-framework COMPILE_FLAGS -Werror)
+    append_target_property(mmseqs-framework LINK_FLAGS -Werror)
+endif()
+
 if (CYGWIN OR ${HAVE_NEON})
     target_compile_definitions(mmseqs-framework PUBLIC -D_GNU_SOURCE=1)
 endif ()

src/commons/DBReader.cpp

@@ -163,7 +163,7 @@ template <typename T> bool DBReader<T>::open(int accessType){
         size_t prevOffset = 0; // makes 0 or empty string
         sortedByOffset = true;
         for (size_t i = 0; i < size; i++) {
-            sortedByOffset *= index[i].offset >= prevOffset;
+            sortedByOffset = sortedByOffset && index[i].offset >= prevOffset;
             prevOffset = index[i].offset;
         }
 

src/linclust/kmermatcher.h

@@ -12,9 +12,7 @@ struct KmerPosition {
     unsigned int id;
     unsigned short seqLen;
     short pos;
-    KmerPosition(){}
-    KmerPosition(size_t kmer, unsigned int id, unsigned short seqLen, short pos):
-            kmer(kmer), id(id), seqLen(seqLen), pos(pos) {}
+
     static bool compareRepSequenceAndIdAndPos(const KmerPosition &first, const KmerPosition &second){
         if(first.kmer < second.kmer )
             return true;

src/test/TestCounting.cpp

@@ -1,85 +1,29 @@
-#include <iostream>
-#include <list>
-#include <algorithm>
-#include <math.h>
-#include <CacheFriendlyOperations.h>
-#include <map>
-
-const char* binary_name = "test_counting";
+#include "Util.h"
 
 #include <iostream>
 #include <chrono>
-#include <ctime>
-#include <immintrin.h> // AVX
-
-void print128_num(__m128i var)
-{
-    uint8_t *val = (uint8_t*) &var;
-    printf("Numerical: %i %i %i %i %i %i %i %i %i %i %i %i %i %i %i %i \n",
-           val[0], val[1], val[2], val[3], val[4], val[5],
-           val[6], val[7], val[8], val[9], val[10], val[11],
-           val[12], val[13], val[14], val[15]);
-}
-// Compute reverse complement of k-mer in 2-bit-per-nucleotide encoding (A: 00, C: 01, T: 10, G: 11)
-uint64_t revComplement(const u_int64_t kmer, const int k) {
-    // broadcast 64bit to 128 bit
-    __m128i x = _mm_cvtsi64_si128(kmer);
-
-    // create lookup (set 16 bytes in 128 bit)
-    // a lookup entry at the index of two nucleotides (4 bit) describes the reverse
-    // complement of these two nucleotides in the higher 4 bits (lookup1) or in the
-    // lower 4 bits (lookup2)
-    __m128i lookup1 = _mm_set_epi8(0x50,0x10,0xD0,0x90,0x40,0x00,0xC0,0x80,0x70,
-                                   0x30,0xF0,0xB0,0x60,0x20,0xE0,0xA0);
-    __m128i lookup2 = _mm_set_epi8(0x05,0x01,0x0D,0x09,0x04,0x00,0x0C,0x08,0x07,
-                                   0x03,0x0F,0x0B,0x06,0x02,0x0E,0x0A);
-    // set upper 8 bytes to 0 and revert order of lower 8 bytes
-    __m128i upper = _mm_set_epi8(0xFF,0xFF,0xFF,0xFF,0xFF,0xFF,0xFF,0xFF,0,1,2,3,4,5,6,7);
 
-    __m128i kmer1 = _mm_and_si128(x, _mm_set1_epi8(0x0F)); // get lower 4 bits
-    __m128i kmer2 = _mm_and_si128(x, _mm_set1_epi8(0xF0)); // get higher 4 bits
+const char* binary_name = "test_counting";
 
-//    // shift right by 2 nucleotides
-//    print128_num(kmer2);
-//    kmer2 >>= 4;
-//    kmer2 = _mm_srli_epi64(kmer2, 4);
+//u_int64_t revcomp64_v2 (const u_int64_t& x, size_t sizeKmer)
+//{
+//    u_int64_t res = x;
 //
-//    print128_num(kmer2);
-//    std::cout << kmer2 << std::endl;
-    // use _mm_shuffle_epi8 to look up reverse complement
-    kmer1 =_mm_shuffle_epi8(lookup1, kmer1);
-    kmer2 = _mm_shuffle_epi8(lookup2, kmer2);
-
-    // _mm_or_si128: bitwise OR
-    x = _mm_or_si128(kmer1, kmer2);
-
-    // set upper 8 bytes to 0 and revert order of lower 8 bytes
-    x = _mm_shuffle_epi8(x, upper);
-
-    // shift out the unused nucleotide positions (1 <= k <=32 )
-    // broadcast 128 bit to 64 bit
-    return (((uint64_t)_mm_cvtsi128_si64(x)) >> (uint64_t)(64-2*k));
-}
-
-u_int64_t revcomp64_v2 (const u_int64_t& x, size_t sizeKmer)
-{
-    u_int64_t res = x;
-
-    res = ((res>> 2 & 0x3333333333333333) | (res & 0x3333333333333333) <<  2);
-    res = ((res>> 4 & 0x0F0F0F0F0F0F0F0F) | (res & 0x0F0F0F0F0F0F0F0F) <<  4);
-    res = ((res>> 8 & 0x00FF00FF00FF00FF) | (res & 0x00FF00FF00FF00FF) <<  8);
-    res = ((res>>16 & 0x0000FFFF0000FFFF) | (res & 0x0000FFFF0000FFFF) << 16);
-    res = ((res>>32 & 0x00000000FFFFFFFF) | (res & 0x00000000FFFFFFFF) << 32);
-    res = res ^ 0xAAAAAAAAAAAAAAAA;
-
-    return (res >> (2*( 32 - sizeKmer))) ;
-}
+//    res = ((res>> 2 & 0x3333333333333333) | (res & 0x3333333333333333) <<  2);
+//    res = ((res>> 4 & 0x0F0F0F0F0F0F0F0F) | (res & 0x0F0F0F0F0F0F0F0F) <<  4);
+//    res = ((res>> 8 & 0x00FF00FF00FF00FF) | (res & 0x00FF00FF00FF00FF) <<  8);
+//    res = ((res>>16 & 0x0000FFFF0000FFFF) | (res & 0x0000FFFF0000FFFF) << 16);
+//    res = ((res>>32 & 0x00000000FFFFFFFF) | (res & 0x00000000FFFFFFFF) << 32);
+//    res = res ^ 0xAAAAAAAAAAAAAAAA;
+//
+//    return (res >> (2*( 32 - sizeKmer))) ;
+//}
 
-int main(int argc, char ** avgv){
+int main(int, char **){
     auto start = std::chrono::system_clock::now();
     size_t revComp = 0;
     for(u_int64_t i = 0; i < 10001010101011; i++){
-        revComp += revComplement(i, 21);
+        revComp += Util::revComplement(i, 21);
     }
     auto end = std::chrono::system_clock::now();
     auto elapsed = end - start;