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fixes 'using namespace std' in header files and compilation on mac #95

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12 changes: 10 additions & 2 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -36,8 +36,16 @@ endif(COMPILATION_ARCH MATCHES "OFF")

if(ENABLE_AVX2 MATCHES "OFF")
message("Disabling AVX2 instructions")
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -mno-avx2")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mno-avx2")
# Only add -mno-avx2 for GCC or for Intel architectures where it's meaningful
if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU" OR
(NOT APPLE AND CMAKE_SYSTEM_PROCESSOR MATCHES "x86_64|AMD64"))
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -mno-avx2")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mno-avx2")
elseif(CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_SYSTEM_PROCESSOR MATCHES "x86_64|AMD64")
# For clang on x86_64, use -mno-avx2 but suppress the warning if it's unused
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wno-unused-command-line-argument -mno-avx2")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unused-command-line-argument -mno-avx2")
endif()
endif(ENABLE_AVX2 MATCHES "OFF")

# Manages build types
Expand Down
4 changes: 2 additions & 2 deletions src/Bifrost.cpp
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Expand Up @@ -333,7 +333,7 @@ bool check_ProgramOptions(CCDBG_Build_opt& opt) {
}
}

v_files = move(files_tmp);
v_files = std::move(files_tmp);

delete[] buffer;
};
Expand Down Expand Up @@ -672,7 +672,7 @@ int main(int argc, char **argv){
ColoredCDBG<>& ccdbg_a = (ccdbg1_len > ccdbg2_len) ? ccdbg1 : ccdbg2;
ColoredCDBG<>& ccdbg_b = (ccdbg1_len > ccdbg2_len) ? ccdbg2 : ccdbg1;

if (success) success = ccdbg_a.merge(move(ccdbg_b), lopt.nb_threads, lopt.verbose);
if (success) success = ccdbg_a.merge(std::move(ccdbg_b), lopt.nb_threads, lopt.verbose);

if (success) success = ccdbg_a.simplify(lopt.deleteIsolated, lopt.clipTips, lopt.verbose);
if (success) success = ccdbg_a.write(lopt.prefixFilenameOut, lopt.nb_threads, lopt.writeIndexFile, lopt.compressOutput, lopt.verbose);
Expand Down
10 changes: 6 additions & 4 deletions src/BitContainer.cpp
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@@ -1,5 +1,7 @@
#include "BitContainer.hpp"

using namespace std;

BitContainer::BitContainer() : setBits(localBitVector) {}

BitContainer::BitContainer(const BitContainer& o) {
Expand Down Expand Up @@ -580,7 +582,7 @@ void BitContainer::remove(const size_t pair_id) {

setBits = (reinterpret_cast<uintptr_t>(t_bmp.detach()) & pointerMask) | localTinyBitmap;

*this = move(new_uc);
*this = std::move(new_uc);
}
else setBits = (reinterpret_cast<uintptr_t>(t_bmp.detach()) & pointerMask) | localTinyBitmap;
}
Expand Down Expand Up @@ -630,7 +632,7 @@ void BitContainer::remove(const size_t pair_id) {

for (; it != it_end; ++it) new_uc.add(*it);

*this = move(new_uc);
*this = std::move(new_uc);
}
else if ((setBits & flagMask) == ptrBitmap) bitmap->r.runOptimize();
}
Expand Down Expand Up @@ -704,7 +706,7 @@ void BitContainer::removeSortedVector(const vector<uint32_t>& v) {

setBits = (reinterpret_cast<uintptr_t>(t_bmp.detach()) & pointerMask) | localTinyBitmap;

*this = move(new_uc);
*this = std::move(new_uc);
}
else setBits = (reinterpret_cast<uintptr_t>(t_bmp.detach()) & pointerMask) | localTinyBitmap;
}
Expand Down Expand Up @@ -752,7 +754,7 @@ void BitContainer::removeSortedVector(const vector<uint32_t>& v) {

for (const_iterator it = begin(), it_end = end(); it != it_end; ++it) new_uc.add(*it);

*this = move(new_uc);
*this = std::move(new_uc);
}
else if ((setBits & flagMask) == ptrBitmap) bitmap->r.runOptimize();
}
Expand Down
8 changes: 4 additions & 4 deletions src/BitContainer.hpp
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Expand Up @@ -103,8 +103,8 @@ class BitContainer {
size_t size() const;
inline size_t cardinality() const { return size(); }

bool write(ostream& stream_out) const;
bool read(istream& stream_in);
bool write(std::ostream& stream_out) const;
bool read(std::istream& stream_in);

size_t getSizeInBytes() const;

Expand All @@ -130,8 +130,8 @@ class BitContainer {

private:

void addSortedVector(const vector<uint32_t>& v);
void removeSortedVector(const vector<uint32_t>& v);
void addSortedVector(const std::vector<uint32_t>& v);
void removeSortedVector(const std::vector<uint32_t>& v);

inline void releaseMemory(){

Expand Down
18 changes: 9 additions & 9 deletions src/BlockedBloomFilter.cpp
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Expand Up @@ -27,7 +27,7 @@ BlockedBloomFilter::BlockedBloomFilter(const BlockedBloomFilter& o) : table_(n
}

BlockedBloomFilter::BlockedBloomFilter(BlockedBloomFilter&& o) : table_(o.table_), blocks_(o.blocks_), nb_bits_per_elem(o.nb_bits_per_elem),
k_(o.k_), M_u64(o.M_u64), seed1(o.seed1), seed2(o.seed2), ush(move(o.ush)) {
k_(o.k_), M_u64(o.M_u64), seed1(o.seed1), seed2(o.seed2), ush(std::move(o.ush)) {

o.table_ = nullptr;

Expand Down Expand Up @@ -80,7 +80,7 @@ BlockedBloomFilter& BlockedBloomFilter::operator=(BlockedBloomFilter&& o) {
seed1 = o.seed1;
seed2 = o.seed2;

ush = move(o.ush);
ush = std::move(o.ush);

o.table_ = nullptr;

Expand Down Expand Up @@ -160,7 +160,7 @@ DualBlockedBloomFilter BlockedBloomFilter::transferToDBBF(const uint64_t idx_bbf
dbbf.seed1 = seed1;
dbbf.seed2 = seed2;

dbbf.ush[idx_bbf_norm] = move(ush);
dbbf.ush[idx_bbf_norm] = std::move(ush);
dbbf.table_ = new DualBlockedBloomFilter::BBF_Block[blocks_ << 1];

for (size_t i = 0; i < blocks_; ++i) {
Expand Down Expand Up @@ -622,7 +622,7 @@ DualBlockedBloomFilter::DualBlockedBloomFilter(const DualBlockedBloomFilter& o)
}

DualBlockedBloomFilter::DualBlockedBloomFilter(DualBlockedBloomFilter&& o) : table_(o.table_), blocks_(o.blocks_), nb_bits_per_elem(o.nb_bits_per_elem),
k_(o.k_), M_u64(o.M_u64), seed1(o.seed1), seed2(o.seed2), ush{move(o.ush[0]), move(o.ush[1])} {
k_(o.k_), M_u64(o.M_u64), seed1(o.seed1), seed2(o.seed2), ush{std::move(o.ush[0]), std::move(o.ush[1])} {

o.table_ = nullptr;

Expand All @@ -645,8 +645,8 @@ DualBlockedBloomFilter& DualBlockedBloomFilter::operator=(const DualBlockedBloom
seed1 = o.seed1;
seed2 = o.seed2;

ush[0] = o.ush[0];
ush[1] = o.ush[1];
ush[0] = std::move(o.ush[0]);
ush[1] = std::move(o.ush[1]);

if (blocks_ != 0) {

Expand Down Expand Up @@ -677,8 +677,8 @@ DualBlockedBloomFilter& DualBlockedBloomFilter::operator=(DualBlockedBloomFilter
seed1 = o.seed1;
seed2 = o.seed2;

ush[0] = move(o.ush[0]);
ush[1] = move(o.ush[1]);
ush[0] = std::move(o.ush[0]);
ush[1] = std::move(o.ush[1]);

o.table_ = nullptr;

Expand Down Expand Up @@ -927,7 +927,7 @@ BlockedBloomFilter DualBlockedBloomFilter::transferToBBF(const uint64_t idx_bbf)
bbf.seed2 = seed2;
bbf.M_u64 = M_u64;

bbf.ush = move(ush[idx_bbf_norm]);
bbf.ush = std::move(ush[idx_bbf_norm]);
bbf.table_ = new BlockedBloomFilter::BBF_Block[blocks_];

for (size_t i = 0; i < blocks_; ++i) {
Expand Down
14 changes: 8 additions & 6 deletions src/ColorSet.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,8 @@

#include "ColorSet.hpp"

using namespace std;

UnitigColors::UnitigColors() : setBits(localBitVector) {}

UnitigColors::UnitigColors(const UnitigColors& o) {
Expand Down Expand Up @@ -721,7 +723,7 @@ void UnitigColors::remove(const UnitigMapBase& um, const size_t color_id) {

setBits = (reinterpret_cast<uintptr_t>(t_bmp.detach()) & pointerMask) | localTinyBitmap;

*this = move(new_uc);
*this = std::move(new_uc);
}
else setBits = (reinterpret_cast<uintptr_t>(t_bmp.detach()) & pointerMask) | localTinyBitmap;
}
Expand Down Expand Up @@ -771,7 +773,7 @@ void UnitigColors::remove(const UnitigMapBase& um, const size_t color_id) {

for (; it != it_end; ++it) new_uc.add(it.getColorID() * um_km_sz + it.getKmerPosition());

*this = move(new_uc);
*this = std::move(new_uc);
}
else if ((setBits & flagMask) == ptrBitmap) bitmap->r.runOptimize();
}
Expand Down Expand Up @@ -1097,8 +1099,8 @@ bool UnitigColors::optimizeFullColors(const UnitigMapBase& um){

UnitigColors* uc = new UnitigColors[2];

uc[0] = move(full_uc);
uc[1] = move(non_full_uc);
uc[0] = std::move(full_uc);
uc[1] = std::move(non_full_uc);

setBits = (reinterpret_cast<uintptr_t>(uc) & pointerMask) | ptrUnitigColors;

Expand All @@ -1121,8 +1123,8 @@ UnitigColors UnitigColors::makeFullColors(const UnitigMapBase& um) const {

UnitigColors* uc = new UnitigColors[2];

uc[0] = move(full_uc);
uc[1] = move(non_full_uc);
uc[0] = std::move(full_uc);
uc[1] = std::move(non_full_uc);

new_uc.setBits = (reinterpret_cast<uintptr_t>(uc) & pointerMask) | ptrUnitigColors;

Expand Down
12 changes: 6 additions & 6 deletions src/ColorSet.hpp
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Expand Up @@ -29,12 +29,12 @@ class UnitigColors {

public:

typedef pair<UnitigColors, size_t> SharedUnitigColors;
typedef std::pair<UnitigColors, size_t> SharedUnitigColors;

/** @class UnitigColors_const_iterator
* @brief See UnitigColors::const_iterator
*/
class UnitigColors_const_iterator : public std::iterator<std::forward_iterator_tag, pair<size_t, size_t>> {
class UnitigColors_const_iterator : public std::iterator<std::forward_iterator_tag, std::pair<size_t, size_t>> {

friend class UnitigColors;

Expand Down Expand Up @@ -70,9 +70,9 @@ class UnitigColors {
* @return a pair p of integers representing the position of a k-mer in the unitig (p.first)
* and the ID of the color associated with the k-mer at the given position (p.second).
*/
inline pair<size_t, size_t> operator*() const {
inline std::pair<size_t, size_t> operator*() const {

return make_pair(ck_id % um_sz, ck_id / um_sz);
return std::make_pair(ck_id % um_sz, ck_id / um_sz);
}

/**
Expand Down Expand Up @@ -281,15 +281,15 @@ class UnitigColors {
* opened prior to the call of this function and it won't be closed by this function.
* @return a boolean indicating if the write was successful.
*/
bool write(ostream& stream_out, const bool copy_UnitigColors = true) const;
bool write(std::ostream& stream_out, const bool copy_UnitigColors = true) const;

/**
* Read a UnitigColors from a stream.
* @param stream_in is an in stream from which the UnitigColors must be read. It must be
* opened prior to the call of this function and it won't be closed by this function.
* @return a boolean indicating if the write was successful.
*/
bool read(istream& stream_in);
bool read(std::istream& stream_in);

/**
* Size of the UnitigColors in bytes.
Expand Down
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