% cumulative self self total time seconds seconds calls ms/call ms/call name 11.81 196.60 196.60 myList::checkString(std::string const&, int, int) 10.12 364.96 168.36 missMatchNumber(std::string, std::string, int, int) 9.88 529.33 164.36 138559832 0.00 0.00 _fini 7.56 655.20 125.88 3937446119 0.00 0.00 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) 6.83 768.90 113.70 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) 5.79 865.33 96.43 1103210846 0.00 0.00 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) 4.71 943.64 78.31 3693798105 0.00 0.00 ShortyString::ShortyString(std::string const&, int) 3.96 1009.49 65.84 529397792 0.00 0.01 std::vector >::_M_check_len(unsigned int, char const*) const 2.57 1052.33 42.84 1397173708 0.00 0.00 std::vector >::push_back(int const&) 2.08 1086.89 34.57 1198094656 0.00 0.00 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) 1.89 1118.40 31.51 1663943608 0.00 0.00 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const 1.61 1145.26 26.86 TrieNode::addToTrie(readPointer, int) 1.55 1171.13 25.87 3634312314 0.00 0.00 UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) 1.18 1190.78 19.64 readPointer::stringData() 1.13 1209.57 18.79 getIndex(char) 1.08 1227.47 17.91 1412210695 0.00 0.00 ReadSeededFastaFile(std::string const&, std::vector >*) 0.91 1242.62 15.14 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator*() const 0.81 1256.12 13.50 3086620571 0.00 0.00 ShortyString::~ShortyString() 0.66 1267.08 10.96 27931064 0.00 0.00 std::vector >::_M_check_len(unsigned int, char const*) const 0.61 1277.25 10.17 3688985037 0.00 0.00 ShortyString::ShortyString(std::string const&, std::vector > const&) 0.56 1286.56 9.31 3222388240 0.00 0.00 std::deque >::deque(std::deque > const&) 0.53 1295.43 8.87 2635651173 0.00 0.00 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, UtilsMath::median_event_point const&) 0.53 1304.27 8.84 4097652014 0.00 0.00 Contig* std::__copy_move_backward::__copy_move_b(Contig*, Contig*, Contig*) 0.52 1312.94 8.67 __gnu_cxx::new_allocator >::construct(triple*, triple const&) 0.49 1321.08 8.14 842549144 0.00 0.00 void std::__introsort_loop<__gnu_cxx::__normal_iterator > >, int>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int) 0.48 1329.08 8.00 47882985 0.00 0.00 std::vector, std::allocator > >::_M_fill_insert(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, unsigned int, triple const&) 0.47 1336.95 7.87 3187563338 0.00 0.00 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_unique(std::pair const&) 0.46 1344.58 7.63 3971005539 0.00 0.00 SeededRead** std::__copy_move_backward_a2(SeededRead**, SeededRead**, SeededRead**) 0.44 1351.87 7.29 844621234 0.00 0.00 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) 0.44 1359.13 7.26 3541563139 0.00 0.00 Contig::~Contig() 0.43 1366.30 7.17 std::vector >::begin() 0.43 1373.44 7.15 2544037281 0.00 0.00 std::_Deque_iterator std::__uninitialized_copy_a, std::_Deque_iterator, SeededRead>(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator, std::allocator&) 0.38 1379.74 6.29 1724816198 0.00 0.00 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) 0.37 1385.97 6.23 readPointer::readPointer() 0.36 1392.01 6.04 3674274660 0.00 0.00 void std::__final_insertion_sort<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) 0.36 1397.98 5.97 std::_Vector_base >::_M_allocate(unsigned int) 0.36 1403.94 5.96 1300701146 0.00 0.00 std::vector >::operator=(std::vector > const&) 0.36 1409.88 5.94 mar_types* std::__copy_move_backward_a(mar_types*, mar_types*, mar_types*) 0.35 1415.77 5.89 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, Vote const&) 0.34 1421.46 5.69 649493343 0.00 0.00 UtilsFile::OpenFile(std::string const&, std::string const&) 0.33 1426.95 5.50 730437480 0.00 0.00 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) 0.33 1432.43 5.48 101771331 0.00 0.00 Vote* std::__copy_move::__copy_m(Vote const*, Vote const*, Vote*) 0.32 1437.79 5.36 2323744019 0.00 0.00 std::_Deque_base >::~_Deque_base() 0.32 1443.04 5.25 886464451 0.00 0.00 triple* std::__uninitialized_copy_a*, triple*, triple >(triple*, triple*, triple*, std::allocator >&) 0.31 1448.26 5.22 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::__normal_iterator(triple* const&) 0.30 1453.26 5.00 1416853474 0.00 0.00 ReadProcessor::ReadProcessor(std::string const&) 0.29 1458.13 4.87 2734359181 0.00 0.00 std::deque >::_M_destroy_data(std::_Deque_iterator, std::_Deque_iterator, std::allocator const&) 0.29 1462.96 4.83 2166422463 0.00 0.00 SeededRead** std::__copy_move_a2(SeededRead**, SeededRead**, SeededRead**) 0.29 1467.79 4.83 1644735383 0.00 0.00 std::_Vector_base, std::allocator > >::~_Vector_base() 0.27 1472.32 4.53 730437481 0.00 0.00 std::_Vector_base >::~_Vector_base() 0.26 1476.59 4.27 1084630574 0.00 0.00 void std::__final_insertion_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) 0.25 1480.76 4.17 std::vector >::vector() 0.24 1484.80 4.04 1033249085 0.00 0.00 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) 0.24 1488.80 4.00 318999000 0.00 0.00 UtilsFile::Log(std::ostream*, std::string const&) 0.24 1492.71 3.92 625631572 0.00 0.00 std::_Rb_tree, std::less, std::allocator >::end() const 0.21 1496.19 3.48 1270915671 0.00 0.00 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) 0.20 1499.58 3.38 1234869252 0.00 0.00 void std::_Destroy(SeededRead*) 0.19 1502.71 3.14 1914486784 0.00 0.00 bool std::operator==(std::_Deque_iterator const&, std::_Deque_iterator const&) 0.19 1505.86 3.14 1180800494 0.00 0.00 std::_Rb_tree, std::less, std::allocator >::begin() const 0.19 1508.97 3.12 1523755262 0.00 0.00 void std::__introsort_loop<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj) 0.18 1512.02 3.04 1623116001 0.00 0.00 std::deque >::_M_reserve_map_at_back(unsigned int) 0.18 1515.06 3.04 857768503 0.00 0.00 Vote* std::__copy_move::__copy_m(Vote*, Vote*, Vote*) 0.18 1518.06 3.00 std::vector >::size() const 0.18 1521.01 2.94 std::vector, std::allocator > >::~vector() 0.17 1523.90 2.90 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::~_Rb_tree() 0.17 1526.72 2.82 873253357 0.00 0.00 std::pair* std::copy_backward*, std::pair*>(std::pair*, std::pair*, std::pair*) 0.15 1529.29 2.57 1735969416 0.00 0.00 OverlapGraph::ContigInfo* std::copy_backward(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) 0.15 1531.83 2.54 858076371 0.00 0.00 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const 0.15 1534.36 2.52 std::vector >::operator[](unsigned int) 0.14 1536.64 2.29 1526430335 0.00 0.00 std::deque >::end() const 0.14 1538.93 2.29 1180800494 0.00 0.00 std::vector, std::allocator > >::end() 0.13 1541.16 2.23 myList::myList(readPointer) 0.13 1543.38 2.21 115695890 0.00 0.00 std::vector >::operator=(std::vector > const&) 0.13 1545.58 2.20 std::vector >::~vector() 0.13 1547.74 2.17 myList::size() 0.13 1549.90 2.15 385741013 0.00 0.00 std::_Vector_base >::~_Vector_base() 0.13 1551.99 2.09 539451719 0.00 0.00 std::list, std::allocator > >::operator=(std::list, std::allocator > > const&) 0.12 1554.02 2.03 bool __gnu_cxx::operator!= > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) 0.12 1556.01 1.99 NavidIntIntStruct::NavidIntIntStruct() 0.11 1557.87 1.86 148011011 0.00 0.00 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) 0.11 1559.66 1.79 std::vector, std::allocator > >::operator=(std::vector, std::allocator > > const&) 0.11 1561.43 1.77 1755802966 0.00 0.00 std::vector, std::allocator > >::max_size() const 0.11 1563.20 1.77 myList::destruct() 0.11 1564.96 1.76 603285812 0.00 0.00 triple* std::__copy_move_backward::__copy_move_b*, triple*>(triple*, triple*, triple*) 0.10 1566.70 1.74 1506635566 0.00 0.00 std::pair* std::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) 0.10 1568.44 1.74 304749023 0.00 0.00 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree_impl::_M_initialize() 0.10 1570.12 1.68 474907109 0.00 0.00 __static_initialization_and_destruction_0(int, int) 0.10 1571.73 1.61 628666150 0.00 0.00 void std::sort<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) 0.10 1573.34 1.60 myList::~myList() 0.10 1574.92 1.58 529397792 0.00 0.00 std::_Rb_tree, std::less, std::allocator >::begin() 0.09 1576.43 1.51 475846366 0.00 0.00 OverlapGraph::AllocateData() 0.09 1577.94 1.51 triple* std::copy*, triple*>(triple*, triple*, triple*) 0.09 1579.44 1.50 127331022 0.00 0.00 std::vector, std::allocator > >::_M_erase_at_end(std::pair*) 0.09 1580.93 1.49 std::_Rb_tree, std::less, std::allocator >::~_Rb_tree() 0.09 1582.37 1.44 606974957 0.00 0.00 void std::iter_swap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) 0.08 1583.77 1.40 __gnu_cxx::new_allocator::max_size() const 0.08 1585.13 1.36 std::pair* std::vector, std::allocator > >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > >(unsigned int, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >) 0.08 1586.44 1.31 109105613 0.00 0.00 std::_Rb_tree, std::less, std::allocator >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, int const&) 0.08 1587.74 1.30 279401951 0.00 0.00 bool __gnu_cxx::operator< *, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) 0.07 1588.98 1.25 636508560 0.00 0.00 void std::__heap_select<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) 0.07 1590.23 1.25 507052032 0.00 0.00 __gnu_cxx::new_allocator > >::allocate(unsigned int, void const*) 0.07 1591.47 1.24 __gnu_cxx::__normal_iterator > >::base() const 0.07 1592.70 1.23 730437481 0.00 0.00 void std::_Destroy*, std::pair >(std::pair*, std::pair*, std::allocator >&) 0.07 1593.93 1.23 448288348 0.00 0.00 void std::__adjust_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) 0.07 1595.14 1.22 __gnu_cxx::new_allocator > >::new_allocator() 0.07 1596.35 1.20 UtilsFile::CloseFile(std::basic_fstream >*) 0.07 1597.52 1.17 std::set, OverlapGraph::IntPairEq, std::allocator > >::set() 0.07 1598.62 1.10 std::allocator >::allocator > >(std::allocator > > const&) 0.06 1599.69 1.07 2674989 0.00 0.07 OverlapGraph::MergeReads(std::vector, std::allocator > > const&) 0.06 1600.76 1.07 __static_initialization_and_destruction_0(int, int) 0.06 1601.82 1.06 void std::_Destroy(mar_types*, mar_types*, std::allocator&) 0.06 1602.84 1.02 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_get_Node_allocator() const 0.06 1603.85 1.00 std::pair::pair() 0.06 1604.84 0.99 184878960 0.00 0.00 std::vector >::push_back(UtilsMath::median_event_point const&) 0.06 1605.83 0.99 385741013 0.00 0.00 __gnu_cxx::new_allocator::construct(UtilsMath::median_event_point*, UtilsMath::median_event_point const&) 0.06 1606.77 0.94 std::vector >::push_back(OverlapGraph::ContigInfo const&) 0.05 1607.68 0.91 std::vector, std::allocator > >::vector() 0.05 1608.58 0.90 77640232 0.00 0.00 bool __gnu_cxx::operator==*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) 0.05 1609.48 0.90 7737 0.12 45.34 OverlapGraph::BuildGraph() 0.05 1610.36 0.88 529397792 0.00 0.00 std::_Rb_tree_iterator::operator==(std::_Rb_tree_iterator const&) const 0.05 1611.19 0.83 void std::__reverse<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::random_access_iterator_tag) 0.05 1612.02 0.82 101771331 0.00 0.00 std::vector, std::allocator > >::push_back(std::pair const&) 0.05 1612.84 0.82 __gnu_cxx::__normal_iterator > >::operator*() const 0.05 1613.64 0.81 OverlapGraph::ContigInfo* std::__uninitialized_move_a >(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, std::allocator&) 0.05 1614.45 0.81 std::vector >::begin() 0.05 1615.26 0.81 std::_Rb_tree, std::less, std::allocator >::_Rb_tree_impl, false>::~_Rb_tree_impl() 0.05 1616.05 0.79 __static_initialization_and_destruction_0(int, int) 0.05 1616.84 0.79 std::vector >::swap(std::vector >&) 0.05 1617.62 0.79 int* std::uninitialized_copy(int*, int*, int*) 0.05 1618.40 0.78 __gnu_cxx::__normal_iterator > >::base() const 0.05 1619.16 0.76 2422750 0.00 0.00 mar_types* std::copy(mar_types*, mar_types*, mar_types*) 0.05 1619.92 0.76 std::_Vector_base, std::allocator > >::_M_get_Tp_allocator() 0.05 1620.67 0.75 std::back_insert_iterator > > std::__copy_move_a2 > >, std::back_insert_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::back_insert_iterator > >) 0.04 1621.41 0.74 __gnu_cxx::new_allocator::new_allocator(__gnu_cxx::new_allocator const&) 0.04 1622.15 0.74 std::_Vector_base >::_M_get_Tp_allocator() 0.04 1622.88 0.73 12451411 0.00 0.00 main 0.04 1623.61 0.72 77624758 0.00 0.00 Vote::operator+=(Vote const&) 0.04 1624.29 0.69 275580450 0.00 0.00 std::deque >::begin() 0.04 1624.96 0.67 606974957 0.00 0.00 std::__niter_base<__gnu_cxx::__normal_iterator > >, true>::__b(__gnu_cxx::__normal_iterator > >) 0.04 1625.62 0.66 void std::__reverse<__gnu_cxx::__normal_iterator >(__gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator, std::random_access_iterator_tag) 0.04 1626.28 0.66 void std::sort_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) 0.04 1626.92 0.65 57785273 0.00 0.00 TrieNode::searchWithErrorWholeSeed(std::string const&, int, int) 0.04 1627.58 0.65 std::pair* std::__copy_move_backward_a*, std::pair*>(std::pair*, std::pair*, std::pair*) 0.04 1628.17 0.60 196537847 0.00 0.00 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) 0.04 1628.78 0.60 std::allocator >::allocator() 0.04 1629.37 0.59 537187764 0.00 0.00 std::_Vector_base, std::allocator > >::_Vector_impl::_Vector_impl() 0.04 1629.95 0.58 __gnu_cxx::new_allocator::destroy(OverlapGraph::ContigInfo*) 0.03 1630.53 0.58 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree_impl::~_Rb_tree_impl() 0.03 1631.09 0.56 332322227 0.00 0.00 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) 0.03 1631.63 0.55 518771239 0.00 0.00 std::_Rb_tree, std::less, std::allocator >::_M_put_node(std::_Rb_tree_node*) 0.03 1632.17 0.54 529397792 0.00 0.00 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator--() 0.03 1632.71 0.54 116345246 0.00 0.00 std::deque >::~deque() 0.03 1633.25 0.54 362166824 0.00 0.00 __gnu_cxx::new_allocator::construct(std::string*, std::string const&) 0.03 1633.78 0.53 161323238 0.00 0.00 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) 0.03 1634.31 0.53 236425176 0.00 0.00 __gnu_cxx::__enable_if::__value, void>::__type std::__fill_a(char*, char*, int const&) 0.03 1634.83 0.53 std::vector >::swap(std::vector >&) 0.03 1635.35 0.52 std::vector, std::allocator > >::~vector() 0.03 1635.87 0.52 __gnu_cxx::__normal_iterator > >::difference_type __gnu_cxx::operator- > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) 0.03 1636.38 0.52 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::base() const 0.03 1636.89 0.51 __gnu_cxx::__normal_iterator > >::__normal_iterator(OverlapGraph::ContigInfo* const&) 0.03 1637.39 0.50 97728652 0.00 0.00 void std::__push_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) 0.03 1637.89 0.50 75448568 0.00 0.00 void std::swap >(triple&, triple&) 0.03 1638.38 0.49 408260573 0.00 0.00 std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) 0.03 1638.86 0.47 std::_Rb_tree_iterator::_Rb_tree_iterator(std::_Rb_tree_node*) 0.03 1639.32 0.46 std::vector, std::allocator > >::size() const 0.03 1639.75 0.43 OverlapGraph::IntPairEq::operator()(std::pair const&, std::pair const&) const 0.03 1640.18 0.43 std::_Vector_base >::_M_get_Tp_allocator() const 0.03 1640.60 0.42 463889692 0.00 0.00 void std::_Destroy_aux::__destroy(Contig*, Contig*) 0.02 1641.01 0.41 void std::reverse<__gnu_cxx::__normal_iterator >(__gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator) 0.02 1641.40 0.40 OverlapGraph::ContigInfo* std::__copy_move_backward_a2(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) 0.02 1641.80 0.40 317564878 0.00 0.00 std::list, std::allocator > >::_M_check_equal_allocators(std::list, std::allocator > >&) 0.02 1642.19 0.40 void std::_Destroy(UtilsMath::median_event_point*, UtilsMath::median_event_point*, std::allocator&) 0.02 1642.58 0.38 77934596 0.00 0.00 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair const&) 0.02 1642.95 0.38 48124627 0.00 0.00 triple* std::__uninitialized_copy::uninitialized_copy*, triple*>(triple*, triple*, triple*) 0.02 1643.34 0.38 48116890 0.00 0.00 std::vector >::push_back(RawRead const&) 0.02 1643.71 0.38 __gnu_cxx::__normal_iterator > >::base() const 0.02 1644.06 0.34 TrieNode::~TrieNode() 0.02 1644.38 0.33 271331188 0.00 0.00 __static_initialization_and_destruction_0(int, int) 0.02 1644.71 0.33 55809948 0.00 0.00 std::_Deque_iterator::_M_set_node(SeededRead**) 0.02 1645.05 0.33 std::vector, std::allocator > >::~vector() 0.02 1645.37 0.32 96299604 0.00 0.00 std::vector, std::allocator > >::_M_erase_at_end(std::pair*) 0.02 1645.68 0.32 48149802 0.00 0.00 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) 0.02 1646.01 0.32 std::vector >::~vector() 0.02 1646.31 0.30 __gnu_cxx::new_allocator >::~new_allocator() 0.02 1646.60 0.29 111619896 0.00 0.00 std::_Deque_base >::_M_allocate_node() 0.02 1646.88 0.29 std::basic_string, std::allocator > std::operator+, std::allocator >(std::basic_string, std::allocator > const&, char const*) 0.02 1647.17 0.28 std::_Rb_tree, std::less, std::allocator >::_S_key(std::_Rb_tree_node const*) 0.02 1647.45 0.28 771482026 0.00 0.00 std::__niter_base::__b(mar_types*) 0.02 1647.73 0.28 std::vector >::max_size() const 0.02 1647.99 0.26 158981148 0.00 0.00 operator<<(std::ostream&, ShortyString const&) 0.02 1648.25 0.26 int* std::__copy_move_a2 > >, int*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int*) 0.01 1648.49 0.24 25559691 0.00 0.00 std::deque >::end() 0.01 1648.73 0.24 std::_Vector_base >::_M_get_Tp_allocator() 0.01 1648.96 0.23 155249516 0.00 0.00 std::_List_iterator >::operator++() 0.01 1649.19 0.23 96233780 0.00 0.00 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) 0.01 1649.42 0.23 9651173 0.00 0.00 std::_Vector_base >::_Vector_impl::_Vector_impl() 0.01 1649.65 0.23 ReadProcessor::TotalPairs() const 0.01 1649.87 0.22 TrieNode::Insert(int, mar_types) 0.01 1650.08 0.21 1056643 0.00 0.00 std::vector, std::allocator > >::operator=(std::vector, std::allocator > > const&) 0.01 1650.29 0.21 std::pair* std::copy*, std::pair*>(std::pair*, std::pair*, std::pair*) 0.01 1650.49 0.20 92439480 0.00 0.00 global constructors keyed to _ZN12ShortyStringC2Ev 0.01 1650.69 0.20 28266 0.01 15.48 Assembler::MakeContigs(bool, Cluster const&, SeededRead const&) 0.01 1650.88 0.19 std::less::operator()(int const&, int const&) const 0.01 1651.07 0.19 std::vector >::push_back(Contig const&) 0.01 1651.26 0.18 int* std::__copy_move_a(int const*, int const*, int*) 0.01 1651.43 0.18 55809948 0.00 0.00 std::_Vector_base, std::allocator > >::_Vector_impl::~_Vector_impl() 0.01 1651.61 0.17 OverlapGraph::ContigInfo::ContigInfo(ShortyString const&, int, int, int, mar_types) 0.01 1651.78 0.17 __gnu_cxx::__normal_iterator > >::difference_type __gnu_cxx::operator- > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) 0.01 1651.95 0.17 std::_Deque_iterator::_Deque_iterator(std::_Deque_iterator const&) 0.01 1652.12 0.17 __gnu_cxx::__enable_if::__value, void>::__type std::__fill_a(int*, int*, int const&) 0.01 1652.28 0.16 void std::_Destroy_aux::__destroy >(std::_Deque_iterator, std::_Deque_iterator) 0.01 1652.43 0.15 std::stack > >::empty() const 0.01 1652.59 0.15 38781760 0.00 0.00 std::_Rb_tree, std::less, std::allocator >::_M_create_node(int const&) 0.01 1652.73 0.15 44790 0.00 0.00 mar_types* std::__copy_move_a2 > >, mar_types*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*) 0.01 1652.88 0.14 __gnu_cxx::__normal_iterator > >::operator*() const 0.01 1653.02 0.14 55809948 0.00 0.00 int* std::__copy_move_backward_a(int*, int*, int*) 0.01 1653.16 0.14 43219050 0.00 0.00 std::vector >::~vector() 0.01 1653.30 0.14 ShortyString::Votes(std::vector > const&) 0.01 1653.44 0.14 OverlapGraph::ContigInfo::size() const 0.01 1653.58 0.14 std::vector, std::allocator > >::push_back(triple const&) 0.01 1653.72 0.14 void std::_Destroy<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::allocator >&) 0.01 1653.86 0.14 77624758 0.00 0.00 std::__niter_base<__gnu_cxx::__normal_iterator > >, true>::__b(__gnu_cxx::__normal_iterator > >) 0.01 1653.99 0.14 std::_Rb_tree, std::less, std::allocator >::_M_end() 0.01 1654.12 0.13 66875224 0.00 0.00 UtilsString::OverlapFromCommonReadMapping(ShortyString const&, ShortyString const&, std::vector, std::allocator > > const&, std::vector, std::allocator > > const&, ReadProcessor const*, int*, int*, ShortyString*) 0.01 1654.25 0.13 48149802 0.00 0.00 std::vector, std::allocator > >::end() const 0.01 1654.38 0.13 28236462 0.00 0.00 std::_Vector_base >::_Vector_base(unsigned int, std::allocator const&) 0.01 1654.51 0.13 21447747 0.00 0.00 std::vector >::push_back(std::string const&) 0.01 1654.63 0.12 std::stack > >::stack(std::deque > const&) 0.01 1654.76 0.12 237084657 0.00 0.00 std::__niter_base::__b(char*) 0.01 1654.88 0.12 97678121 0.00 0.00 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) 0.01 1654.99 0.12 87014606 0.00 0.00 Hash::Insert(std::string const&, int, int, int, int) 0.01 1655.12 0.12 19302346 0.00 0.00 triple* std::__copy_move_backward_a2*, triple*>(triple*, triple*, triple*) 0.01 1655.23 0.12 std::vector >::size() const 0.01 1655.36 0.12 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const 0.01 1655.47 0.12 std::_Vector_base >::_Vector_base() 0.01 1655.60 0.12 void std::_Destroy<__gnu_cxx::__normal_iterator > >, int>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::allocator&) 0.01 1655.71 0.12 58525952 0.00 0.00 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_put_node(std::_Rb_tree_node >*) 0.01 1655.83 0.12 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) 0.01 1655.93 0.11 58947341 0.00 0.00 Contig::Contig(Contig const&) 0.01 1656.05 0.11 9412154 0.00 0.00 void std::__unguarded_linear_insert<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj) 0.01 1656.15 0.11 7406691 0.00 0.00 __static_initialization_and_destruction_0(int, int) 0.01 1656.27 0.11 44790 0.00 0.01 Contig* std::__uninitialized_copy_a(Contig*, Contig*, Contig*, std::allocator&) 0.01 1656.38 0.11 std::vector, std::allocator > >::vector() 0.01 1656.48 0.11 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree_impl::_Rb_tree_impl() 0.01 1656.60 0.11 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) 0.01 1656.70 0.10 184878960 0.00 0.00 __gnu_cxx::new_allocator >::max_size() const 0.01 1656.81 0.10 std::allocator >::~allocator() 0.01 1656.91 0.10 std::stack > >::top() 0.01 1657.01 0.10 77624758 0.00 0.00 std::list, std::allocator > >::_M_erase(std::_List_iterator >) 0.01 1657.11 0.10 67677006 0.00 0.00 std::list, std::allocator > >::begin() 0.01 1657.21 0.10 16982099 0.00 0.00 mar_types* std::copy<__gnu_cxx::__normal_iterator > >, mar_types*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*) 0.01 1657.31 0.10 684149 0.00 0.00 ReadProcessor::GetMarLen(int, mar_types) const 0.01 1657.41 0.10 __gnu_cxx::new_allocator >::new_allocator() 0.01 1657.51 0.10 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator++() 0.01 1657.61 0.10 std::_Vector_base >::_Vector_base() 0.01 1657.71 0.10 OverlapGraph::ContigInfo* std::__uninitialized_copy_a(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, std::allocator&) 0.01 1657.80 0.09 77624758 0.00 0.00 void std::fill(char*, char*, int const&) 0.01 1657.89 0.09 21589830 0.00 0.00 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::~_Rb_tree() 0.01 1657.98 0.09 19323731 0.00 0.00 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) 0.01 1658.07 0.09 std::_Rb_tree, std::less, std::allocator >::_M_destroy_node(std::_Rb_tree_node*) 0.01 1658.15 0.09 10409062 0.00 0.00 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::get_allocator() const 0.01 1658.24 0.09 std::vector >::size() const 0.01 1658.33 0.09 std::vector >::operator[](unsigned int) 0.00 1658.40 0.08 47060770 0.00 0.00 Contig* std::__uninitialized_copy::uninitialized_copy(Contig*, Contig*, Contig*) 0.00 1658.48 0.08 11627676 0.00 0.00 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, RawRead const&) 0.00 1658.57 0.08 446402 0.00 0.02 __gnu_cxx::__normal_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) 0.00 1658.64 0.08 15474 0.01 0.01 OverlapGraph::Traverse(int, int, int, int) 0.00 1658.72 0.08 13130 0.01 0.30 Trie::Insert(std::string const&, int, mar_types) 0.00 1658.81 0.08 std::__niter_base<__gnu_cxx::__normal_iterator > >, true>::__b(__gnu_cxx::__normal_iterator > >) 0.00 1658.88 0.07 96407108 0.00 0.00 std::_Rb_tree, std::less, std::allocator >::get_allocator() const 0.00 1658.95 0.07 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator*() const 0.00 1659.03 0.07 std::vector, std::allocator > >::size() const 0.00 1659.11 0.07 std::_Vector_base, std::allocator > >::_M_deallocate(std::pair*, unsigned int) 0.00 1659.18 0.07 std::set, std::allocator >::set() 0.00 1659.25 0.07 55809948 0.00 0.00 void std::_Destroy*>(std::pair*, std::pair*) 0.00 1659.32 0.07 55059010 0.00 0.00 std::_Deque_base >::_M_initialize_map(unsigned int) 0.00 1659.39 0.07 21589830 0.00 0.00 Vote* std::copy(Vote*, Vote*, Vote*) 0.00 1659.46 0.07 9177919 0.00 0.00 std::vector >::end() 0.00 1659.53 0.07 6533878 0.00 0.00 Contig::operator=(Contig const&) 0.00 1659.60 0.07 std::allocator > >::allocator() 0.00 1659.67 0.07 std::_Vector_base, std::allocator > >::_Vector_impl::_Vector_impl() 0.00 1659.74 0.07 std::_Vector_base, std::allocator > >::_Vector_base() 0.00 1659.81 0.07 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_end() 0.00 1659.88 0.07 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) 0.00 1659.94 0.07 77624758 0.00 0.00 std::list, std::allocator > >::empty() const 0.00 1660.01 0.07 std::stack > >::pop() 0.00 1660.07 0.06 101771331 0.00 0.00 std::_Vector_base >::_Vector_impl::~_Vector_impl() 0.00 1660.13 0.06 58246520 0.00 0.00 std::vector >::push_back(Vote const&) 0.00 1660.19 0.06 48023296 0.00 0.00 __gnu_cxx::new_allocator::construct(Contig*, Contig const&) 0.00 1660.25 0.06 3393446 0.00 0.00 TrieNode::searchWithErrorAllowedNonRecursive(std::string const&, int) 0.00 1660.31 0.06 ShortyString::Str(std::string const&) 0.00 1660.37 0.06 bool __gnu_cxx::operator== > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) 0.00 1660.43 0.06 std::_Vector_base, std::allocator > >::_M_deallocate(std::pair*, unsigned int) 0.00 1660.49 0.06 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_destroy_node(std::_Rb_tree_node >*) 0.00 1660.55 0.06 void std::swap(Vote*&, Vote*&) 0.00 1660.61 0.06 std::vector, std::allocator > >::operator[](unsigned int) 0.00 1660.66 0.06 std::vector >::operator[](unsigned int) 0.00 1660.71 0.05 4833964 0.00 0.00 __static_initialization_and_destruction_0(int, int) 0.00 1660.76 0.05 648620 0.00 0.00 std::_Vector_base >::_Vector_base(unsigned int, std::allocator const&) 0.00 1660.81 0.05 13130 0.00 0.02 std::vector >::push_back(mar_types const&) 0.00 1660.86 0.05 Contig::Add(Contig const&) 0.00 1660.91 0.05 myList::addToList(myList*) 0.00 1660.96 0.05 __gnu_cxx::new_allocator::new_allocator() 0.00 1661.01 0.05 std::vector >::size() const 0.00 1661.06 0.05 std::allocator >::allocator() 0.00 1661.11 0.05 std::_Vector_base, std::allocator > >::~_Vector_base() 0.00 1661.16 0.05 std::vector >::vector() 0.00 1661.21 0.05 std::vector >::operator[](unsigned int) 0.00 1661.26 0.05 int* std::vector >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator > > >(unsigned int, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) 0.00 1661.31 0.04 12087143 0.00 0.00 __gnu_cxx::__normal_iterator > >::difference_type __gnu_cxx::operator- > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) 0.00 1661.35 0.04 OverlapGraph::SortAdj::operator()(triple const&, triple const&) const 0.00 1661.39 0.04 std::_Identity::operator()(int const&) const 0.00 1661.44 0.04 std::__niter_base*, false>::__b(std::pair*) 0.00 1661.48 0.04 27250186 0.00 0.00 std::vector >::operator=(std::vector > const&) 0.00 1661.52 0.04 19961827 0.00 0.00 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_create_node(std::pair const&) 0.00 1661.56 0.04 19302346 0.00 0.00 mar_types* std::__uninitialized_copy::uninitialized_copy<__gnu_cxx::__normal_iterator > >, mar_types*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*) 0.00 1661.60 0.04 6612552 0.00 0.00 int* std::__uninitialized_copy_a<__gnu_cxx::__normal_iterator > >, int*, int>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int*, std::allocator&) 0.00 1661.64 0.04 4847094 0.00 0.00 std::_Vector_base, std::allocator > >::_Vector_impl::_Vector_impl() 0.00 1661.68 0.04 __gnu_cxx::new_allocator::construct(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo const&) 0.00 1661.72 0.04 __gnu_cxx::new_allocator > >::deallocate(std::_Rb_tree_node >*, unsigned int) 0.00 1661.76 0.04 bool __gnu_cxx::operator!= > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) 0.00 1661.80 0.04 std::_List_iterator >::operator*() const 0.00 1661.84 0.04 std::vector, std::allocator > >::size() const 0.00 1661.88 0.04 std::allocator >::allocator() 0.00 1661.92 0.04 std::_Vector_base, std::allocator > >::_Vector_base() 0.00 1661.96 0.04 std::map, std::allocator > >::map() 0.00 1662.00 0.04 mar_types* std::vector >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator > > >(unsigned int, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) 0.00 1662.04 0.04 std::vector >::operator[](unsigned int) 0.00 1662.08 0.04 std::iterator_traits<__gnu_cxx::__normal_iterator > > >::iterator_category std::__iterator_category<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > > const&) 0.00 1662.12 0.04 __gnu_cxx::new_allocator >::deallocate(triple*, unsigned int) 0.00 1662.15 0.04 std::_Vector_base, std::allocator > >::_M_allocate(unsigned int) 0.00 1662.18 0.03 75448568 0.00 0.00 std::_Rb_tree, std::less, std::allocator >::_S_value(std::_Rb_tree_node const*) 0.00 1662.21 0.03 10841858 0.00 0.00 OverlapGraph::ContigInfo* std::__copy_move_backward::__copy_move_b(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) 0.00 1662.24 0.03 2881044 0.00 0.00 TrieNode::addToTrie(myList*, int) 0.00 1662.27 0.03 1242568 0.00 0.00 ShortyString::GetConfidentClone() const 0.00 1662.30 0.03 7737 0.00 0.12 std::vector, std::allocator > >::push_back(std::pair const&) 0.00 1662.33 0.03 44 0.68 0.68 ShortyString::operator+=(std::string const&) 0.00 1662.36 0.03 GetFirstLine(std::basic_fstream >&, char*) 0.00 1662.39 0.03 __gnu_cxx::new_allocator >::construct(triple*, triple const&) 0.00 1662.42 0.03 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) 0.00 1662.45 0.03 std::vector >::operator[](unsigned int) const 0.00 1662.48 0.03 std::char_traits::compare(char const*, char const*, unsigned int) 0.00 1662.51 0.03 std::_Vector_base >::_Vector_impl::_Vector_impl() 0.00 1662.54 0.03 std::_Vector_base >::_M_deallocate(readPointer*, unsigned int) 0.00 1662.57 0.03 RawRead* std::__copy_move_backward::__copy_move_b(RawRead*, RawRead*, RawRead*) 0.00 1662.60 0.03 void std::reverse<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) 0.00 1662.62 0.03 Cluster::GetMt(int) const 0.00 1662.65 0.03 std::_Vector_base >::_M_get_Tp_allocator() const 0.00 1662.67 0.02 77624758 0.00 0.00 void std::_Destroy<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::allocator >&) 0.00 1662.69 0.02 11504238 0.00 0.00 Vote* std::uninitialized_copy(Vote*, Vote*, Vote*) 0.00 1662.71 0.02 11477978 0.00 0.00 Contig::GetMt(int) const 0.00 1662.73 0.02 9651173 0.00 0.00 std::pair* std::__copy_move_backward_a2*, std::pair*>(std::pair*, std::pair*, std::pair*) 0.00 1662.75 0.02 3532923 0.00 0.00 Contig* std::__uninitialized_move_a >(Contig*, Contig*, Contig*, std::allocator&) 0.00 1662.77 0.02 2485131 0.00 0.00 ShortyString::ShortyString(std::string const&, int) 0.00 1662.79 0.02 1894596 0.00 0.00 ReadProcessor::ReadProcessor(std::string const&) 0.00 1662.81 0.02 960198 0.00 0.00 TrieNode::searchWithErrorAllowed(std::string const&, int, int) 0.00 1662.83 0.02 960142 0.00 0.00 std::deque >::begin() const 0.00 1662.85 0.02 722176 0.00 0.00 Vote* std::__uninitialized_copy::uninitialized_copy(Vote*, Vote*, Vote*) 0.00 1662.87 0.02 13249 0.00 0.04 std::_Vector_base, std::allocator > >::~_Vector_base() 0.00 1662.89 0.02 13130 0.00 0.00 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) 0.00 1662.91 0.02 111 0.18 0.27 ShortyString::operator+=(ShortyString const&) 0.00 1662.93 0.02 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::__normal_iterator(std::pair* const&) 0.00 1662.95 0.02 ShortyString::operator!=(std::string const&) const 0.00 1662.97 0.02 UtilsMath::median_event_point::operator<(UtilsMath::median_event_point const&) const 0.00 1662.99 0.02 __gnu_cxx::__normal_iterator > >::base() const 0.00 1663.01 0.02 std::vector >::max_size() const 0.00 1663.03 0.02 std::vector, std::allocator > >::capacity() const 0.00 1663.05 0.02 std::vector, std::allocator > >::max_size() const 0.00 1663.07 0.02 std::vector >::capacity() const 0.00 1663.09 0.02 std::allocator >::~allocator() 0.00 1663.11 0.02 void std::_Destroy_aux::__destroy(std::string*, std::string*) 0.00 1663.13 0.02 void std::_Destroy_aux::__destroy<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) 0.00 1663.15 0.02 void std::_Destroy_aux::__destroy*>(std::pair*, std::pair*) 0.00 1663.17 0.02 std::__alloc_swap, true>::_S_do_it(std::allocator&, std::allocator&) 0.00 1663.19 0.02 std::__niter_base<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, true>::__b(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) 0.00 1663.21 0.02 std::string* std::__uninitialized_copy::uninitialized_copy(std::string*, std::string*, std::string*) 0.00 1663.23 0.02 std::set, OverlapGraph::IntPairEq, std::allocator > >::insert(std::pair const&) 0.00 1663.25 0.02 std::set, std::allocator >::insert(int const&) 0.00 1663.27 0.02 std::deque >::deque() 0.00 1663.29 0.02 std::vector >::_M_erase_at_end(Vote*) 0.00 1663.31 0.02 Vote* std::vector >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator > > >(unsigned int, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) 0.00 1663.33 0.02 std::vector, std::allocator > >::_M_erase_at_end(triple*) 0.00 1663.35 0.02 triple* std::vector, std::allocator > >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > >(unsigned int, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >) 0.00 1663.37 0.02 std::vector, std::allocator > >::begin() 0.00 1663.39 0.02 std::vector >::vector() 0.00 1663.41 0.02 std::vector >::vector() 0.00 1663.43 0.02 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_erase(std::_Rb_tree_node >*) 0.00 1663.45 0.02 std::_Rb_tree, std::less, std::allocator >::_M_erase(std::_Rb_tree_node*) 0.00 1663.47 0.02 std::pair* std::__uninitialized_move_a*, std::pair*, std::allocator > >(std::pair*, std::pair*, std::pair*, std::allocator >&) 0.00 1663.48 0.01 15620066 0.00 0.00 std::_Vector_base >::_M_allocate(unsigned int) 0.00 1663.49 0.01 29004034 0.00 0.00 __gnu_cxx::__normal_iterator > >::__normal_iterator(UtilsMath::median_event_point* const&) 0.00 1663.51 0.01 22997690 0.00 0.00 std::_Vector_base >::_Vector_impl::_Vector_impl(std::allocator const&) 0.00 1663.52 0.01 12087143 0.00 0.00 std::pair >, bool>::pair(std::_Rb_tree_const_iterator > const&, bool const&) 0.00 1663.53 0.01 5806846 0.00 0.00 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) 0.00 1663.54 0.01 3840572 0.00 0.00 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_destroy_node(std::_Rb_tree_node >*) 0.00 1663.55 0.01 3546341 0.00 0.00 std::pair::~pair() 0.00 1663.56 0.01 3339671 0.00 0.00 ShortyString::operator=(std::string const&) 0.00 1663.57 0.01 2623439 0.00 0.00 int* std::copy<__gnu_cxx::__normal_iterator > >, int*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int*) 0.00 1663.58 0.01 2447689 0.00 0.00 __gnu_cxx::__normal_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) 0.00 1663.59 0.01 2416982 0.00 0.00 operator>>(std::istream&, Vote&) 0.00 1663.60 0.01 502466 0.00 0.00 std::pair* std::__uninitialized_copy_a*, std::pair*, std::pair >(std::pair*, std::pair*, std::pair*, std::allocator >&) 0.00 1663.61 0.01 311513 0.00 0.00 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) 0.00 1663.62 0.01 280832 0.00 0.00 std::pair* std::__uninitialized_copy_a<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*, std::pair >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*, std::allocator >&) 0.00 1663.62 0.01 22395 0.00 0.00 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator+(int const&) const 0.00 1663.63 0.01 13140 0.00 0.00 mar_types* std::__copy_move_backward::__copy_move_b(mar_types const*, mar_types const*, mar_types*) 0.00 1663.64 0.01 13130 0.00 0.00 Contig::IsGoodSeed(std::basic_fstream >*, Contig const&) const 0.00 1663.65 0.01 global constructors keyed to _ZN4Vote7MAX_VALE 0.00 1663.66 0.01 global constructors keyed to _ZN7RawReadC2Eiiiii 0.00 1663.67 0.01 global constructors keyed to _ZN8TrieNodeC2Ev 0.00 1663.68 0.01 SeededRead::SeededRead(SeededRead const&) 0.00 1663.69 0.01 ShortyString::ShortyString(ShortyString const&) 0.00 1663.70 0.01 ShortyString::ShortyString() 0.00 1663.71 0.01 TrieNode::Search(std::string const&) 0.00 1663.72 0.01 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) 0.00 1663.73 0.01 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) 0.00 1663.74 0.01 bool __gnu_cxx::operator!= > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) 0.00 1663.76 0.01 Cluster::GetGen(int) const 0.00 1663.77 0.01 Cluster::GetIndex(int) const 0.00 1663.78 0.01 __gnu_cxx::__normal_iterator > >::base() const 0.00 1663.79 0.01 std::vector >::end() const 0.00 1663.80 0.01 std::vector >::capacity() const 0.00 1663.81 0.01 std::vector >::capacity() const 0.00 1663.82 0.01 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::end() const 0.00 1663.83 0.01 std::_Identity >::operator()(std::pair const&) const 0.00 1663.84 0.01 std::allocator >::~allocator() 0.00 1663.85 0.01 std::allocator::allocator(std::allocator const&) 0.00 1663.86 0.01 std::_Deque_base >::_M_get_Tp_allocator() 0.00 1663.87 0.01 std::_Vector_base >::_M_deallocate(Vote*, unsigned int) 0.00 1663.88 0.01 std::_Vector_base >::_Vector_impl::_Vector_impl() 0.00 1663.88 0.01 std::_Vector_base >::~_Vector_base() 0.00 1663.89 0.01 std::_Vector_base, std::allocator > >::_Vector_impl::_Vector_impl() 0.00 1663.90 0.01 std::_Vector_base, std::allocator > >::_Vector_impl::~_Vector_impl() 0.00 1663.91 0.01 std::__niter_base::__b(int*) 0.00 1663.92 0.01 std::string* std::__copy_move_backward::__copy_move_b(std::string*, std::string*, std::string*) 0.00 1663.93 0.01 RawRead* std::__uninitialized_copy::uninitialized_copy(RawRead*, RawRead*, RawRead*) 0.00 1663.94 0.01 std::_Rb_tree_const_iterator::_Rb_tree_const_iterator(std::_Rb_tree_node const*) 0.00 1663.95 0.01 std::pair, bool>::pair(std::_Rb_tree_const_iterator const&, bool const&) 0.00 1663.96 0.01 std::vector >::insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) 0.00 1663.97 0.01 std::vector, std::allocator > >::end() 0.00 1663.98 0.01 std::vector >::~vector() 0.00 1663.99 0.01 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_S_key(std::_Rb_tree_node > const*) 0.00 1664.01 0.01 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_erase(std::_Rb_tree_node >*) 0.00 1664.02 0.01 std::_Rb_tree, std::less, std::allocator >::_S_right(std::_Rb_tree_node_base*) 0.00 1664.03 0.01 void std::partial_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) 0.00 1664.04 0.01 triple* std::copy_backward*, triple*>(triple*, triple*, triple*) 0.00 1664.05 0.01 std::pair* std::__uninitialized_copy_a*, std::pair*, std::pair >(std::pair*, std::pair*, std::pair*, std::allocator >&) 0.00 1664.06 0.01 void std::sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) 0.00 1664.07 0.01 void std::_Destroy(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, std::allocator&) 0.00 1664.08 0.01 void std::_Destroy*>(std::pair*, std::pair*) 0.00 1664.08 0.01 2674989 0.00 0.00 std::vector >::begin() 0.00 1664.09 0.01 960142 0.00 0.00 std::deque >::_M_destroy_data_aux(std::_Deque_iterator, std::_Deque_iterator) 0.00 1664.09 0.01 480071 0.00 0.00 std::_Deque_base >::_M_deallocate_map(SeededRead**, unsigned int) 0.00 1664.10 0.01 __gnu_cxx::new_allocator >::~new_allocator() 0.00 1664.10 0.01 __gnu_cxx::__normal_iterator > >::__normal_iterator(readPointer* const&) 0.00 1664.11 0.01 __gnu_cxx::new_allocator::max_size() const 0.00 1664.11 0.01 void std::_Destroy_aux::__destroy*>(triple*, triple*) 0.00 1664.11 0.00 13931508 0.00 0.00 __gnu_cxx::__normal_iterator > >::__normal_iterator(Contig* const&) 0.00 1664.11 0.00 9828241 0.00 0.00 std::allocator >::~allocator() 0.00 1664.11 0.00 4845505 0.00 0.00 SeededRead** std::copy_backward(SeededRead**, SeededRead**, SeededRead**) 0.00 1664.11 0.00 4238020 0.00 0.00 std::pair::operator=(std::pair const&) 0.00 1664.11 0.00 3840572 0.00 0.00 std::_Deque_iterator::_Deque_iterator(std::_Deque_iterator const&) 0.00 1664.11 0.00 3096309 0.00 0.00 std::pair >, bool>::pair(std::_Rb_tree_iterator > const&, bool const&) 0.00 1664.11 0.00 2925217 0.00 0.00 std::pair* std::__copy_move_backward_a2*, std::pair*>(std::pair*, std::pair*, std::pair*) 0.00 1664.11 0.00 2902821 0.00 0.00 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) 0.00 1664.11 0.00 2902821 0.00 0.00 __gnu_cxx::new_allocator::max_size() const 0.00 1664.11 0.00 2880428 0.00 0.00 TrieNode::traceTrie() 0.00 1664.11 0.00 2674989 0.00 0.00 std::vector, std::allocator > >::size() const 0.00 1664.11 0.00 2674989 0.00 0.00 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::begin() const 0.00 1664.11 0.00 2447689 0.00 0.00 std::_Vector_base, std::allocator > >::_M_allocate(unsigned int) 0.00 1664.11 0.00 2357247 0.00 0.00 std::pair* std::__copy_move::__copy_m*, std::pair*>(std::pair*, std::pair*, std::pair*) 0.00 1664.11 0.00 2132137 0.00 0.00 std::_Vector_base >::~_Vector_base() 0.00 1664.11 0.00 1965076 0.00 0.00 SeededRead** std::copy(SeededRead**, SeededRead**, SeededRead**) 0.00 1664.11 0.00 1920887 0.00 0.00 TrieNode::searchWithError(std::string const&, int) 0.00 1664.11 0.00 1920286 0.00 0.00 std::allocator::allocator() 0.00 1664.11 0.00 1920284 0.00 0.00 std::_Deque_base >::_M_destroy_nodes(SeededRead**, SeededRead**) 0.00 1664.11 0.00 1528377 0.00 0.00 std::_Deque_base >::_Deque_base(std::allocator const&, unsigned int) 0.00 1664.11 0.00 1208491 0.00 0.00 ShortyString::push_back(char, Vote const&) 0.00 1664.11 0.00 1208491 0.00 0.00 ShortyString::operator==(std::string const&) const 0.00 1664.11 0.00 1136472 0.00 0.00 std::vector, std::allocator > >::begin() 0.00 1664.11 0.00 1004933 0.00 0.00 __gnu_cxx::new_allocator >::deallocate(std::pair*, unsigned int) 0.00 1664.11 0.00 982537 0.00 0.00 int* std::copy(int*, int*, int*) 0.00 1664.11 0.00 960143 0.00 0.00 std::_Deque_base >::_Deque_impl::_Deque_impl() 0.00 1664.11 0.00 960143 0.00 0.00 std::vector >::end() 0.00 1664.11 0.00 960142 0.00 0.00 __gnu_cxx::new_allocator::~new_allocator() 0.00 1664.11 0.00 656399 0.00 0.00 void std::_Destroy_aux::__destroy(SeededRead*, SeededRead*) 0.00 1664.11 0.00 648620 0.00 0.00 std::vector >::begin() const 0.00 1664.11 0.00 648620 0.00 0.00 Contig* std::__copy_move_backward_a2(Contig*, Contig*, Contig*) 0.00 1664.11 0.00 502466 0.00 0.00 std::_Deque_base >::_M_get_Tp_allocator() const 0.00 1664.11 0.00 480071 0.00 0.00 std::_Deque_base >::_Deque_base() 0.00 1664.11 0.00 480071 0.00 0.00 Vote* std::__uninitialized_copy_a(Vote*, Vote*, Vote*, std::allocator&) 0.00 1664.11 0.00 307868 0.00 0.00 std::pair::pair(std::pair const&) 0.00 1664.11 0.00 241223 0.00 0.00 OverlapGraph::ContigInfo* std::__uninitialized_copy::uninitialized_copy(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) 0.00 1664.11 0.00 223950 0.00 0.00 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, std::string const&) 0.00 1664.11 0.00 186838 0.00 0.00 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) 0.00 1664.11 0.00 176329 0.00 0.00 __gnu_cxx::new_allocator >::construct(std::pair*, std::pair const&) 0.00 1664.11 0.00 176329 0.00 0.00 std::vector, std::allocator > >::end() const 0.00 1664.11 0.00 156765 0.00 0.00 ReadProcessor::LocateRead(std::string const&) const 0.00 1664.11 0.00 140416 0.00 0.00 std::_Rb_tree, std::less, std::allocator >::_Rb_tree_impl, false>::_M_initialize() 0.00 1664.11 0.00 131539 0.00 0.00 std::vector, std::allocator > >::begin() const 0.00 1664.11 0.00 131300 0.00 0.00 Contig::PrintContigFormat(std::basic_fstream >*) const 0.00 1664.11 0.00 118170 0.00 0.00 __gnu_cxx::__normal_iterator > > std::__copy_move_a2 > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) 0.00 1664.11 0.00 91910 0.00 0.00 std::vector >::_M_check_len(unsigned int, char const*) const 0.00 1664.11 0.00 91910 0.00 0.00 Vote* std::__copy_move_a2(Vote*, Vote*, Vote*) 0.00 1664.11 0.00 88164 0.00 0.00 __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >::base() const 0.00 1664.11 0.00 88164 0.00 0.00 std::_Vector_base, std::allocator > >::_M_get_Tp_allocator() 0.00 1664.11 0.00 78901 0.00 0.00 mar_types* std::__copy_move::__copy_m(mar_types const*, mar_types const*, mar_types*) 0.00 1664.11 0.00 70208 0.00 0.00 std::vector, std::allocator > >::begin() const 0.00 1664.11 0.00 70208 0.00 0.00 std::allocator::allocator() 0.00 1664.11 0.00 70208 0.00 0.00 void std::_Destroy_aux::__destroy(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) 0.00 1664.11 0.00 70208 0.00 0.00 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Contig const&) 0.00 1664.11 0.00 70208 0.00 0.00 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::__copy_move_a2 const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) 0.00 1664.11 0.00 70208 0.00 0.00 std::pair* std::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) 0.00 1664.11 0.00 65769 0.00 0.00 __gnu_cxx::new_allocator::max_size() const 0.00 1664.11 0.00 65769 0.00 0.00 void std::_Destroy*, triple >(triple*, triple*, std::allocator >&) 0.00 1664.11 0.00 65650 0.00 0.00 Contig::PrintGeoFormat(std::basic_fstream >*) const 0.00 1664.11 0.00 64810 0.00 0.00 void std::_Destroy(int*, int*) 0.00 1664.11 0.00 61670 0.00 0.00 ReadProcessor::GetMar(int, mar_types) const 0.00 1664.11 0.00 52520 0.00 0.02 SeededRead::~SeededRead() 0.00 1664.11 0.00 52520 0.00 0.00 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) 0.00 1664.11 0.00 52520 0.00 0.00 void std::_Destroy >(std::_Deque_iterator, std::_Deque_iterator) 0.00 1664.11 0.00 52519 0.00 0.00 std::vector >::vector(std::vector > const&) 0.00 1664.11 0.00 49336 0.00 0.00 __gnu_cxx::new_allocator > >::new_allocator() 0.00 1664.11 0.00 47879 0.00 0.00 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) 0.00 1664.11 0.00 44790 0.00 0.00 ReadProcessor::~ReadProcessor() 0.00 1664.11 0.00 39390 0.00 0.00 std::_Deque_base >::_M_create_nodes(SeededRead**, SeededRead**) 0.00 1664.11 0.00 33997 0.00 0.00 std::_Deque_iterator::_M_set_node(SeededRead**) 0.00 1664.11 0.00 30142 0.00 0.00 TrieNode::destructNode() 0.00 1664.11 0.00 26854 0.00 0.00 std::_Deque_base >::_M_allocate_map(unsigned int) 0.00 1664.11 0.00 26272 0.00 0.00 std::_Vector_base, std::allocator > >::~_Vector_base() 0.00 1664.11 0.00 26260 0.00 0.00 __static_initialization_and_destruction_0(int, int) 0.00 1664.11 0.00 26260 0.00 0.00 Contig::Contig(bool, int, int, ShortyString const&, int, ReadProcessor const*) 0.00 1664.11 0.00 26260 0.00 0.00 __gnu_cxx::new_allocator::construct(mar_types*, mar_types const&) 0.00 1664.11 0.00 26260 0.00 0.00 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) 0.00 1664.11 0.00 26260 0.00 0.00 Contig::PrintFastaFormat(std::basic_fstream >*) const 0.00 1664.11 0.00 26260 0.00 0.00 readPointer* std::__uninitialized_copy::uninitialized_copy(readPointer*, readPointer*, readPointer*) 0.00 1664.11 0.00 26260 0.00 0.00 std::deque >::push_back(SeededRead const&) 0.00 1664.11 0.00 24668 0.00 0.00 std::pair* std::__copy_move::__copy_m const*, std::pair*>(std::pair const*, std::pair const*, std::pair*) 0.00 1664.11 0.00 24668 0.00 0.00 std::pair* std::__uninitialized_copy::uninitialized_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*>(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*) 0.00 1664.11 0.00 22395 0.00 0.00 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) 0.00 1664.11 0.00 20071 0.00 0.00 std::_Deque_base >::_M_get_map_allocator() const 0.00 1664.11 0.00 20071 0.00 0.00 std::allocator::~allocator() 0.00 1664.11 0.00 13249 0.00 0.00 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::__unguarded_partition<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj) 0.00 1664.11 0.00 13167 0.00 0.00 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) 0.00 1664.11 0.00 13141 0.00 0.00 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_put_node(std::_Rb_tree_node >*) 0.00 1664.11 0.00 13137 0.00 0.00 std::_Vector_base >::_M_deallocate(mar_types*, unsigned int) 0.00 1664.11 0.00 13134 0.00 0.00 Vote* std::__copy_move_a(Vote*, Vote*, Vote*) 0.00 1664.11 0.00 13131 0.00 0.00 ShortyString::ShortyString(std::string const&) 0.00 1664.11 0.00 13130 0.00 0.00 ShortyString::ShortyString(std::string const&, std::vector > const&) 0.00 1664.11 0.00 13130 0.00 0.00 Contig::AddRead(int, int, int, mar_types) 0.00 1664.11 0.00 13130 0.00 0.00 __gnu_cxx::new_allocator::deallocate(SeededRead**, unsigned int) 0.00 1664.11 0.00 13130 0.00 0.00 std::vector >::size() const 0.00 1664.11 0.00 13130 0.00 0.00 readPointer* std::__copy_move_backward::__copy_move_b(readPointer*, readPointer*, readPointer*) 0.00 1664.11 0.00 13130 0.00 0.00 std::vector >::_M_erase_at_end(readPointer*) 0.00 1664.11 0.00 13130 0.00 0.00 std::vector >::begin() 0.00 1664.11 0.00 13130 0.00 0.00 std::vector >::end() 0.00 1664.11 0.00 13129 0.00 0.00 __gnu_cxx::__normal_iterator > >::__normal_iterator(Vote const* const&) 0.00 1664.11 0.00 13129 0.00 0.00 std::allocator::allocator() 0.00 1664.11 0.00 13129 0.00 0.00 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Rb_tree_impl, false>::_Rb_tree_impl() 0.00 1664.11 0.00 13129 0.00 0.00 void std::_Destroy(Vote*, Vote*) 0.00 1664.11 0.00 12334 0.00 0.00 void std::__insertion_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) 0.00 1664.11 0.00 12334 0.00 0.00 Contig* std::uninitialized_copy(Contig*, Contig*, Contig*) 0.00 1664.11 0.00 12334 0.00 0.00 void std::_Destroy<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) 0.00 1664.11 0.00 7737 0.00 0.00 __static_initialization_and_destruction_0(int, int) 0.00 1664.11 0.00 7737 0.00 0.00 std::_Deque_base >::_M_deallocate_node(SeededRead*) 0.00 1664.11 0.00 7737 0.00 0.00 Vote* std::uninitialized_copy<__gnu_cxx::__normal_iterator > >, Vote*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, Vote*) 0.00 1664.11 0.00 2496 0.00 0.00 std::deque >::_M_reallocate_map(unsigned int, bool) 0.00 1664.11 0.00 2419 0.00 0.00 bool std::operator!=(std::_Deque_iterator const&, std::_Deque_iterator const&) 0.00 1664.11 0.00 596 0.00 0.00 std::_Deque_iterator::difference_type std::operator-(std::_Deque_iterator const&, std::_Deque_iterator const&) 0.00 1664.11 0.00 314 0.00 0.00 ShortyString::operator+(ShortyString const&) 0.00 1664.11 0.00 312 0.00 0.00 ShortyString::operator+(std::string const&) 0.00 1664.11 0.00 199 0.00 0.00 ShortyString::ReverseComplement() const 0.00 1664.11 0.00 133 0.00 0.00 ShortyString::ReadVotesFromFile(std::istream&) 0.00 1664.11 0.00 133 0.00 0.00 ShortyString::Print() const 0.00 1664.11 0.00 56 0.00 0.00 SeededRead** std::__copy_move_a(SeededRead**, SeededRead**, SeededRead**) 0.00 1664.11 0.00 44 0.00 0.00 ShortyString::PrintScores(std::ostream&) const 0.00 1664.11 0.00 32 0.00 0.00 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) 0.00 1664.11 0.00 30 0.00 0.00 std::_Deque_iterator std::__uninitialized_copy::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) 0.00 1664.11 0.00 27 0.00 0.00 ShortyString::RepresentativeVotes() const 0.00 1664.11 0.00 22 0.00 0.00 ShortyString::reverse() 0.00 1664.11 0.00 18 0.00 0.00 std::deque >::_M_push_back_aux(SeededRead const&) 0.00 1664.11 0.00 17 0.00 0.00 mar_types* std::__copy_move_a2(mar_types*, mar_types*, mar_types*) 0.00 1664.11 0.00 14 0.00 0.00 UtilsString::Complement(std::string const&) 0.00 1664.11 0.00 10 0.00 0.00 TrieNode::TrieNode() 0.00 1664.11 0.00 8 0.00 0.00 std::vector >::~vector() 0.00 1664.11 0.00 7 0.00 0.12 Hash::Insert(std::string const&, int, int, int) 0.00 1664.11 0.00 7 0.00 0.00 std::vector >::operator[](unsigned int) 0.00 1664.11 0.00 7 0.00 0.00 UtilsMath::median_event_point* std::__copy_move_a(UtilsMath::median_event_point*, UtilsMath::median_event_point*, UtilsMath::median_event_point*) 0.00 1664.11 0.00 6 0.00 0.00 std::_Deque_iterator::operator++() 0.00 1664.11 0.00 6 0.00 0.00 SeededRead** std::__copy_move_backward_a(SeededRead**, SeededRead**, SeededRead**) 0.00 1664.11 0.00 5 0.00 0.00 __gnu_cxx::new_allocator::destroy(SeededRead*) 0.00 1664.11 0.00 5 0.00 0.00 void std::__push_heap<__gnu_cxx::__normal_iterator > >, int, UtilsMath::median_event_point>(__gnu_cxx::__normal_iterator > >, int, int, UtilsMath::median_event_point) 0.00 1664.11 0.00 4 0.00 0.00 TrieNode::TrieNode() 0.00 1664.11 0.00 4 0.00 0.00 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) 0.00 1664.11 0.00 4 0.00 0.00 __gnu_cxx::new_allocator::construct(SeededRead*, SeededRead const&) 0.00 1664.11 0.00 4 0.00 0.00 std::vector, std::allocator > >::end() const 0.00 1664.11 0.00 4 0.00 0.00 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::get_allocator() const 0.00 1664.11 0.00 4 0.00 0.00 std::_List_base, std::allocator > >::_M_clear() 0.00 1664.11 0.00 4 0.00 0.00 std::_List_base, std::allocator > >::_List_base(std::allocator > const&) 0.00 1664.11 0.00 4 0.00 0.00 std::__niter_base*, false>::__b(std::pair*) 0.00 1664.11 0.00 4 0.00 0.00 std::_Deque_iterator::operator++() 0.00 1664.11 0.00 4 0.00 0.00 Vote* std::__uninitialized_copy::uninitialized_copy<__gnu_cxx::__normal_iterator > >, Vote*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, Vote*) 0.00 1664.11 0.00 4 0.00 0.00 std::deque >::_M_pop_back_aux() 0.00 1664.11 0.00 4 0.00 0.00 std::deque >::pop_back() 0.00 1664.11 0.00 4 0.00 0.00 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::resize(unsigned int, std::list, std::allocator > >) 0.00 1664.11 0.00 4 0.00 0.00 Vote* std::__copy_move_a(Vote const*, Vote const*, Vote*) 0.00 1664.11 0.00 4 0.00 0.00 void std::_Destroy, std::allocator > >*, std::list, std::allocator > > >(std::list, std::allocator > >*, std::list, std::allocator > >*, std::allocator, std::allocator > > >&) 0.00 1664.11 0.00 3 0.00 0.00 ShortyString::~ShortyString() 0.00 1664.11 0.00 3 0.00 0.00 Hash::Hash(int) 0.00 1664.11 0.00 3 0.00 0.00 Hash::LeftShiftHashVal(char, char, int) const 0.00 1664.11 0.00 2 0.00 0.00 UtilsString::PrintContig(std::string const&, std::string const&) 0.00 1664.11 0.00 2 0.00 0.00 ShortyString::push_back(char) 0.00 1664.11 0.00 2 0.00 15.69 Assembler::Assemble() 0.00 1664.11 0.00 2 0.00 0.00 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) 0.00 1664.11 0.00 2 0.00 0.00 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) 0.00 1664.11 0.00 2 0.00 0.00 __gnu_cxx::new_allocator::deallocate(int*, unsigned int) 0.00 1664.11 0.00 2 0.00 0.00 __gnu_cxx::new_allocator::construct(int*, int const&) 0.00 1664.11 0.00 2 0.00 0.00 __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >::__normal_iterator(std::pair const* const&) 0.00 1664.11 0.00 2 0.00 7.84 std::vector >::_M_check_len(unsigned int, char const*) const 0.00 1664.11 0.00 2 0.00 0.00 std::vector, std::allocator > >::begin() const 0.00 1664.11 0.00 2 0.00 0.00 std::vector >::max_size() const 0.00 1664.11 0.00 2 0.00 0.00 std::vector >::_M_check_len(unsigned int, char const*) const 0.00 1664.11 0.00 2 0.00 0.00 std::allocator > >::~allocator() 0.00 1664.11 0.00 2 0.00 0.00 std::allocator::allocator() 0.00 1664.11 0.00 2 0.00 0.00 std::_List_base, std::allocator > >::_List_base() 0.00 1664.11 0.00 2 0.00 0.00 std::_Vector_base, std::allocator > >, std::allocator, std::allocator > > > >::~_Vector_base() 0.00 1664.11 0.00 2 0.00 0.00 std::__niter_base<__gnu_cxx::__normal_iterator > >, true>::__b(__gnu_cxx::__normal_iterator > >) 0.00 1664.11 0.00 2 0.00 0.00 std::_Deque_iterator::operator--() 0.00 1664.11 0.00 2 0.00 0.00 int* std::__copy_move_backward::__copy_move_b(int const*, int const*, int*) 0.00 1664.11 0.00 2 0.00 0.00 void std::list, std::allocator > >::_M_initialize_dispatch > >(std::_List_const_iterator >, std::_List_const_iterator >, std::__false_type) 0.00 1664.11 0.00 2 0.00 0.00 std::stack > >::push(SeededRead const&) 0.00 1664.11 0.00 2 0.00 0.00 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Rb_tree_impl, false>::_M_initialize() 0.00 1664.11 0.00 2 0.00 0.00 mar_types* std::__copy_move_a(mar_types*, mar_types*, mar_types*) 0.00 1664.11 0.00 2 0.00 0.00 int* std::__copy_move_a(int*, int*, int*) 0.00 1664.11 0.00 2 0.00 0.00 mar_types* std::__uninitialized_move_a >(mar_types*, mar_types*, mar_types*, std::allocator&) 0.00 1664.11 0.00 2 0.00 0.00 mar_types* std::__copy_move_backward_a2(mar_types*, mar_types*, mar_types*) 0.00 1664.11 0.00 1 0.00 0.00 ShortyString::ShortyString() 0.00 1664.11 0.00 1 0.00 0.00 Hash::~Hash() 0.00 1664.11 0.00 1 0.00 0.00 Cluster::Cluster() 0.00 1664.11 0.00 1 0.00 0.00 Assembler::Assembler(std::vector > const&, ReadProcessor*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*) 0.00 1664.11 0.00 1 0.00 0.00 __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >::operator++() 0.00 1664.11 0.00 1 0.00 0.00 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) 0.00 1664.11 0.00 1 0.00 0.00 ShortyString::operator[](int) const 0.00 1664.11 0.00 1 0.00 0.00 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::_M_check_len(unsigned int, char const*) const 0.00 1664.11 0.00 1 0.00 0.00 std::vector, std::allocator > >::max_size() const 0.00 1664.11 0.00 1 0.00 0.00 std::allocator >::allocator() 0.00 1664.11 0.00 1 0.00 0.00 std::_Vector_base >::_M_allocate(unsigned int) 0.00 1664.11 0.00 1 0.00 0.00 std::_Vector_base >::_Vector_impl::_Vector_impl() 0.00 1664.11 0.00 1 0.00 0.00 std::_Vector_base >::_M_deallocate(UtilsMath::median_event_point*, unsigned int) 0.00 1664.11 0.00 1 0.00 0.00 std::_Vector_base, std::allocator > >, std::allocator, std::allocator > > > >::_Vector_impl::~_Vector_impl() 0.00 1664.11 0.00 1 0.00 0.00 std::_Vector_base, std::allocator > >::_M_allocate(unsigned int) 0.00 1664.11 0.00 1 0.00 0.00 std::__niter_base::__b(short*) 0.00 1664.11 0.00 1 0.00 0.00 std::_Deque_iterator::_S_buffer_size() 0.00 1664.11 0.00 1 0.00 0.00 std::_List_const_iterator >::operator++() 0.00 1664.11 0.00 1 0.00 0.00 std::vector, std::allocator > >::~vector() 0.00 1664.11 0.00 1 0.00 0.00 int* std::__copy_move_a2(int*, int*, int*) 0.00 1664.11 0.00 1 0.00 0.00 RawRead* std::__copy_move_backward_a2(RawRead*, RawRead*, RawRead*) 0.00 1664.11 0.00 1 0.00 0.17 std::back_insert_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, std::back_insert_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::back_insert_iterator > >) 0.00 1664.11 0.00 1 0.00 0.00 operator>>(std::istream&, ShortyString&) % the percentage of the total running time of the time program used by this function. cumulative a running sum of the number of seconds accounted seconds for by this function and those listed above it. self the number of seconds accounted for by this seconds function alone. This is the major sort for this listing. calls the number of times this function was invoked, if this function is profiled, else blank. self the average number of milliseconds spent in this ms/call function per call, if this function is profiled, else blank. total the average number of milliseconds spent in this ms/call function and its descendents per call, if this function is profiled, else blank. name the name of the function. This is the minor sort for this listing. The index shows the location of the function in the gprof listing. If the index is in parenthesis it shows where it would appear in the gprof listing if it were to be printed. Call graph (explanation follows) granularity: each sample hit covers 4 byte(s) for 0.00% of 12019.48 seconds index % time self children called name [1] 89.5 9656.99 1105.70 2099102434+146066409 [1] 2521.32 16.25 138559832+3439465140 _fini [4] 1930.95 0.00 3937446119+3549628993 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [5] 1479.26 45.57 1103210846+1 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 1201.29 0.00 3693798105 ShortyString::ShortyString(std::string const&, int) [7] 396.85 529.72 3634312314+385741013 UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) [9] 274.74 0.73 1412210695+39618061 ReadSeededFastaFile(std::string const&, std::vector >*) [26] 84.29 162.95 730437480 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [28] 207.09 0.00 3086620571 ShortyString::~ShortyString() [34] 168.21 4.30 27931064 std::vector >::_M_check_len(unsigned int, char const*) const [43] 33.06 128.96 385741013 std::_Vector_base >::~_Vector_base() [46] 156.01 0.00 3688985037 ShortyString::ShortyString(std::string const&, std::vector > const&) [48] 111.83 29.90 844621234 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] 122.72 0.00 47882985+4833964 std::vector, std::allocator > >::_M_fill_insert(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, unsigned int, triple const&) [50] 46.63 65.46 857768503 Vote* std::__copy_move::__copy_m(Vote*, Vote*, Vote*) [52] 111.37 0.00 3541563139 Contig::~Contig() [53] 87.29 23.81 649493343+184878960 UtilsFile::OpenFile(std::string const&, std::string const&) [54] 61.36 37.58 318999000 UtilsFile::Log(std::ostream*, std::string const&) [58] 76.70 18.30 1416853474+2668229 ReadProcessor::ReadProcessor(std::string const&) [59] 91.43 0.00 1300701146 std::vector >::operator=(std::vector > const&) [60] 53.38 23.80 1270915671 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 65.50 0.00 1084630574+77624758 void std::__final_insertion_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [71] 61.97 0.00 1033249085+507059769 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [75] 47.86 0.00 1523755262+48132364 void std::__introsort_loop<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj) [86] 33.90 10.35 115695890 std::vector >::operator=(std::vector > const&) [88] 38.96 0.01 858076371 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [92] 25.77 1.84 474907109 __static_initialization_and_destruction_0(int, int) [100] 27.08 0.00 603285812 triple* std::__copy_move_backward::__copy_move_b*, triple*>(triple*, triple*, triple*) [101] 23.16 0.00 475846366 OverlapGraph::AllocateData() [112] 19.10 0.00 507052032 __gnu_cxx::new_allocator > >::allocate(unsigned int, void const*) [120] 18.87 0.07 448288348 void std::__adjust_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [121] 9.97 0.00 57785273 TrieNode::searchWithErrorWholeSeed(std::string const&, int, int) [138] 8.13 0.00 161323238 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [145] 8.05 0.00 236425176 __gnu_cxx::__enable_if::__value, void>::__type std::__fill_a(char*, char*, int const&) [146] 7.67 0.27 97728652 void std::__push_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [147] 7.52 0.00 408260573 std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [151] 5.83 0.00 48124627 triple* std::__uninitialized_copy::uninitialized_copy*, triple*>(triple*, triple*, triple*) [161] 1.07 3.06 6533878+2674989 Contig::operator=(Contig const&) [174] 3.53 0.40 96233780 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [177] 2.15 0.00 43219050 std::vector >::~vector() [208] 1.99 0.00 48149802 std::vector, std::allocator > >::end() const [213] 1.69 0.31 58947341+2674989 Contig::Contig(Contig const&) [214] 1.84 0.00 87014606+1 Hash::Insert(std::string const&, int, int, int, int) [220] 1.69 0.00 7406691 __static_initialization_and_destruction_0(int, int) [227] 1.53 0.00 684149 ReadProcessor::GetMarLen(int, mar_types) const [232] 1.23 0.22 11627676 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, RawRead const&) [235] 1.38 0.00 21589830 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::~_Rb_tree() [237] 1.38 0.00 19323731 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [238] 1.07 0.24 55059010+960143 std::_Deque_base >::_M_initialize_map(unsigned int) [242] 1.23 0.07 15474 OverlapGraph::Traverse(int, int, int, int) [245] 1.07 0.00 21589830 Vote* std::copy(Vote*, Vote*, Vote*) [257] 1.07 0.00 9177919 std::vector >::end() [258] 0.92 0.00 48023296 __gnu_cxx::new_allocator::construct(Contig*, Contig const&) [268] 0.61 0.23 27250186 std::vector >::operator=(std::vector > const&) [283] 0.69 0.00 12087143 __gnu_cxx::__normal_iterator > >::difference_type __gnu_cxx::operator- > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [297] 0.61 0.00 4847094 std::_Vector_base, std::allocator > >::_Vector_impl::_Vector_impl() [308] 0.00 0.52 2880428 TrieNode::traceTrie() [317] 0.46 0.00 2881044+30 TrieNode::addToTrie(myList*, int) [330] 0.46 0.00 10841858 OverlapGraph::ContigInfo* std::__copy_move_backward::__copy_move_b(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [331] 0.46 0.00 1242568+22 ShortyString::GetConfidentClone() const [332] 0.46 0.00 44 ShortyString::operator+=(std::string const&) [333] 0.31 0.15 111 ShortyString::operator+=(ShortyString const&) [334] 0.15 0.23 2447689 __gnu_cxx::__normal_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [346] 0.31 0.02 1894596 ReadProcessor::ReadProcessor(std::string const&) [358] 0.31 0.00 11504238 Vote* std::uninitialized_copy(Vote*, Vote*, Vote*) [364] 0.31 0.00 2485131 ShortyString::ShortyString(std::string const&, int) [366] 0.31 0.00 960198 TrieNode::searchWithErrorAllowed(std::string const&, int, int) [367] 0.31 0.00 13130 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [368] 0.23 0.00 15620066 std::_Vector_base >::_M_allocate(unsigned int) [382] 0.15 0.07 311513 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] 0.15 0.00 22997690 std::_Vector_base >::_Vector_impl::_Vector_impl(std::allocator const&) [404] 0.15 0.00 5806846 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [405] 0.15 0.00 3840572 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_destroy_node(std::_Rb_tree_node >*) [406] 0.00 0.15 131300+39390 Contig::PrintContigFormat(std::basic_fstream >*) const [408] 0.15 0.00 22395 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator+(int const&) const [410] 0.15 0.00 13140 mar_types* std::__copy_move_backward::__copy_move_b(mar_types const*, mar_types const*, mar_types*) [411] 0.00 0.12 70208 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Contig const&) [428] 0.08 0.00 2674989 std::vector >::begin() [446] 0.00 0.02 13167+13153 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] 0.00 0.01 52519 std::vector >::vector(std::vector > const&) [514] 0.00 0.01 26260 std::deque >::push_back(SeededRead const&) [549] 0.00 0.00 241223 OverlapGraph::ContigInfo* std::__uninitialized_copy::uninitialized_copy(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [583] 0.00 0.00 4845505 SeededRead** std::copy_backward(SeededRead**, SeededRead**, SeededRead**) [680] 0.00 0.00 1920887 TrieNode::searchWithError(std::string const&, int) [691] 0.00 0.00 1004933 __gnu_cxx::new_allocator >::deallocate(std::pair*, unsigned int) [697] 0.00 0.00 307868 std::pair::pair(std::pair const&) [705] 0.00 0.00 223950+67185 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, std::string const&) [706] 0.00 0.00 186838 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [707] 0.00 0.00 156765 ReadProcessor::LocateRead(std::string const&) const [709] 0.00 0.00 140416 std::_Rb_tree, std::less, std::allocator >::_Rb_tree_impl, false>::_M_initialize() [710] 0.00 0.00 131539 std::vector, std::allocator > >::begin() const [711] 0.00 0.00 118170 __gnu_cxx::__normal_iterator > > std::__copy_move_a2 > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [712] 0.00 0.00 91910 Vote* std::__copy_move_a2(Vote*, Vote*, Vote*) [714] 0.00 0.00 78901 mar_types* std::__copy_move::__copy_m(mar_types const*, mar_types const*, mar_types*) [717] 0.00 0.00 70208 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::__copy_move_a2 const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [720] 0.00 0.00 52520 void std::_Destroy >(std::_Deque_iterator, std::_Deque_iterator) [724] 0.00 0.00 47879 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [726] 0.00 0.00 39390 std::_Deque_base >::_M_create_nodes(SeededRead**, SeededRead**) [728] 0.00 0.00 33997 std::_Deque_iterator::_M_set_node(SeededRead**) [729] 0.00 0.00 30142 TrieNode::destructNode() [730] 0.00 0.00 26854 std::_Deque_base >::_M_allocate_map(unsigned int) [731] 0.00 0.00 26272 std::_Vector_base, std::allocator > >::~_Vector_base() [732] 0.00 0.00 26260 Contig::Contig(bool, int, int, ShortyString const&, int, ReadProcessor const*) [734] 0.00 0.00 20071 std::allocator::~allocator() [739] 0.00 0.00 13134 Vote* std::__copy_move_a(Vote*, Vote*, Vote*) [742] 0.00 0.00 13131 ShortyString::ShortyString(std::string const&) [743] 0.00 0.00 13129 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Rb_tree_impl, false>::_Rb_tree_impl() [750] 0.00 0.00 7737 std::_Deque_base >::_M_deallocate_node(SeededRead*) [756] 0.00 0.00 2496 std::deque >::_M_reallocate_map(unsigned int, bool) [758] 0.00 0.00 2419 bool std::operator!=(std::_Deque_iterator const&, std::_Deque_iterator const&) [759] 0.00 0.00 596 std::_Deque_iterator::difference_type std::operator-(std::_Deque_iterator const&, std::_Deque_iterator const&) [760] 0.00 0.00 312+177 ShortyString::operator+(std::string const&) [762] 0.00 0.00 314 ShortyString::operator+(ShortyString const&) [761] 0.00 0.00 199+22 ShortyString::ReverseComplement() const [763] 0.00 0.00 133 ShortyString::Print() const [764] 0.00 0.00 56 SeededRead** std::__copy_move_a(SeededRead**, SeededRead**, SeededRead**) [765] 0.00 0.00 32 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [766] 0.00 0.00 30 std::_Deque_iterator std::__uninitialized_copy::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [767] 0.00 0.00 27 ShortyString::RepresentativeVotes() const [768] 0.00 0.00 22 ShortyString::reverse() [769] 0.00 0.00 18 std::deque >::_M_push_back_aux(SeededRead const&) [770] 0.00 0.00 17 mar_types* std::__copy_move_a2(mar_types*, mar_types*, mar_types*) [771] 0.00 0.00 10 TrieNode::TrieNode() [773] 0.00 0.00 6 SeededRead** std::__copy_move_backward_a(SeededRead**, SeededRead**, SeededRead**) [776] 0.00 0.00 4 std::vector, std::allocator > >::end() const [782] 0.00 0.00 4 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::resize(unsigned int, std::list, std::allocator > >) [788] 0.00 0.00 4 std::_List_base, std::allocator > >::_M_clear() [783] 0.00 0.00 4 std::deque >::pop_back() [787] 0.00 0.00 4 Vote* std::__copy_move_a(Vote const*, Vote const*, Vote*) [789] 0.00 0.00 4 std::deque >::_M_pop_back_aux() [786] 0.00 0.00 3 ShortyString::~ShortyString() [791] 0.00 0.00 3 Hash::LeftShiftHashVal(char, char, int) const [793] 0.00 0.00 2 __gnu_cxx::new_allocator::deallocate(int*, unsigned int) [796] 0.00 0.00 2 std::allocator > >::~allocator() [800] 0.00 0.00 2 ShortyString::push_back(char) [794] 0.00 0.00 2 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [795] 0.00 0.00 2 int* std::__copy_move_backward::__copy_move_b(int const*, int const*, int*) [805] 0.00 0.00 1+1 std::vector, std::allocator > >::~vector() [825] 0.00 0.00 2 int* std::__copy_move_a(int*, int*, int*) [809] 0.00 0.00 2 std::_Deque_iterator::operator--() [804] 0.00 0.00 1 Cluster::Cluster() [812] ----------------------------------------------- 0.01 2.53 2674989/3187563338 std::set, std::allocator >::insert(int const&) [198] 0.02 8.90 9412154/3187563338 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [117] 0.05 20.86 22053227/3187563338 std::vector >::swap(std::vector >&) [85] 0.19 73.43 77632495/3187563338 std::vector >::operator[](unsigned int) [67] 0.38 146.84 155257253/3187563338 std::vector, std::allocator > >::~vector() [41] 0.44 167.70 177310480/3187563338 std::vector >::push_back(OverlapGraph::ContigInfo const&) [36] 1.31 500.71 529397792/3187563338 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree_impl::~_Rb_tree_impl() [19] 1.43 546.22 577514682/3187563338 std::_Rb_tree, std::less, std::allocator >::~_Rb_tree() [13] 1.43 546.22 577514682/3187563338 std::set, OverlapGraph::IntPairEq, std::allocator > >::set() [18] 2.61 1001.43 1058795584/3187563338 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::~_Rb_tree() [8] [2] 25.1 7.87 3014.85 3187563338 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_unique(std::pair const&) [2] 65.84 2914.88 529397792/529397792 std::vector >::_M_check_len(unsigned int, char const*) const [3] 1.20 29.85 99693459/109105613 std::_Rb_tree, std::less, std::allocator >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, int const&) [93] 1.58 0.46 529397792/529397792 std::_Rb_tree, std::less, std::allocator >::begin() [212] 0.88 0.00 529397792/529397792 std::_Rb_tree_iterator::operator==(std::_Rb_tree_iterator const&) const [280] 0.06 0.02 12087143/77934596 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair const&) [253] 0.01 0.06 9412154/12087143 std::pair >, bool>::pair(std::_Rb_tree_const_iterator > const&, bool const&) [441] ----------------------------------------------- 65.84 2914.88 529397792/529397792 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_unique(std::pair const&) [2] [3] 24.8 65.84 2914.88 529397792 std::vector >::_M_check_len(unsigned int, char const*) const [3] 1225.79 140.35 4087341360/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 1225.79 140.35 4087341360/2099102434 std::vector >::_M_check_len(unsigned int, char const*) const [43] 158.77 18.18 529397792/2099102434 void std::__final_insertion_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [71] 3.29 1.17 114145920/1198094656 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [33] 1.19 0.00 1180800494/1755802966 std::vector, std::allocator > >::max_size() const [172] ----------------------------------------------- 3439465140 _fini [4] 1724816198 UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) [9] 0.00 0.00 499/2099102434 std::back_insert_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, std::back_insert_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::back_insert_iterator > >) [598] 0.00 0.00 499/2099102434 bool std::operator!=, std::allocator >(std::basic_string, std::allocator > const&, std::basic_string, std::allocator > const&) [597] 0.80 0.09 2674989/2099102434 Cluster::GetIndex(int) const [272] 3.48 0.40 11603908/2099102434 Trie::Insert(std::string const&, int, mar_types) [175] 13.64 1.56 45474813/2099102434 OverlapGraph::ContigInfo::ContigInfo(ShortyString const&, int, int, int, mar_types) [124] 35.69 4.09 119021490/2099102434 std::vector, std::allocator > >::push_back(triple const&) [84] 40.11 4.59 133749450/2099102434 std::vector >::swap(std::vector >&) [87] 245.54 28.11 818756912/2099102434 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, Vote const&) [15] 368.32 42.17 1228135368/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [12] 581.00 66.52 1937320110/2099102434 bool __gnu_cxx::operator!= > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [14] 811.81 92.95 2706940188/2099102434 __gnu_cxx::new_allocator::max_size() const [11] [4] 21.1 2521.32 16.25 138559832+3439465140 _fini [4] 15.35 0.00 866365509/1506635566 std::pair* std::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [115] 0.90 0.00 48149802/271331188 __static_initialization_and_destruction_0(int, int) [252] 0.00 0.00 1/1 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::_M_check_len(unsigned int, char const*) const [815] 0.00 0.00 1/1 operator>>(std::istream&, ShortyString&) [827] 0.00 0.00 1/1 std::vector, std::allocator > >::max_size() const [816] 0.00 0.00 1/1 std::_Vector_base >::_M_deallocate(UtilsMath::median_event_point*, unsigned int) [820] 0.00 0.00 1/14 UtilsString::Complement(std::string const&) [772] 1 UtilsFile::OpenFile(std::string const&, std::string const&) [54] 1 Contig::~Contig() [53] 1 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [5] 1 ReadSeededFastaFile(std::string const&, std::vector >*) [26] 1 Hash::LeftShiftHashVal(char, char, int) const [793] 1 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 1 ShortyString::ShortyString(std::string const&, int) [7] 3439465140 _fini [4] ----------------------------------------------- 3549628993 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [5] 1 _fini [4] 14665308 std::vector, std::allocator > >::_M_fill_insert(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, unsigned int, triple const&) [50] 183350579 TrieNode::searchWithErrorWholeSeed(std::string const&, int, int) [138] 0.72 0.08 2416982/2099102434 RawRead* std::__uninitialized_copy::uninitialized_copy(RawRead*, RawRead*, RawRead*) [249] 0.72 0.08 2416982/2099102434 std::string* std::__copy_move_backward::__copy_move_b(std::string*, std::string*, std::string*) [285] 1.45 0.17 4833964/2099102434 __static_initialization_and_destruction_0(int, int) [211] 55.53 6.36 185167275/2099102434 getIndex(char) [62] 165.69 18.97 552470473/2099102434 myList::size() [37] 365.83 41.89 1219827041/2099102434 myList::checkString(std::string const&, int, int) [16] 531.51 60.86 1772297514/2099102434 std::_Vector_base >::_M_allocate(unsigned int) [17] [5] 16.1 1930.95 0.00 3937446119+3549628993 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [5] 3674994298 ShortyString::ShortyString(std::string const&, std::vector > const&) [48] 4833964 __static_initialization_and_destruction_0(int, int) [227] 4833964 std::_Vector_base, std::allocator > >::_Vector_impl::_Vector_impl() [308] 4833964 std::vector, std::allocator > >::_M_fill_insert(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, unsigned int, triple const&) [50] 3549628993 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [5] ----------------------------------------------- 1 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 1 _fini [4] 0.06 0.01 207871/2099102434 mar_types* std::__uninitialized_copy_a<__gnu_cxx::__normal_iterator > >, mar_types*, mar_types>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*, std::allocator&) [452] 0.09 0.01 288962/2099102434 std::vector >::end() const [439] 0.12 0.01 412850/2099102434 std::_Rb_tree_const_iterator::operator++() [374] 0.19 0.02 619831/2099102434 Contig* std::__copy_move_backward_a2(Contig*, Contig*, Contig*) [390] 0.19 0.02 648620/2099102434 std::vector >::begin() const [386] 0.50 0.06 1683262/2099102434 std::allocator > >::~allocator() [313] 0.68 0.08 2262139/2099102434 void std::_Destroy(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, std::allocator&) [234] 0.68 0.08 2262139/2099102434 std::allocator >::~allocator() [233] 0.68 0.08 2262139/2099102434 std::_Rb_tree, std::less, std::allocator >::_M_erase(std::_Rb_tree_node*) [230] 0.73 0.08 2447689/2099102434 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::end() const [282] 0.80 0.09 2674989/2099102434 std::set, OverlapGraph::IntPairEq, std::allocator > >::~set() [278] 1.36 0.16 4524278/2099102434 std::_Vector_base >::~_Vector_base() [194] 3.21 0.37 10707693/2099102434 OverlapGraph::BuildGraph() [23] 4.78 0.55 15926951/2099102434 int* std::vector >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator > > >(unsigned int, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [143] 4.86 0.56 16201587/2099102434 mar_types* std::vector >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator > > >(unsigned int, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [152] 5.94 0.68 19791088/2099102434 std::vector, std::allocator > >::size() const [129] 15.85 1.82 52865362/2099102434 int* std::__copy_move_a2 > >, int*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int*) [98] 17.50 2.00 58339616/2099102434 std::vector, std::allocator > >::operator=(std::vector, std::allocator > > const&) [42] 23.28 2.67 77617115/2099102434 void std::__heap_select<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [61] 152.87 17.50 509734758/2099102434 OverlapGraph::MergeReads(std::vector, std::allocator > > const&) [40] 158.75 18.18 529357842/2099102434 __gnu_cxx::__normal_iterator > >::__normal_iterator(OverlapGraph::ContigInfo* const&) [39] 1225.79 140.35 4087341360/2099102434 std::vector >::_M_check_len(unsigned int, char const*) const [3] [6] 12.7 1479.26 45.57 1103210846+1 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 45.57 0.00 96887489/1397173708 std::vector >::push_back(int const&) [32] 507052032 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [75] 8024967 ReadSeededFastaFile(std::string const&, std::vector >*) [26] 13249 void std::__introsort_loop<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj) [86] 13249 std::vector >::operator=(std::vector > const&) [88] 13249 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] 1 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] ----------------------------------------------- 1 _fini [4] 13130 ShortyString::ShortyString(std::string const&) [743] 3688985037 ShortyString::ShortyString(std::string const&, std::vector > const&) [48] 0.00 0.00 2/2099102434 ShortyString::ShortyString(std::string const&) [635] 0.36 0.04 1208491/2099102434 RawRead* std::__uninitialized_copy::uninitialized_copy(RawRead*, RawRead*, RawRead*) [249] 1.08 0.12 3591444/2099102434 ShortyString::ShortyString() [202] [7] 10.0 1201.29 0.00 3693798105 ShortyString::ShortyString(std::string const&, int) [7] 0.00 0.00 1208469/1208491 ShortyString::push_back(char, Vote const&) [695] 22 ShortyString::GetConfidentClone() const [332] 1 ShortyString::ShortyString(std::string const&) [743] 1 ShortyString::~ShortyString() [791] 1 ShortyString::push_back(char) [794] ----------------------------------------------- [8] 8.4 2.90 1009.71 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::~_Rb_tree() [8] 2.61 1001.43 1058795584/3187563338 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_unique(std::pair const&) [2] 3.62 0.00 577514682/625631572 std::_Rb_tree, std::less, std::allocator >::end() const [178] 2.05 0.00 529397792/539451719 std::list, std::allocator > >::operator=(std::list, std::allocator > > const&) [210] ----------------------------------------------- 385741013 UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) [9] 628666150 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [28] 704740013 UtilsFile::Log(std::ostream*, std::string const&) [58] 961830966 UtilsFile::OpenFile(std::string const&, std::string const&) [54] 401.59 45.98 1339075185/2099102434 UtilsFile::CloseFile(std::basic_fstream >*) [20] [9] 7.7 396.85 529.72 3634312314+385741013 UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) [9] 41.58 131.07 805320026/2635651173 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, UtilsMath::median_event_point const&) [22] 24.77 134.77 628666150/628666150 void std::sort<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [47] 51.29 61.45 1157223039/3222388240 std::deque >::deque(std::deque > const&) [31] 31.62 0.00 1157223039/2734359181 std::deque >::_M_destroy_data(std::_Deque_iterator, std::_Deque_iterator, std::allocator const&) [70] 15.19 9.71 385741013/385741013 __gnu_cxx::new_allocator::construct(UtilsMath::median_event_point*, UtilsMath::median_event_point const&) [108] 19.41 0.00 771482026/1914486784 bool std::operator==(std::_Deque_iterator const&, std::_Deque_iterator const&) [81] 8.88 0.00 385741013/1526430335 std::deque >::end() const [111] 1724816198 Contig::~Contig() [53] 1724816198 _fini [4] 385741013 std::_Vector_base >::~_Vector_base() [46] 29004034 Hash::Insert(std::string const&, int, int, int, int) [220] 385741013 UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) [9] ----------------------------------------------- [10] 7.6 5.94 904.76 mar_types* std::__copy_move_backward_a(mar_types*, mar_types*, mar_types*) [10] 811.81 92.95 2706940188/2099102434 Contig::~Contig() [53] ----------------------------------------------- [11] 7.5 1.40 904.76 __gnu_cxx::new_allocator::max_size() const [11] 811.81 92.95 2706940188/2099102434 _fini [4] ----------------------------------------------- [12] 6.3 113.70 638.67 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [12] 368.32 42.17 1228135368/2099102434 _fini [4] 102.88 11.78 343056370/2099102434 ReadSeededFastaFile(std::string const&, std::vector >*) [26] 81.88 0.00 2670341755/1397173708 std::vector >::push_back(int const&) [32] 31.51 0.00 1663943608/1663943608 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [96] 0.13 0.00 77624758/158981148 operator<<(std::ostream&, ShortyString const&) [359] ----------------------------------------------- [13] 6.1 1.49 733.21 std::_Rb_tree, std::less, std::allocator >::~_Rb_tree() [13] 1.43 546.22 577514682/3187563338 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_unique(std::pair const&) [2] 166.49 19.06 555168922/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] ----------------------------------------------- [14] 5.4 2.03 647.52 bool __gnu_cxx::operator!= > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [14] 581.00 66.52 1937320110/2099102434 _fini [4] ----------------------------------------------- [15] 5.3 5.89 631.20 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, Vote const&) [15] 245.54 28.11 818756912/2099102434 _fini [4] 198.96 22.78 663429030/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] 1.81 99.48 143784439/148011011 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [57] 27.13 0.00 884916593/1397173708 std::vector >::push_back(int const&) [32] 6.61 0.76 22053227/2099102434 std::vector >::operator=(std::vector > const&) [88] ----------------------------------------------- [16] 5.0 196.60 407.71 myList::checkString(std::string const&, int, int) [16] 365.83 41.89 1219827041/2099102434 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [5] ----------------------------------------------- [17] 5.0 5.97 592.37 std::_Vector_base >::_M_allocate(unsigned int) [17] 531.51 60.86 1772297514/2099102434 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [5] ----------------------------------------------- [18] 4.6 1.17 547.65 std::set, OverlapGraph::IntPairEq, std::allocator > >::set() [18] 1.43 546.22 577514682/3187563338 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_unique(std::pair const&) [2] ----------------------------------------------- [19] 4.2 0.58 502.02 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree_impl::~_Rb_tree_impl() [19] 1.31 500.71 529397792/3187563338 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_unique(std::pair const&) [2] ----------------------------------------------- [20] 3.7 1.20 447.57 UtilsFile::CloseFile(std::basic_fstream >*) [20] 401.59 45.98 1339075185/2099102434 UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) [9] ----------------------------------------------- 0.00 0.03 2/28266 Assembler::Assemble() [474] 0.08 177.45 11466/28266 Assembler::ProcessNewSeeds() [38] 0.12 259.97 16798/28266 Assembler::MakeCluster(bool, std::vector, std::allocator > > const&, Cluster*, Cluster*, Contig*, Contig*) [27] [21] 3.6 0.20 437.45 28266 Assembler::MakeContigs(bool, Cluster const&, SeededRead const&) [21] 0.90 349.89 7737/7737 OverlapGraph::BuildGraph() [23] 0.66 50.52 11315750/12451411 main [78] 20.69 2.37 68975489/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [145] 10.24 1.17 34159067/2099102434 std::vector >::operator=(std::vector > const&) [88] 0.03 0.92 7737/7737 std::vector, std::allocator > >::push_back(std::pair const&) [265] 0.03 0.00 84568/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] 0.01 0.00 3546341/3546341 std::pair::~pair() [518] 0.00 0.01 13130/13130 std::vector >::end() [538] 0.00 0.00 13130/13130 ShortyString::ShortyString(std::string const&, std::vector > const&) [563] 0.00 0.00 5786/2099102434 std::vector >::~vector() [208] 0.00 0.00 52637/1397173708 std::vector >::push_back(int const&) [32] 0.00 0.00 26260/26260 __gnu_cxx::new_allocator::construct(mar_types*, mar_types const&) [735] ----------------------------------------------- 0.10 0.31 29004034/2635651173 UtilsMath::median_event_point::operator<(UtilsMath::median_event_point const&) const [340] 0.11 0.33 31421017/2635651173 std::vector >::vector() [335] 0.62 1.96 184878960/2635651173 std::vector >::push_back(UtilsMath::median_event_point const&) [169] 0.62 1.96 184878960/2635651173 std::vector >::begin() [185] 1.30 4.09 385741013/2635651173 void std::_Destroy(UtilsMath::median_event_point*, UtilsMath::median_event_point*, std::allocator&) [154] 19.91 62.78 385741013/2635651173 std::_Vector_base >::~_Vector_base() [46] 32.46 102.32 628666150/2635651173 void std::sort<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [47] 41.58 131.07 805320026/2635651173 UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) [9] [22] 3.3 96.69 304.82 2635651173 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, UtilsMath::median_event_point const&) [22] 85.68 110.62 813545110/842549144 void std::__introsort_loop<__gnu_cxx::__normal_iterator > >, int>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int) [35] 49.39 28.01 1542964052/1644735383 std::_Vector_base, std::allocator > >::~_Vector_base() [64] 23.02 0.00 771482026/1234869252 void std::_Destroy(SeededRead*) [94] 6.90 0.00 385741013/1914486784 bool std::operator==(std::_Deque_iterator const&, std::_Deque_iterator const&) [81] 1.09 0.00 67676000/67677006 std::list, std::allocator > >::begin() [255] 0.11 0.00 29004034/29004034 __gnu_cxx::__normal_iterator > >::__normal_iterator(UtilsMath::median_event_point* const&) [432] ----------------------------------------------- 0.90 349.89 7737/7737 Assembler::MakeContigs(bool, Cluster const&, SeededRead const&) [21] [23] 2.9 0.90 349.89 7737 OverlapGraph::BuildGraph() [23] 1.07 173.95 2674989/2674989 OverlapGraph::MergeReads(std::vector, std::allocator > > const&) [40] 152.07 17.41 507067506/2099102434 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [75] 3.21 0.37 10707693/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 0.80 0.09 2674989/2099102434 ShortyString::ShortyString(std::string const&, std::vector > const&) [48] 0.80 0.09 2674989/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] 0.01 0.01 2682726/116345246 std::deque >::~deque() [134] 0.00 0.00 2674989/58246520 std::vector >::push_back(Vote const&) [455] ----------------------------------------------- [24] 2.7 8.67 315.40 __gnu_cxx::new_allocator >::construct(triple*, triple const&) [24] 283.00 32.40 943639770/2099102434 ReadSeededFastaFile(std::string const&, std::vector >*) [26] ----------------------------------------------- 0.30 57.80 25559691/127331022 std::_Deque_iterator::_Deque_iterator(std::_Deque_iterator const&) [77] 1.20 230.13 101771331/127331022 std::vector, std::allocator > >::size() const [30] [25] 2.4 1.50 287.93 127331022 std::vector, std::allocator > >::_M_erase_at_end(std::pair*) [25] 1.23 244.14 730437481/730437481 void std::_Destroy*, std::pair >(std::pair*, std::pair*, std::allocator >&) [29] 38.19 4.37 127331022/2099102434 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [92] ----------------------------------------------- 39618061 ReadSeededFastaFile(std::string const&, std::vector >*) [26] 1 _fini [4] 8024967 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 0.00 0.00 1/2099102434 Assembler::Assemble() [474] 0.00 0.00 11572/2099102434 Assembler::MakeCluster(bool, std::vector, std::allocator > > const&, Cluster*, Cluster*, Contig*, Contig*) [27] 0.00 0.00 13129/2099102434 ReadProcessor::NumUsed(int) [515] 0.00 0.00 14687/2099102434 Assembler::ProcessNewSeeds() [38] 35.22 4.03 117450198/2099102434 main [78] 102.88 11.78 343056370/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [12] 283.00 32.40 943639770/2099102434 __gnu_cxx::new_allocator >::construct(triple*, triple const&) [24] [26] 2.3 274.74 0.73 1412210695+39618061 ReadSeededFastaFile(std::string const&, std::vector >*) [26] 0.40 0.32 5684107/116345246 std::deque >::~deque() [134] 0.00 0.01 13129/52520 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [545] 11315694 std::vector >::~vector() [208] 5657847 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::~_Rb_tree() [237] 39618061 ReadSeededFastaFile(std::string const&, std::vector >*) [26] ----------------------------------------------- [27] 2.2 0.00 260.68 Assembler::MakeCluster(bool, std::vector, std::allocator > > const&, Cluster*, Cluster*, Contig*, Contig*) [27] 0.12 259.97 16798/28266 Assembler::MakeContigs(bool, Cluster const&, SeededRead const&) [21] 0.00 0.52 23144/52520 SeededRead::~SeededRead() [251] 0.00 0.05 11572/12451411 main [78] 0.01 0.00 23144/2099102434 std::vector >::operator=(std::vector > const&) [88] 0.00 0.00 11572/2099102434 ReadSeededFastaFile(std::string const&, std::vector >*) [26] 0.00 0.00 5786/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] 0.00 0.00 5786/2099102434 std::vector >::vector(std::vector > const&) [514] 0.00 0.00 5786/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] ----------------------------------------------- 637998000 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] 27.72 3.17 92439480/2099102434 std::back_insert_iterator > > std::__copy_move_a2 > >, std::back_insert_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::back_insert_iterator > >) [95] [28] 2.1 84.29 162.95 730437480 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [28] 69.49 2.34 730437481/730437481 std::_Vector_base >::~_Vector_base() [68] 32.37 38.79 730437481/3222388240 std::deque >::deque(std::deque > const&) [31] 19.96 0.00 730437481/2734359181 std::deque >::_M_destroy_data(std::_Deque_iterator, std::_Deque_iterator, std::allocator const&) [70] 628666150 UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) [9] ----------------------------------------------- 1.23 244.14 730437481/730437481 std::vector, std::allocator > >::_M_erase_at_end(std::pair*) [25] [29] 2.0 1.23 244.14 730437481 void std::_Destroy*, std::pair >(std::pair*, std::pair*, std::allocator >&) [29] 219.06 25.08 730437481/2099102434 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [92] ----------------------------------------------- [30] 1.9 0.46 231.33 std::vector, std::allocator > >::size() const [30] 1.20 230.13 101771331/127331022 std::vector, std::allocator > >::_M_erase_at_end(std::pair*) [25] ----------------------------------------------- 0.07 0.09 25559691/3222388240 std::basic_string, std::allocator > std::operator+, std::allocator >(std::basic_string, std::allocator > const&, char const*) [247] 0.07 0.09 25559691/3222388240 std::vector, std::allocator > >::vector() [375] 0.16 0.19 55809948/3222388240 std::vector, std::allocator > >::~vector() [266] 0.16 0.19 55809948/3222388240 std::vector >::operator[](unsigned int) [344] 0.16 0.19 55809948/3222388240 std::vector >::~vector() [281] 2.11 2.53 730437481/3222388240 void std::_Destroy(mar_types*, mar_types*, std::allocator&) [162] 17.10 20.48 385741013/3222388240 UtilsFile::Log(std::ostream*, std::string const&) [58] 32.37 38.79 730437481/3222388240 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [28] 51.29 61.45 1157223039/3222388240 UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) [9] [31] 1.9 103.50 124.00 3222388240 std::deque >::deque(std::deque > const&) [31] 77.74 43.55 2488227333/2544037281 std::_Deque_iterator std::__uninitialized_copy_a, std::_Deque_iterator, SeededRead>(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator, std::allocator&) [51] 2.04 0.66 167429844/537187764 std::_Vector_base, std::allocator > >::_Vector_impl::_Vector_impl() [187] ----------------------------------------------- 0.00 0.00 13130/1397173708 std::vector >::push_back(mar_types const&) [387] 0.00 0.00 13130/1397173708 std::vector >::size() const [592] 0.00 0.00 13249/1397173708 void std::swap(OverlapGraph::ContigInfo*&, OverlapGraph::ContigInfo*&) [558] 0.00 0.00 22395/1397173708 triple const& std::__median, OverlapGraph::SortAdj>(triple const&, triple const&, triple const&, OverlapGraph::SortAdj) [380] 0.00 0.00 26498/1397173708 OverlapGraph::ContigInfo::operator=(OverlapGraph::ContigInfo const&) [551] 0.00 0.00 52637/1397173708 Assembler::MakeContigs(bool, Cluster const&, SeededRead const&) [21] 0.00 0.00 52639/1397173708 main [78] 0.01 0.00 13130/1397173708 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] 0.01 0.00 13130/1397173708 std::deque >::push_back(SeededRead const&) [549] 0.01 0.00 52520/1397173708 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [545] 0.01 0.00 20986/1397173708 std::vector >::operator=(std::vector > const&) [88] 0.01 0.00 26259/1397173708 std::vector >::vector(std::vector > const&) [514] 0.03 0.00 1056643/1397173708 std::vector >::insert(__gnu_cxx::__normal_iterator > >, unsigned int, Vote const&) [291] 0.03 0.00 1056643/1397173708 triple* std::vector, std::allocator > >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > >(unsigned int, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >) [196] 0.08 0.00 2674989/1397173708 std::__lg(int) [444] 0.73 0.00 23804298/1397173708 bool __gnu_cxx::operator== > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [289] 0.76 0.00 24860941/1397173708 std::vector, std::allocator > >::push_back(triple const&) [84] 2.83 0.00 92439480/1397173708 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [57] 3.06 0.00 6502930/1397173708 Contig::operator=(Contig const&) [174] 27.13 0.00 884916593/1397173708 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, Vote const&) [15] 45.57 0.00 96887489/1397173708 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 57.87 0.00 1887279540/1397173708 triple* std::copy*, triple*>(triple*, triple*, triple*) [76] 81.88 0.00 2670341755/1397173708 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [12] [32] 1.8 220.03 0.00 1397173708 std::vector >::push_back(int const&) [32] 0.00 0.00 52520/116345246 std::deque >::~deque() [134] ----------------------------------------------- 3.29 1.17 114145920/1198094656 std::vector >::_M_check_len(unsigned int, char const*) const [3] 4.48 1.59 155241873/1198094656 void std::__heap_select<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [61] 15.27 5.41 529357842/1198094656 OverlapGraph::ContigInfo* std::__uninitialized_move_a >(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, std::allocator&) [113] 17.51 6.21 606974957/1198094656 bool __gnu_cxx::operator==*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [107] 117.94 41.81 4087341360/1198094656 triple* std::__uninitialized_copy_a*, triple*, triple >(triple*, triple*, triple*, std::allocator >&) [45] [33] 1.8 158.50 56.19 1198094656 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [33] 40.43 15.76 4087341360/4097652014 Contig* std::__copy_move_backward::__copy_move_b(Contig*, Contig*, Contig*) [79] ----------------------------------------------- 1 ShortyString::~ShortyString() [791] 66 ShortyString::Print() const [764] 26260 ShortyString::ShortyString(std::string const&) [743] 3083002778 ShortyString::ShortyString(std::string const&, std::vector > const&) [48] 0.00 0.00 22/2099102434 ShortyString::PrintScores(std::ostream&) const [607] 1.08 0.12 3591444/2099102434 ShortyString::ShortyString() [202] [34] 1.7 207.09 0.00 3086620571 ShortyString::~ShortyString() [34] 44 ShortyString::GetConfidentClone() const [332] ----------------------------------------------- 0.28 0.36 29004034/842549144 bool __gnu_cxx::operator!= > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [116] 85.68 110.62 813545110/842549144 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, UtilsMath::median_event_point const&) [22] [35] 1.6 85.96 110.99 842549144 void std::__introsort_loop<__gnu_cxx::__normal_iterator > >, int>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int) [35] 63.78 47.20 3674274660/3674274660 void std::__final_insertion_sort<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [55] ----------------------------------------------- [36] 1.6 0.94 194.09 std::vector >::push_back(OverlapGraph::ContigInfo const&) [36] 0.44 167.70 177310480/3187563338 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_unique(std::pair const&) [2] 23.28 2.67 77624758/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] ----------------------------------------------- [37] 1.6 2.17 184.66 myList::size() [37] 165.69 18.97 552470473/2099102434 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [5] ----------------------------------------------- 1 Assembler::ProcessNewSeeds() [38] [38] 1.5 0.00 178.44 0+1 Assembler::ProcessNewSeeds() [38] 0.08 177.45 11466/28266 Assembler::MakeContigs(bool, Cluster const&, SeededRead const&) [21] 0.00 0.66 29372/52520 SeededRead::~SeededRead() [251] 0.00 0.18 40946/12451411 main [78] 0.02 0.00 68763/2099102434 std::vector >::operator=(std::vector > const&) [88] 0.02 0.00 67208/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] 0.01 0.00 20472/2099102434 std::vector >::vector(std::vector > const&) [514] 0.00 0.00 14687/2099102434 ReadSeededFastaFile(std::string const&, std::vector >*) [26] 0.00 0.00 7344/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] 0.00 0.00 7343/2099102434 std::vector >::~vector() [208] 0.00 0.00 13129/13130 std::vector >::size() const [592] 0.00 0.00 13129/52520 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [545] 0.00 0.00 2/2 __gnu_cxx::new_allocator::construct(int*, int const&) [621] 0.00 0.00 2/116345246 std::deque >::~deque() [134] 0.00 0.00 1/2 std::stack > >::push(SeededRead const&) [807] 1 Assembler::ProcessNewSeeds() [38] ----------------------------------------------- [39] 1.5 0.51 176.93 __gnu_cxx::__normal_iterator > >::__normal_iterator(OverlapGraph::ContigInfo* const&) [39] 158.75 18.18 529357842/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] ----------------------------------------------- 1.07 173.95 2674989/2674989 OverlapGraph::BuildGraph() [23] [40] 1.5 1.07 173.95 2674989 OverlapGraph::MergeReads(std::vector, std::allocator > > const&) [40] 152.87 17.50 509734758/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 1.60 0.18 5349978/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 0.80 0.09 2674989/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] 0.80 0.09 2674989/2099102434 std::vector >::end() [258] 0.00 0.00 7737/2099102434 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [75] ----------------------------------------------- [41] 1.4 0.52 173.30 std::vector, std::allocator > >::~vector() [41] 0.38 146.84 155257253/3187563338 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_unique(std::pair const&) [2] 23.28 2.67 77624758/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 0.13 0.00 77624758/158981148 operator<<(std::ostream&, ShortyString const&) [359] ----------------------------------------------- [42] 1.4 1.79 171.57 std::vector, std::allocator > >::operator=(std::vector, std::allocator > > const&) [42] 135.97 15.57 453376022/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 17.50 2.00 58339616/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 0.12 0.40 39464818/196537847 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] 0.02 0.00 4703949/539451719 std::list, std::allocator > >::operator=(std::list, std::allocator > > const&) [210] ----------------------------------------------- 2674989 Contig::Contig(Contig const&) [214] 232882011 void std::__final_insertion_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [71] 1225.79 140.35 4087341360/2099102434 std::vector >::_M_check_len(unsigned int, char const*) const [3] [43] 1.4 168.21 4.30 27931064 std::vector >::_M_check_len(unsigned int, char const*) const [43] 1.00 1.53 77624758/77624758 std::list, std::allocator > >::empty() const [200] 1.76 0.00 77624758/155249516 std::_List_iterator >::operator++() [217] 157924505 void std::__adjust_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [121] ----------------------------------------------- [44] 1.4 168.36 0.00 missMatchNumber(std::string, std::string, int, int) [44] ----------------------------------------------- 0.46 13.99 77624758/886464451 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator++() [127] 1.65 50.36 279441901/886464451 void std::__heap_select<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [61] 3.14 95.40 529397792/886464451 std::vector >::begin() [56] [45] 1.4 5.25 159.75 886464451 triple* std::__uninitialized_copy_a*, triple*, triple >(triple*, triple*, triple*, std::allocator >&) [45] 117.94 41.81 4087341360/1198094656 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [33] ----------------------------------------------- 385741013 UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) [9] [46] 1.3 33.06 128.96 385741013 std::_Vector_base >::~_Vector_base() [46] 19.91 62.78 385741013/2635651173 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, UtilsMath::median_event_point const&) [22] 40.91 5.36 1157223039/2323744019 std::_Deque_base >::~_Deque_base() [80] 385741013 std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [151] ----------------------------------------------- 24.77 134.77 628666150/628666150 UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) [9] [47] 1.3 24.77 134.77 628666150 void std::sort<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [47] 32.46 102.32 628666150/2635651173 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, UtilsMath::median_event_point const&) [22] ----------------------------------------------- 3674994298 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [5] 0.80 0.09 2674989/2099102434 OverlapGraph::BuildGraph() [23] 3.39 0.39 11315750/2099102434 main [78] [48] 1.3 156.01 0.00 3688985037 ShortyString::ShortyString(std::string const&, std::vector > const&) [48] 3688985037 ShortyString::ShortyString(std::string const&, int) [7] 3083002778 ShortyString::~ShortyString() [34] ----------------------------------------------- 13249 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 39389 std::vector >::~vector() [208] 88164 std::vector >::vector(std::vector > const&) [514] 9177919 std::vector >::end() [258] 0.00 0.00 1/2099102434 Hash::Hash(int) [504] 0.00 0.00 5786/2099102434 Assembler::MakeCluster(bool, std::vector, std::allocator > > const&, Cluster*, Cluster*, Contig*, Contig*) [27] 0.00 0.00 7344/2099102434 Assembler::ProcessNewSeeds() [38] 0.32 0.04 1056643/2099102434 __gnu_cxx::new_allocator::construct(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo const&) [264] 0.32 0.04 1056643/2099102434 std::vector >::_M_erase_at_end(Vote*) [254] 0.32 0.04 1056643/2099102434 std::vector, std::allocator > >::capacity() const [349] 0.32 0.04 1056643/2099102434 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [342] 0.63 0.07 2113286/2099102434 bool __gnu_cxx::operator!= > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [295] 0.80 0.09 2674989/2099102434 OverlapGraph::BuildGraph() [23] 0.80 0.09 2674989/2099102434 OverlapGraph::MergeReads(std::vector, std::allocator > > const&) [40] 0.95 0.11 3169929/2099102434 triple* std::vector, std::allocator > >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > >(unsigned int, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >) [196] 7.14 0.82 23804298/2099102434 std::vector, std::allocator > >::push_back(triple const&) [84] 16.67 1.91 55571531/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [57] 23.28 2.67 77624758/2099102434 std::vector >::push_back(OverlapGraph::ContigInfo const&) [36] 198.96 22.78 663429030/2099102434 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, Vote const&) [15] [49] 1.2 111.83 29.90 844621234 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] 24.25 0.00 433182754/1724816198 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [69] 5.65 0.00 318999000/1506635566 std::pair* std::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [115] 637998000 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [28] 318999000 UtilsFile::Log(std::ostream*, std::string const&) [58] ----------------------------------------------- 4833964 std::vector, std::allocator > >::_M_fill_insert(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, unsigned int, triple const&) [50] 4833964 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [5] 8588826 TrieNode::searchWithErrorWholeSeed(std::string const&, int, int) [138] 0.00 0.00 1/2099102434 ShortyString::ShortyString() [650] 0.00 0.00 13130/2099102434 std::vector, std::allocator > >::insert(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, unsigned int, triple const&) [569] 0.00 0.00 13130/2099102434 std::_Vector_base, std::allocator > >::_Vector_base() [566] 3.44 0.39 11477978/2099102434 std::_Vector_base >::_M_deallocate(readPointer*, unsigned int) [180] 6.88 0.79 22955956/2099102434 std::_Vector_base >::_Vector_impl::_Vector_impl() [149] [50] 1.0 122.72 0.00 47882985+4833964 std::vector, std::allocator > >::_M_fill_insert(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, unsigned int, triple const&) [50] 0.00 0.00 39390/91910 std::vector >::_M_check_len(unsigned int, char const*) const [713] 0.00 0.00 13130/13130 std::vector >::begin() [747] 14665308 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [5] 4833964 TrieNode::searchWithErrorWholeSeed(std::string const&, int, int) [138] 4833964 std::vector, std::allocator > >::_M_fill_insert(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, unsigned int, triple const&) [50] ----------------------------------------------- 0.16 0.09 55809948/2544037281 std::_Vector_base, std::allocator > >::_M_deallocate(std::pair*, unsigned int) [319] 77.74 43.55 2488227333/2544037281 std::deque >::deque(std::deque > const&) [31] [51] 1.0 77.90 43.64 2544037281 std::_Deque_iterator std::__uninitialized_copy_a, std::_Deque_iterator, SeededRead>(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator, std::allocator&) [51] 23.30 15.77 1141738185/1623116001 std::deque >::_M_reserve_map_at_back(unsigned int) [91] 4.57 0.00 463387226/463889692 void std::_Destroy_aux::__destroy(Contig*, Contig*) [171] ----------------------------------------------- 857768503 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [92] [52] 0.9 46.63 65.46 857768503 Vote* std::__copy_move::__copy_m(Vote*, Vote*, Vote*) [52] 57.10 0.00 1937320110/3971005539 SeededRead** std::__copy_move_backward_a2(SeededRead**, SeededRead**, SeededRead**) [72] 3.48 4.88 101771331/2166422463 SeededRead** std::__copy_move_a2(SeededRead**, SeededRead**, SeededRead**) [119] 1937320110 Contig::~Contig() [53] ----------------------------------------------- 1 _fini [4] 4 std::deque >::_M_pop_back_aux() [786] 600 std::deque >::_M_reallocate_map(unsigned int, bool) [758] 600 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [405] 1818 bool std::operator!=(std::_Deque_iterator const&, std::_Deque_iterator const&) [759] 9146 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, RawRead const&) [235] 13130 std::deque >::push_back(SeededRead const&) [549] 1208491 ShortyString::reverse() [769] 1242520 ShortyString::GetConfidentClone() const [332] 2097151 ShortyString::operator+=(ShortyString const&) [334] 2097151 ShortyString::operator+=(std::string const&) [333] 2674989 Contig::operator=(Contig const&) [174] 3827941 __static_initialization_and_destruction_0(int, int) [100] 21589830 Vote* std::copy(Vote*, Vote*, Vote*) [257] 91296551 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [145] 475846366 OverlapGraph::AllocateData() [112] 568095230 ReadProcessor::ReadProcessor(std::string const&) [59] 1724816198 UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) [9] 1937320110 Vote* std::__copy_move::__copy_m(Vote*, Vote*, Vote*) [52] 0.00 0.00 4/2099102434 std::_Vector_base >::_M_deallocate(Contig*, unsigned int) [625] 0.00 0.00 13130/2099102434 std::deque >::_S_buffer_size() [568] 0.00 0.00 13249/2099102434 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::__unguarded_partition<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj) [537] 3.44 0.39 11477978/2099102434 Contig::GetMt(int) const [181] 6.61 0.76 22053227/2099102434 std::_Rb_tree, std::less, std::allocator >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, int const&) [93] 8.24 0.94 27469656/2099102434 std::vector >::operator[](unsigned int) [144] 70.90 8.12 236425176/2099102434 ReadProcessor::Debug() const [63] 811.81 92.95 2706940188/2099102434 mar_types* std::__copy_move_backward_a(mar_types*, mar_types*, mar_types*) [10] [53] 0.9 111.37 0.00 3541563139 Contig::~Contig() [53] 1 Cluster::Cluster() [812] ----------------------------------------------- 184878960 UtilsFile::OpenFile(std::string const&, std::string const&) [54] 1 _fini [4] 0.72 0.08 2416982/2099102434 __static_initialization_and_destruction_0(int, int) [286] 27.72 3.17 92439480/2099102434 std::iterator_traits<__gnu_cxx::__normal_iterator > > >::iterator_category std::__iterator_category<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > > const&) [97] 55.45 6.35 184878960/2099102434 void std::__reverse<__gnu_cxx::__normal_iterator >(__gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator, std::random_access_iterator_tag) [74] 55.45 6.35 184878960/2099102434 void std::__reverse<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::random_access_iterator_tag) [73] 55.45 6.35 184878960/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [57] [54] 0.9 87.29 23.81 649493343+184878960 UtilsFile::OpenFile(std::string const&, std::string const&) [54] 17.43 0.00 637998000/2734359181 std::deque >::_M_destroy_data(std::_Deque_iterator, std::_Deque_iterator, std::allocator const&) [70] 6.38 0.00 277318440/1526430335 std::deque >::end() const [111] 961830966 UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) [9] 184878960 UtilsFile::OpenFile(std::string const&, std::string const&) [54] ----------------------------------------------- 63.78 47.20 3674274660/3674274660 void std::__introsort_loop<__gnu_cxx::__normal_iterator > >, int>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int) [35] [55] 0.9 63.78 47.20 3674274660 void std::__final_insertion_sort<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [55] 47.20 0.00 1224758220/1724816198 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [69] ----------------------------------------------- [56] 0.9 7.17 98.54 std::vector >::begin() [56] 3.14 95.40 529397792/886464451 triple* std::__uninitialized_copy_a*, triple*, triple >(triple*, triple*, triple*, std::allocator >&) [45] ----------------------------------------------- 0.01 0.73 1056643/148011011 std::vector >::_M_erase_at_end(Vote*) [254] 0.01 0.73 1056643/148011011 std::vector >::insert(__gnu_cxx::__normal_iterator > >, unsigned int, Vote const&) [291] 0.03 1.46 2113286/148011011 triple* std::vector, std::allocator > >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > >(unsigned int, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >) [196] 1.81 99.48 143784439/148011011 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, Vote const&) [15] [57] 0.9 1.86 102.41 148011011 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [57] 55.45 6.35 184878960/2099102434 UtilsFile::OpenFile(std::string const&, std::string const&) [54] 16.67 1.91 55571531/2099102434 std::vector >::operator=(std::vector > const&) [88] 16.67 1.91 55571531/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] 2.83 0.00 92439480/1397173708 std::vector >::push_back(int const&) [32] 0.21 0.03 92439480/2323744019 std::_Deque_base >::~_Deque_base() [80] 0.23 0.00 92439480/275580450 std::deque >::begin() [299] 0.10 0.00 184878960/184878960 __gnu_cxx::new_allocator >::max_size() const [433] 0.06 0.00 55571531/58246520 std::vector >::push_back(Vote const&) [455] ----------------------------------------------- 318999000 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] [58] 0.8 61.36 37.58 318999000 UtilsFile::Log(std::ostream*, std::string const&) [58] 17.10 20.48 385741013/3222388240 std::deque >::deque(std::deque > const&) [31] 704740013 UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) [9] ----------------------------------------------- 2668229 ReadProcessor::ReadProcessor(std::string const&) [59] 15474 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [707] 156765 ReadProcessor::ReadProcessor(std::string const&) [358] 3441556 void std::__push_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [147] 19345116 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [238] 96233780 triple* std::__copy_move_backward::__copy_move_b*, triple*>(triple*, triple*, triple*) [101] 144358407 triple* std::__uninitialized_copy::uninitialized_copy*, triple*>(triple*, triple*, triple*) [161] 439407125 void std::__adjust_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [121] 513554962 __gnu_cxx::new_allocator > >::allocate(unsigned int, void const*) [120] 0.01 0.00 44790/2099102434 mar_types* std::__copy_move_a2 > >, mar_types*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*) [394] 0.79 0.09 2623439/2099102434 mar_types* std::copy<__gnu_cxx::__normal_iterator > >, mar_types*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*) [155] 1.57 0.18 5246878/2099102434 int* std::copy<__gnu_cxx::__normal_iterator > >, int*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int*) [225] 11.58 1.33 38604692/2099102434 mar_types* std::__uninitialized_copy::uninitialized_copy<__gnu_cxx::__normal_iterator > >, mar_types*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*) [130] 14.15 1.62 10310654/2099102434 Contig* std::__copy_move_backward::__copy_move_b(Contig*, Contig*, Contig*) [79] 19.76 2.26 65885078/2099102434 Contig* std::__uninitialized_copy::uninitialized_copy(Contig*, Contig*, Contig*) [114] 23.28 2.67 77624758/2099102434 std::__niter_base<__gnu_cxx::__normal_iterator > >, true>::__b(__gnu_cxx::__normal_iterator > >) [105] [59] 0.8 76.70 18.30 1416853474+2668229 ReadProcessor::ReadProcessor(std::string const&) [59] 5.83 1.09 48116890/48116890 std::vector >::push_back(RawRead const&) [153] 1.38 1.76 77624758/77624758 void std::fill(char*, char*, int const&) [193] 2.96 0.00 155249516/317564878 std::list, std::allocator > >::_M_check_equal_allocators(std::list, std::allocator > >&) [188] 2.84 0.00 96233780/3971005539 SeededRead** std::__copy_move_backward_a2(SeededRead**, SeededRead**, SeededRead**) [72] 1.99 0.00 21447747/21447747 std::vector >::push_back(std::string const&) [215] 0.20 0.08 2623439/77934596 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair const&) [253] 0.18 0.00 6883112/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [240] 568095230 Contig::~Contig() [53] 11379058 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, RawRead const&) [235] 6502930 std::vector >::end() [258] 206591 __static_initialization_and_destruction_0(int, int) [100] 2668229 ReadProcessor::ReadProcessor(std::string const&) [59] ----------------------------------------------- 70208 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Contig const&) [428] 48124627 void std::__final_insertion_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [71] 1110557879 void std::__introsort_loop<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj) [86] 0.01 0.00 21385/2099102434 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [501] 5.79 0.66 19302346/2099102434 triple* std::__copy_move_backward_a2*, triple*>(triple*, triple*, triple*) [158] 36.78 4.21 122624701/2099102434 std::pair* std::vector, std::allocator > >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > >(unsigned int, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >) [89] [60] 0.8 91.43 0.00 1300701146 std::vector >::operator=(std::vector > const&) [60] 555168922 triple* std::__copy_move_backward::__copy_move_b*, triple*>(triple*, triple*, triple*) [101] 507052032 __gnu_cxx::new_allocator > >::allocate(unsigned int, void const*) [120] 48124627 triple* std::__uninitialized_copy::uninitialized_copy*, triple*>(triple*, triple*, triple*) [161] 48116890 std::_Deque_base >::_M_initialize_map(unsigned int) [242] 48116890 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [177] 19323731 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [238] 186838 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [707] 175862 __gnu_cxx::new_allocator::construct(Contig*, Contig const&) [268] 42770 OverlapGraph::ContigInfo* std::__uninitialized_copy::uninitialized_copy(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [583] 7737 void std::__adjust_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [121] ----------------------------------------------- 0.00 0.01 39950/636508560 std::_Vector_base >::_M_allocate(unsigned int) [550] 0.15 10.26 77584808/636508560 std::_Rb_tree, std::less, std::allocator >::_S_key(std::_Rb_tree_node const*) [137] 1.09 73.94 558883802/636508560 __gnu_cxx::__normal_iterator > >::difference_type __gnu_cxx::operator- > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [66] [61] 0.7 1.25 84.21 636508560 void std::__heap_select<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [61] 1.65 50.36 279441901/886464451 triple* std::__uninitialized_copy_a*, triple*, triple >(triple*, triple*, triple*, std::allocator >&) [45] 23.28 2.67 77617115/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 4.48 1.59 155241873/1198094656 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [33] 0.18 0.00 77617115/606974957 void std::iter_swap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [236] ----------------------------------------------- [62] 0.7 18.79 61.89 getIndex(char) [62] 55.53 6.36 185167275/2099102434 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [5] ----------------------------------------------- [63] 0.7 0.00 79.02 ReadProcessor::Debug() const [63] 70.90 8.12 236425176/2099102434 Contig::~Contig() [53] ----------------------------------------------- 0.30 0.17 101771331/1644735383 std::vector, std::allocator > >::push_back(std::pair const&) [223] 49.39 28.01 1542964052/1644735383 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, UtilsMath::median_event_point const&) [22] [64] 0.6 49.69 28.18 1644735383 std::_Vector_base, std::allocator > >::~_Vector_base() [64] 25.63 2.54 771482026/873253357 std::pair* std::copy_backward*, std::pair*>(std::pair*, std::pair*, std::pair*) [99] ----------------------------------------------- 5357715 OverlapGraph::Traverse(int, int, int, int) [245] 0.00 0.00 13249/2099102434 void std::swap(OverlapGraph::ContigInfo*&, OverlapGraph::ContigInfo*&) [558] 0.12 0.01 412850/2099102434 std::_Rb_tree_const_iterator::operator++() [374] 0.26 0.03 857934/2099102434 std::_Vector_base >::_Vector_impl::~_Vector_impl() [371] 0.32 0.04 1056643/2099102434 OverlapGraph::ContigInfo::ContigInfo(OverlapGraph::ContigInfo const&) [259] 0.32 0.04 1069892/2099102434 std::vector, std::allocator > >::push_back(triple const&) [345] 0.41 0.05 1368147/2099102434 std::_Vector_base, std::allocator > >::~_Vector_base() [325] 0.50 0.06 1683262/2099102434 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree() [314] 0.68 0.08 2262139/2099102434 void std::_Destroy(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, std::allocator&) [234] 0.68 0.08 2262139/2099102434 std::allocator >::~allocator() [233] 0.68 0.08 2262139/2099102434 std::_Rb_tree, std::less, std::allocator >::_M_erase(std::_Rb_tree_node*) [230] 0.80 0.09 2674989/2099102434 global constructors keyed to _ZN12OverlapGraphC2EbRK7ClusterPK10SeededReadPK13ReadProcessorPSt13basic_fstreamIcSt11char_traitsIcEESD_ [276] 0.80 0.09 2674989/2099102434 Cluster::GetGen(int) const [271] 0.80 0.09 2674989/2099102434 OverlapGraph::IntPairEq::operator()(std::pair const&, std::pair const&) const [206] 0.80 0.09 2674989/2099102434 std::set, std::allocator >::~set() [279] 0.80 0.09 2674989/2099102434 std::vector >::~vector() [222] 1.36 0.16 4524278/2099102434 std::_Vector_base >::~_Vector_base() [194] 1.60 0.18 5349978/2099102434 OverlapGraph::MergeReads(std::vector, std::allocator > > const&) [40] 5.94 0.68 19791088/2099102434 std::vector, std::allocator > >::size() const [129] 13.64 1.56 45474813/2099102434 OverlapGraph::SortAdj::operator()(triple const&, triple const&) const [125] 23.28 2.67 77624758/2099102434 std::vector, std::allocator > >::~vector() [41] 23.28 2.67 77624758/2099102434 std::vector >::swap(std::vector >&) [85] 135.97 15.57 453376022/2099102434 std::vector, std::allocator > >::operator=(std::vector, std::allocator > > const&) [42] 166.49 19.06 555168922/2099102434 std::_Rb_tree, std::less, std::allocator >::~_Rb_tree() [13] [65] 0.6 53.38 23.80 1270915671 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 12.61 2.75 555168922/1735969416 OverlapGraph::ContigInfo* std::copy_backward(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [122] 4.91 0.01 96299604/96299604 std::vector, std::allocator > >::_M_erase_at_end(std::pair*) [167] 3.53 0.00 9651173/9651173 std::_Vector_base >::_Vector_impl::_Vector_impl() [183] 0.00 0.00 9651173/9828241 std::allocator >::~allocator() [679] 0.00 0.00 70208/70208 std::vector, std::allocator > >::begin() const [718] 388570435 OverlapGraph::AllocateData() [112] 48149802 std::vector, std::allocator > >::end() const [213] 7065846 Contig::Contig(Contig const&) [214] 7065846 __gnu_cxx::new_allocator::construct(Contig*, Contig const&) [268] 2635729 Contig::operator=(Contig const&) [174] 70208 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Contig const&) [428] 15474 void std::__introsort_loop<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj) [86] ----------------------------------------------- [66] 0.6 0.52 75.03 __gnu_cxx::__normal_iterator > >::difference_type __gnu_cxx::operator- > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [66] 1.09 73.94 558883802/636508560 void std::__heap_select<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [61] ----------------------------------------------- [67] 0.6 0.05 73.62 std::vector >::operator[](unsigned int) [67] 0.19 73.43 77632495/3187563338 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_unique(std::pair const&) [2] ----------------------------------------------- 69.49 2.34 730437481/730437481 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [28] [68] 0.6 69.49 2.34 730437481 std::_Vector_base >::~_Vector_base() [68] 2.34 0.00 101771331/1526430335 std::deque >::end() const [111] ----------------------------------------------- 0.00 0.00 499/1724816198 std::_Vector_base >::_Vector_base() [618] 0.24 0.00 66874725/1724816198 void std::reverse<__gnu_cxx::__normal_iterator >(__gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator) [305] 24.25 0.00 433182754/1724816198 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] 47.20 0.00 1224758220/1724816198 void std::__final_insertion_sort<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [55] [69] 0.6 71.70 0.00 1724816198 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [69] ----------------------------------------------- 0.05 0.00 25559691/2734359181 std::basic_string, std::allocator > std::operator+, std::allocator >(std::basic_string, std::allocator > const&, char const*) [247] 0.05 0.00 25559691/2734359181 std::_Deque_iterator::_Deque_iterator(std::_Deque_iterator const&) [77] 0.10 0.00 55809948/2734359181 std::vector, std::allocator > >::~vector() [266] 0.18 0.00 101771331/2734359181 std::vector, std::allocator > >::push_back(std::pair const&) [223] 17.43 0.00 637998000/2734359181 UtilsFile::OpenFile(std::string const&, std::string const&) [54] 19.96 0.00 730437481/2734359181 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [28] 31.62 0.00 1157223039/2734359181 UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) [9] [70] 0.6 69.38 0.00 2734359181 std::deque >::_M_destroy_data(std::_Deque_iterator, std::_Deque_iterator, std::allocator const&) [70] ----------------------------------------------- 77624758 void std::__final_insertion_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [71] 48149802 std::vector, std::allocator > >::end() const [213] 507082980 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [75] 158.77 18.18 529397792/2099102434 std::vector >::_M_check_len(unsigned int, char const*) const [3] [71] 0.5 65.50 0.00 1084630574+77624758 void std::__final_insertion_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [71] 232882011 std::vector >::_M_check_len(unsigned int, char const*) const [43] 48124627 std::vector >::operator=(std::vector > const&) [60] 77624758 void std::__final_insertion_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [71] ----------------------------------------------- 0.00 0.00 131539/3971005539 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [415] 2.84 0.00 96233780/3971005539 ReadProcessor::ReadProcessor(std::string const&) [59] 3.72 0.00 1937320110/3971005539 __gnu_cxx::new_allocator::new_allocator() [182] 57.10 0.00 1937320110/3971005539 Vote* std::__copy_move::__copy_m(Vote*, Vote*, Vote*) [52] [72] 0.5 63.66 0.00 3971005539 SeededRead** std::__copy_move_backward_a2(SeededRead**, SeededRead**, SeededRead**) [72] ----------------------------------------------- [73] 0.5 0.83 62.03 void std::__reverse<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::random_access_iterator_tag) [73] 55.45 6.35 184878960/2099102434 UtilsFile::OpenFile(std::string const&, std::string const&) [54] 0.21 0.03 92439480/2323744019 std::_Deque_base >::~_Deque_base() [80] ----------------------------------------------- [74] 0.5 0.66 62.14 void std::__reverse<__gnu_cxx::__normal_iterator >(__gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator, std::random_access_iterator_tag) [74] 55.45 6.35 184878960/2099102434 UtilsFile::OpenFile(std::string const&, std::string const&) [54] 0.21 0.03 92439480/2323744019 std::_Deque_base >::~_Deque_base() [80] 0.11 0.00 92439480/1506635566 std::pair* std::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [115] ----------------------------------------------- 507059769 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [75] 7737 std::vector >::end() [258] 140416 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::__copy_move_a2 const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [720] 5419611 OverlapGraph::Traverse(int, int, int, int) [245] 507052032 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 0.00 0.00 7737/2099102434 OverlapGraph::MergeReads(std::vector, std::allocator > > const&) [40] 0.02 0.00 70208/2099102434 void std::_Destroy<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [465] 0.02 0.00 70208/2099102434 std::pair* std::__copy_move_a2*, std::pair*>(std::pair*, std::pair*, std::pair*) [464] 0.80 0.09 2682726/2099102434 std::vector >::~vector() [222] 0.80 0.09 2682726/2099102434 std::vector, std::allocator > >::push_back(std::pair const&) [265] 0.80 0.09 2682726/2099102434 std::set, std::allocator >::begin() const [275] 0.80 0.09 2682726/2099102434 std::set, OverlapGraph::IntPairEq, std::allocator > >::insert(std::pair const&) [269] 0.80 0.09 2682726/2099102434 void std::sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [270] 152.07 17.41 507067506/2099102434 OverlapGraph::BuildGraph() [23] [75] 0.5 61.97 0.00 1033249085+507059769 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [75] 1521217992 void std::__introsort_loop<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj) [86] 507082980 void std::__final_insertion_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [71] 5349978 Contig::Contig(Contig const&) [214] 507059769 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [75] ----------------------------------------------- [76] 0.5 1.51 57.87 triple* std::copy*, triple*>(triple*, triple*, triple*) [76] 57.87 0.00 1887279540/1397173708 std::vector >::push_back(int const&) [32] ----------------------------------------------- [77] 0.5 0.17 58.14 std::_Deque_iterator::_Deque_iterator(std::_Deque_iterator const&) [77] 0.30 57.80 25559691/127331022 std::vector, std::allocator > >::_M_erase_at_end(std::pair*) [25] 0.05 0.00 25559691/2734359181 std::deque >::_M_destroy_data(std::_Deque_iterator, std::_Deque_iterator, std::allocator const&) [70] ----------------------------------------------- 0.00 0.00 2/12451411 Assembler::Assemble() [474] 0.00 0.05 11572/12451411 Assembler::MakeCluster(bool, std::vector, std::allocator > > const&, Cluster*, Cluster*, Contig*, Contig*) [27] 0.00 0.06 13249/12451411 triple::triple(int, int, int) [457] 0.00 0.18 40946/12451411 Assembler::ProcessNewSeeds() [38] 0.06 4.78 1069892/12451411 std::vector, std::allocator > >::begin() [168] 0.66 50.52 11315750/12451411 Assembler::MakeContigs(bool, Cluster const&, SeededRead const&) [21] [78] 0.5 0.73 55.59 12451411 main [78] 35.22 4.03 117450198/2099102434 ReadSeededFastaFile(std::string const&, std::vector >*) [26] 7.43 0.85 24771284/2099102434 std::vector >::~vector() [208] 3.71 0.43 12385642/2099102434 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::~_Rb_tree() [237] 3.39 0.39 11315750/2099102434 ShortyString::ShortyString(std::string const&, std::vector > const&) [48] 0.05 0.04 11342010/116345246 std::deque >::~deque() [134] 0.02 0.00 79018/2099102434 std::vector, std::allocator > >::begin() const [711] 0.01 0.00 39509/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] 0.00 0.00 52639/1397173708 std::vector >::push_back(int const&) [32] 0.00 0.00 13130/52520 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [545] ----------------------------------------------- 0.02 0.01 10310654/4097652014 triple* std::__copy_move_backward_a2*, triple*>(triple*, triple*, triple*) [158] 40.43 15.76 4087341360/4097652014 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [33] [79] 0.5 40.45 15.77 4097652014 Contig* std::__copy_move_backward::__copy_move_b(Contig*, Contig*, Contig*) [79] 14.15 1.62 10310654/2099102434 ReadProcessor::ReadProcessor(std::string const&) [59] ----------------------------------------------- 0.06 0.01 25559691/2323744019 std::basic_string, std::allocator > std::operator+, std::allocator >(std::basic_string, std::allocator > const&, char const*) [247] 0.13 0.02 55809948/2323744019 std::vector, std::allocator > >::~vector() [266] 0.13 0.02 55809948/2323744019 std::vector >::vector() [392] 0.21 0.03 92439480/2323744019 void std::__reverse<__gnu_cxx::__normal_iterator >(__gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator, std::random_access_iterator_tag) [74] 0.21 0.03 92439480/2323744019 void std::__reverse<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::random_access_iterator_tag) [73] 0.21 0.03 92439480/2323744019 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [57] 0.23 0.03 101771331/2323744019 std::vector, std::allocator > >::push_back(std::pair const&) [223] 0.23 0.03 101771331/2323744019 std::stack > >::top() [351] 0.89 0.12 385741013/2323744019 void std::_Destroy(UtilsMath::median_event_point*, UtilsMath::median_event_point*, std::allocator&) [154] 4.49 0.59 162739278/2323744019 std::deque >::~deque() [134] 40.91 5.36 1157223039/2323744019 std::_Vector_base >::~_Vector_base() [46] [80] 0.4 47.71 6.25 2323744019 std::_Deque_base >::~_Deque_base() [80] 6.15 0.00 460459410/1526430335 std::deque >::end() const [111] 0.09 0.00 480071/960142 std::deque >::begin() const [434] ----------------------------------------------- 0.24 0.00 55809948/1914486784 std::_Deque_base >::_M_allocate_node() [262] 6.28 0.00 481377816/1914486784 std::deque >::_M_reserve_map_at_back(unsigned int) [91] 6.90 0.00 385741013/1914486784 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, UtilsMath::median_event_point const&) [22] 9.71 0.00 385741013/1914486784 __gnu_cxx::new_allocator::construct(UtilsMath::median_event_point*, UtilsMath::median_event_point const&) [108] 11.33 0.00 4129302264/1914486784 SeededRead** std::__copy_move_a2(SeededRead**, SeededRead**, SeededRead**) [119] 19.41 0.00 771482026/1914486784 UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) [9] [81] 0.4 53.87 0.00 1914486784 bool std::operator==(std::_Deque_iterator const&, std::_Deque_iterator const&) [81] ----------------------------------------------- 0.01 24.36 37707828/75448568 __gnu_cxx::new_allocator >::deallocate(triple*, unsigned int) [110] 0.02 24.38 37740740/75448568 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [109] [82] 0.4 0.03 48.75 75448568 std::_Rb_tree, std::less, std::allocator >::_S_value(std::_Rb_tree_node const*) [82] 0.50 48.25 75448568/75448568 void std::swap >(triple&, triple&) [83] ----------------------------------------------- 0.50 48.25 75448568/75448568 std::_Rb_tree, std::less, std::allocator >::_S_value(std::_Rb_tree_node const*) [82] [83] 0.4 0.50 48.25 75448568 void std::swap >(triple&, triple&) [83] 14.43 1.65 48116890/2099102434 triple* std::__copy_move_backward::__copy_move_b*, triple*>(triple*, triple*, triple*) [101] 14.43 1.65 48116890/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [145] 14.43 1.65 48116890/2099102434 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [177] ----------------------------------------------- [84] 0.4 0.14 48.50 std::vector, std::allocator > >::push_back(triple const&) [84] 35.69 4.09 119021490/2099102434 _fini [4] 7.14 0.82 23804298/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] 0.76 0.00 24860941/1397173708 std::vector >::push_back(int const&) [32] ----------------------------------------------- [85] 0.4 0.79 47.79 std::vector >::swap(std::vector >&) [85] 23.28 2.67 77624758/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 0.05 20.86 22053227/3187563338 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_unique(std::pair const&) [2] 0.72 0.21 77624758/77624758 Vote::operator+=(Vote const&) [267] ----------------------------------------------- 48132364 void std::__introsort_loop<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj) [86] 13249 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 15474 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 280832 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Contig const&) [428] 1521217992 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [75] 0.00 0.00 13249/2099102434 void std::_Destroy*, std::pair >(std::pair*, std::pair*, std::allocator >&) [561] 0.00 0.00 13249/2099102434 OverlapGraph::ContigInfo::operator=(OverlapGraph::ContigInfo const&) [551] 0.03 0.00 87931/2099102434 void std::_Destroy*, triple >(triple*, triple*, std::allocator >&) [479] 0.63 0.07 2113286/2099102434 OverlapGraph::ContigInfo::ContigInfo(OverlapGraph::ContigInfo const&) [259] [86] 0.4 47.86 0.00 1523755262+48132364 void std::__introsort_loop<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj) [86] 1110557879 std::vector >::operator=(std::vector > const&) [60] 48132364 void std::__introsort_loop<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj) [86] ----------------------------------------------- [87] 0.4 0.53 44.98 std::vector >::swap(std::vector >&) [87] 40.11 4.59 133749450/2099102434 _fini [4] 0.13 0.08 66874725/66875224 UtilsString::OverlapFromCommonReadMapping(ShortyString const&, ShortyString const&, std::vector, std::allocator > > const&, std::vector, std::allocator > > const&, ReadProcessor const*, int*, int*, ShortyString*) [388] 0.07 0.00 58246520/1506635566 std::pair* std::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [115] ----------------------------------------------- 13249 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 22395 TrieNode::destructNode() [730] 0.00 0.00 6/2099102434 Assembler::Assemble() [474] 0.00 0.00 13129/2099102434 ShortyString::ShortyString(ShortyString const&) [512] 0.00 0.00 13249/2099102434 std::_Rb_tree_const_iterator >::operator!=(std::_Rb_tree_const_iterator > const&) const [559] 0.00 0.00 13249/2099102434 std::_Rb_tree_const_iterator >::operator++() [560] 0.00 0.00 13249/2099102434 void std::sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [270] 0.01 0.00 23144/2099102434 Assembler::MakeCluster(bool, std::vector, std::allocator > > const&, Cluster*, Cluster*, Contig*, Contig*) [27] 0.02 0.00 68763/2099102434 Assembler::ProcessNewSeeds() [38] 0.32 0.04 1056643/2099102434 __gnu_cxx::new_allocator::construct(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo const&) [264] 0.80 0.09 2674989/2099102434 OverlapGraph::IntPairEq::operator()(std::pair const&, std::pair const&) const [206] 6.61 0.76 22053227/2099102434 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, Vote const&) [15] 10.24 1.17 34159067/2099102434 Assembler::MakeContigs(bool, Cluster const&, SeededRead const&) [21] 16.67 1.91 55571531/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [57] [88] 0.4 33.90 10.35 115695890 std::vector >::operator=(std::vector > const&) [88] 5.79 4.55 81369639/116345246 std::deque >::~deque() [134] 0.01 0.00 20986/1397173708 std::vector >::push_back(int const&) [32] 0.00 0.00 52520/176329 std::vector, std::allocator > >::end() const [708] 114424 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] 52520 std::vector, std::allocator > >::begin() const [711] 2 std::vector, std::allocator > >::end() const [782] 1 std::vector, std::allocator > >::~vector() [825] ----------------------------------------------- [89] 0.4 1.36 42.03 std::pair* std::vector, std::allocator > >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > >(unsigned int, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >) [89] 36.78 4.21 122624701/2099102434 std::vector >::operator=(std::vector > const&) [60] 0.70 0.05 122624701/304749023 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree_impl::_M_initialize() [218] 0.26 0.00 245249402/518771239 std::_Rb_tree, std::less, std::allocator >::_M_put_node(std::_Rb_tree_node*) [311] 0.04 0.00 48149802/96407108 std::_Rb_tree, std::less, std::allocator >::get_allocator() const [447] ----------------------------------------------- [90] 0.3 0.07 40.99 std::allocator > >::allocator() [90] 36.78 4.21 122624701/2099102434 void std::__adjust_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [121] ----------------------------------------------- 0.21 0.14 111619896/1623116001 std::allocator >::~allocator() [336] 0.69 0.47 369757920/1623116001 std::vector >::push_back(UtilsMath::median_event_point const&) [169] 23.30 15.77 1141738185/1623116001 std::_Deque_iterator std::__uninitialized_copy_a, std::_Deque_iterator, SeededRead>(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator, std::allocator&) [51] [91] 0.3 24.20 16.38 1623116001 std::deque >::_M_reserve_map_at_back(unsigned int) [91] 10.10 0.00 463387226/1234869252 void std::_Destroy(SeededRead*) [94] 6.28 0.00 481377816/1914486784 bool std::operator==(std::_Deque_iterator const&, std::_Deque_iterator const&) [81] ----------------------------------------------- 307868 std::pair::pair(std::pair const&) [705] 38.19 4.37 127331022/2099102434 std::vector, std::allocator > >::_M_erase_at_end(std::pair*) [25] 219.06 25.08 730437481/2099102434 void std::_Destroy*, std::pair >(std::pair*, std::pair*, std::allocator >&) [29] [92] 0.3 38.96 0.01 858076371 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [92] 0.01 0.00 307868/97678121 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [415] 857768503 Vote* std::__copy_move::__copy_m(Vote*, Vote*, Vote*) [52] ----------------------------------------------- 0.11 2.82 9412154/109105613 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [117] 1.20 29.85 99693459/109105613 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_unique(std::pair const&) [2] [93] 0.3 1.31 32.66 109105613 std::_Rb_tree, std::less, std::allocator >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, int const&) [93] 0.90 24.39 77640232/77640232 bool __gnu_cxx::operator==*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [107] 6.61 0.76 22053227/2099102434 Contig::~Contig() [53] ----------------------------------------------- 10.10 0.00 463387226/1234869252 std::deque >::_M_reserve_map_at_back(unsigned int) [91] 23.02 0.00 771482026/1234869252 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, UtilsMath::median_event_point const&) [22] [94] 0.3 33.12 0.00 1234869252 void std::_Destroy(SeededRead*) [94] ----------------------------------------------- [95] 0.3 0.75 31.10 std::back_insert_iterator > > std::__copy_move_a2 > >, std::back_insert_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::back_insert_iterator > >) [95] 27.72 3.17 92439480/2099102434 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [28] 0.20 0.00 92439480/92439480 global constructors keyed to _ZN12ShortyStringC2Ev [391] ----------------------------------------------- 31.51 0.00 1663943608/1663943608 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [12] [96] 0.3 31.51 0.00 1663943608 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [96] ----------------------------------------------- [97] 0.3 0.04 30.90 std::iterator_traits<__gnu_cxx::__normal_iterator > > >::iterator_category std::__iterator_category<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > > const&) [97] 27.72 3.17 92439480/2099102434 UtilsFile::OpenFile(std::string const&, std::string const&) [54] ----------------------------------------------- [98] 0.3 0.26 29.81 int* std::__copy_move_a2 > >, int*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int*) [98] 15.85 1.82 52865362/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 10.76 1.23 35883263/2099102434 void std::__push_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [147] 0.15 0.00 88748625/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [240] ----------------------------------------------- 0.33 0.03 101771331/873253357 std::_Vector_base >::_Vector_base() [329] 25.63 2.54 771482026/873253357 std::_Vector_base, std::allocator > >::~_Vector_base() [64] [99] 0.2 25.96 2.58 873253357 std::pair* std::copy_backward*, std::pair*>(std::pair*, std::pair*, std::pair*) [99] 2.58 0.00 771482026/771482026 std::__niter_base::__b(mar_types*) [197] ----------------------------------------------- 206591 ReadProcessor::ReadProcessor(std::string const&) [59] 531204 ReadProcessor::ReadProcessor(std::string const&) [358] 474169314 __gnu_cxx::__enable_if::__value, void>::__type std::__fill_a(char*, char*, int const&) [146] [100] 0.2 25.77 1.84 474907109 __static_initialization_and_destruction_0(int, int) [100] 1.84 0.00 237084657/237084657 std::__niter_base::__b(char*) [221] 236425176 __gnu_cxx::__enable_if::__value, void>::__type std::__fill_a(char*, char*, int const&) [146] 3827941 Contig::~Contig() [53] ----------------------------------------------- 555168922 std::vector >::operator=(std::vector > const&) [60] 14.43 1.65 48116890/2099102434 void std::swap >(triple&, triple&) [83] [101] 0.2 27.08 0.00 603285812 triple* std::__copy_move_backward::__copy_move_b*, triple*>(triple*, triple*, triple*) [101] 96233780 ReadProcessor::ReadProcessor(std::string const&) [59] ----------------------------------------------- [102] 0.2 26.86 0.00 TrieNode::addToTrie(readPointer, int) [102] ----------------------------------------------- [103] 0.2 0.66 26.08 void std::sort_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [103] 0.14 25.95 77624758/77624758 std::__niter_base<__gnu_cxx::__normal_iterator > >, true>::__b(__gnu_cxx::__normal_iterator > >) [105] ----------------------------------------------- [104] 0.2 0.18 25.95 int* std::__copy_move_a(int const*, int const*, int*) [104] 23.28 2.67 77624758/2099102434 OverlapGraph::AllocateData() [112] ----------------------------------------------- 0.14 25.95 77624758/77624758 void std::sort_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [103] [105] 0.2 0.14 25.95 77624758 std::__niter_base<__gnu_cxx::__normal_iterator > >, true>::__b(__gnu_cxx::__normal_iterator > >) [105] 23.28 2.67 77624758/2099102434 ReadProcessor::ReadProcessor(std::string const&) [59] ----------------------------------------------- [106] 0.2 0.08 25.95 std::__niter_base<__gnu_cxx::__normal_iterator > >, true>::__b(__gnu_cxx::__normal_iterator > >) [106] 23.28 2.67 77624758/2099102434 void std::__adjust_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [121] ----------------------------------------------- 0.90 24.39 77640232/77640232 std::_Rb_tree, std::less, std::allocator >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, int const&) [93] [107] 0.2 0.90 24.39 77640232 bool __gnu_cxx::operator==*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [107] 17.51 6.21 606974957/1198094656 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [33] 0.67 0.00 606974957/606974957 std::__niter_base<__gnu_cxx::__normal_iterator > >, true>::__b(__gnu_cxx::__normal_iterator > >) [300] ----------------------------------------------- 15.19 9.71 385741013/385741013 UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) [9] [108] 0.2 15.19 9.71 385741013 __gnu_cxx::new_allocator::construct(UtilsMath::median_event_point*, UtilsMath::median_event_point const&) [108] 9.71 0.00 385741013/1914486784 bool std::operator==(std::_Deque_iterator const&, std::_Deque_iterator const&) [81] ----------------------------------------------- [109] 0.2 0.11 24.59 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [109] 0.02 24.38 37740740/75448568 std::_Rb_tree, std::less, std::allocator >::_S_value(std::_Rb_tree_node const*) [82] 0.07 0.06 10409062/48149802 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [307] 0.04 0.00 37740740/518771239 std::_Rb_tree, std::less, std::allocator >::_M_put_node(std::_Rb_tree_node*) [311] 0.02 0.00 10409062/58525952 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_put_node(std::_Rb_tree_node >*) [429] ----------------------------------------------- [110] 0.2 0.04 24.38 __gnu_cxx::new_allocator >::deallocate(triple*, unsigned int) [110] 0.01 24.36 37707828/75448568 std::_Rb_tree, std::less, std::allocator >::_S_value(std::_Rb_tree_node const*) [82] ----------------------------------------------- 0.45 0.00 301140141/1526430335 std::deque >::end() [296] 2.34 0.00 101771331/1526430335 std::_Vector_base >::~_Vector_base() [68] 6.15 0.00 460459410/1526430335 std::_Deque_base >::~_Deque_base() [80] 6.38 0.00 277318440/1526430335 UtilsFile::OpenFile(std::string const&, std::string const&) [54] 8.88 0.00 385741013/1526430335 UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) [9] [111] 0.2 24.21 0.00 1526430335 std::deque >::end() const [111] ----------------------------------------------- 388570435 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 2.89 0.33 9651173/2099102434 std::_Rb_tree, std::less, std::allocator >::_M_destroy_node(std::_Rb_tree_node*) [184] 23.28 2.67 77624758/2099102434 int* std::__copy_move_a(int const*, int const*, int*) [104] [112] 0.2 23.16 0.00 475846366 OverlapGraph::AllocateData() [112] 475846366 Contig::~Contig() [53] ----------------------------------------------- [113] 0.2 0.81 21.99 OverlapGraph::ContigInfo* std::__uninitialized_move_a >(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, std::allocator&) [113] 15.27 5.41 529357842/1198094656 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [33] 1.30 0.00 279401951/279401951 bool __gnu_cxx::operator< *, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [244] 0.00 0.00 39950/529397792 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator--() [316] ----------------------------------------------- 0.03 8.81 18824308/47060770 void std::__unguarded_linear_insert<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj) [131] 0.05 13.21 28236462/47060770 std::_Vector_base >::_Vector_base(unsigned int, std::allocator const&) [128] [114] 0.2 0.08 22.02 47060770 Contig* std::__uninitialized_copy::uninitialized_copy(Contig*, Contig*, Contig*) [114] 19.76 2.26 65885078/2099102434 ReadProcessor::ReadProcessor(std::string const&) [59] ----------------------------------------------- 0.00 0.00 1/1506635566 std::back_insert_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, std::back_insert_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::back_insert_iterator > >) [598] 0.01 0.00 11603908/1506635566 Trie::Insert(std::string const&, int, mar_types) [175] 0.07 0.00 58246520/1506635566 std::vector >::swap(std::vector >&) [87] 0.11 0.00 92439480/1506635566 void std::__reverse<__gnu_cxx::__normal_iterator >(__gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator, std::random_access_iterator_tag) [74] 0.18 0.00 158981148/1506635566 __static_initialization_and_destruction_0(int, int) [263] 5.65 0.00 318999000/1506635566 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] 15.35 0.00 866365509/1506635566 _fini [4] [115] 0.2 21.37 0.00 1506635566 std::pair* std::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [115] ----------------------------------------------- [116] 0.2 0.04 20.03 bool __gnu_cxx::operator!= > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [116] 17.40 1.99 58008068/2099102434 Hash::Insert(std::string const&, int, int, int, int) [220] 0.28 0.36 29004034/842549144 void std::__introsort_loop<__gnu_cxx::__normal_iterator > >, int>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int) [35] ----------------------------------------------- [117] 0.2 0.12 19.55 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [117] 0.02 8.90 9412154/3187563338 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_unique(std::pair const&) [2] 0.04 4.42 9412154/28236462 std::_Vector_base >::_Vector_base(unsigned int, std::allocator const&) [128] 2.82 0.32 9412154/2099102434 Contig::Contig(Contig const&) [214] 0.11 2.82 9412154/109105613 std::_Rb_tree, std::less, std::allocator >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, int const&) [93] 0.05 0.02 9412154/77934596 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair const&) [253] 0.02 0.00 9412154/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [240] ----------------------------------------------- [118] 0.2 19.64 0.00 readPointer::stringData() [118] ----------------------------------------------- 3.48 4.88 101771331/2166422463 Vote* std::__copy_move::__copy_m(Vote*, Vote*, Vote*) [52] 4.60 6.45 2064651132/2166422463 std::allocator >::allocator > >(std::allocator > > const&) [133] [119] 0.2 8.08 11.33 2166422463 SeededRead** std::__copy_move_a2(SeededRead**, SeededRead**, SeededRead**) [119] 11.33 0.00 4129302264/1914486784 bool std::operator==(std::_Deque_iterator const&, std::_Deque_iterator const&) [81] ----------------------------------------------- 507052032 std::vector >::operator=(std::vector > const&) [60] [120] 0.2 19.10 0.00 507052032 __gnu_cxx::new_allocator > >::allocate(unsigned int, void const*) [120] 513554962 ReadProcessor::ReadProcessor(std::string const&) [59] ----------------------------------------------- 7737 std::vector >::operator=(std::vector > const&) [60] 70208 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::__copy_move_a2 const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [720] 140416 std::_Rb_tree, std::less, std::allocator >::_Rb_tree_impl, false>::_M_initialize() [710] 2674989 std::vector >::begin() [446] 9412154 __gnu_cxx::__normal_iterator > >::difference_type __gnu_cxx::operator- > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [297] 15620066 std::_Vector_base >::_M_allocate(unsigned int) [382] 157924505 std::vector >::_M_check_len(unsigned int, char const*) const [43] 0.02 0.00 70208/2099102434 std::pair* std::__copy_move_a2*, std::pair*>(std::pair*, std::pair*, std::pair*) [464] 0.02 0.00 70208/2099102434 std::allocator >::allocator() [482] 4.18 0.48 13931508/2099102434 __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >::__normal_iterator(std::pair const* const&) [170] 14.43 1.65 48116890/2099102434 OverlapGraph::ContigInfo* std::__copy_move_backward_a2(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [123] 23.28 2.67 77624758/2099102434 std::__niter_base<__gnu_cxx::__normal_iterator > >, true>::__b(__gnu_cxx::__normal_iterator > >) [106] 36.78 4.21 122624701/2099102434 std::allocator > >::allocator() [90] [121] 0.2 18.87 0.07 448288348 void std::__adjust_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [121] 0.07 0.00 3532923/317564878 std::list, std::allocator > >::_M_check_equal_allocators(std::list, std::allocator > >&) [188] 439407125 ReadProcessor::ReadProcessor(std::string const&) [59] ----------------------------------------------- 1.75 0.38 1180800494/1735969416 std::_Rb_tree, std::less, std::allocator >::begin() const [165] 12.61 2.75 555168922/1735969416 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] [122] 0.1 14.36 3.13 1735969416 OverlapGraph::ContigInfo* std::copy_backward(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [122] 3.13 0.00 555168922/1755802966 std::vector, std::allocator > >::max_size() const [172] ----------------------------------------------- [123] 0.1 0.40 16.08 OverlapGraph::ContigInfo* std::__copy_move_backward_a2(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [123] 14.43 1.65 48116890/2099102434 void std::__adjust_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [121] ----------------------------------------------- [124] 0.1 0.17 15.20 OverlapGraph::ContigInfo::ContigInfo(ShortyString const&, int, int, int, mar_types) [124] 13.64 1.56 45474813/2099102434 _fini [4] ----------------------------------------------- [125] 0.1 0.04 15.20 OverlapGraph::SortAdj::operator()(triple const&, triple const&) const [125] 13.64 1.56 45474813/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] ----------------------------------------------- [126] 0.1 15.14 0.00 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator*() const [126] ----------------------------------------------- [127] 0.1 0.10 14.45 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator++() [127] 0.46 13.99 77624758/886464451 triple* std::__uninitialized_copy_a*, triple*, triple >(triple*, triple*, triple*, std::allocator >&) [45] ----------------------------------------------- 0.04 4.42 9412154/28236462 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [117] 0.04 4.42 9412154/28236462 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [148] 0.04 4.42 9412154/28236462 std::_Vector_base, std::allocator > >::_M_allocate(unsigned int) [150] [128] 0.1 0.13 13.26 28236462 std::_Vector_base >::_Vector_base(unsigned int, std::allocator const&) [128] 0.05 13.21 28236462/47060770 Contig* std::__uninitialized_copy::uninitialized_copy(Contig*, Contig*, Contig*) [114] ----------------------------------------------- [129] 0.1 0.07 13.23 std::vector, std::allocator > >::size() const [129] 5.94 0.68 19791088/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 5.94 0.68 19791088/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] ----------------------------------------------- 0.02 6.45 9651173/19302346 std::pair* std::__copy_move_backward_a2*, std::pair*>(std::pair*, std::pair*, std::pair*) [156] 0.02 6.45 9651173/19302346 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [140] [130] 0.1 0.04 12.90 19302346 mar_types* std::__uninitialized_copy::uninitialized_copy<__gnu_cxx::__normal_iterator > >, mar_types*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*) [130] 11.58 1.33 38604692/2099102434 ReadProcessor::ReadProcessor(std::string const&) [59] ----------------------------------------------- 0.11 12.48 9412154/9412154 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator*() const [132] [131] 0.1 0.11 12.48 9412154 void std::__unguarded_linear_insert<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj) [131] 0.03 8.81 18824308/47060770 Contig* std::__uninitialized_copy::uninitialized_copy(Contig*, Contig*, Contig*) [114] 2.82 0.32 9412154/2099102434 std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [151] 0.11 0.38 37648616/196537847 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] ----------------------------------------------- [132] 0.1 0.00 12.59 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator*() const [132] 0.11 12.48 9412154/9412154 void std::__unguarded_linear_insert<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj) [131] ----------------------------------------------- [133] 0.1 1.10 11.06 std::allocator >::allocator > >(std::allocator > > const&) [133] 4.60 6.45 2064651132/2166422463 SeededRead** std::__copy_move_a2(SeededRead**, SeededRead**, SeededRead**) [119] ----------------------------------------------- 0.00 0.00 2/116345246 Assembler::ProcessNewSeeds() [38] 0.00 0.00 44790/116345246 std::pair* std::uninitialized_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*>(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*) [393] 0.00 0.00 52520/116345246 std::vector >::push_back(int const&) [32] 0.00 0.00 960143/116345246 std::_Deque_base >::_Deque_impl::_Deque_impl() [356] 0.00 0.00 960143/116345246 std::allocator::~allocator() [541] 0.01 0.01 2682726/116345246 OverlapGraph::BuildGraph() [23] 0.05 0.04 11328880/116345246 GetFirstLine(std::basic_fstream >&, char*) [422] 0.05 0.04 11342010/116345246 main [78] 0.14 0.11 1920286/116345246 std::_Deque_base >::_M_initialize_map(unsigned int) [242] 0.40 0.32 5684107/116345246 ReadSeededFastaFile(std::string const&, std::vector >*) [26] 5.79 4.55 81369639/116345246 std::vector >::operator=(std::vector > const&) [88] [134] 0.1 6.46 5.08 116345246 std::deque >::~deque() [134] 4.49 0.59 162739278/2323744019 std::_Deque_base >::~_Deque_base() [80] 0.00 0.00 480071/480071 std::_Deque_base >::_Deque_base() [703] 0.00 0.00 480071/480071 Vote* std::__uninitialized_copy_a(Vote*, Vote*, Vote*, std::allocator&) [704] ----------------------------------------------- [135] 0.1 0.01 11.10 void std::partial_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [135] 0.08 10.87 446402/446402 __gnu_cxx::__normal_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [136] 0.13 0.02 446402/2099102434 __gnu_cxx::__normal_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [346] 0.00 0.00 446402/6612552 int* std::__uninitialized_copy_a<__gnu_cxx::__normal_iterator > >, int*, int>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int*, std::allocator&) [378] ----------------------------------------------- 0.08 10.87 446402/446402 void std::partial_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [135] [136] 0.1 0.08 10.87 446402 __gnu_cxx::__normal_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [136] 4.86 0.56 16201587/2099102434 void std::__push_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [147] 0.08 5.24 13578148/16982099 mar_types* std::copy<__gnu_cxx::__normal_iterator > >, mar_types*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*) [155] 0.09 0.04 18649276/77934596 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair const&) [253] 0.01 0.00 3403951/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [240] ----------------------------------------------- [137] 0.1 0.28 10.42 std::_Rb_tree, std::less, std::allocator >::_S_key(std::_Rb_tree_node const*) [137] 0.15 10.26 77584808/636508560 void std::__heap_select<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [61] ----------------------------------------------- 4833964 std::vector, std::allocator > >::_M_fill_insert(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, unsigned int, triple const&) [50] 50139441 __static_initialization_and_destruction_0(int, int) [227] 0.42 0.05 1405934/2099102434 TrieNode::Search(std::string const&) [320] 0.42 0.05 1405934/2099102434 TrieNode::Insert(int, mar_types) [298] [138] 0.1 9.97 0.00 57785273 TrieNode::searchWithErrorWholeSeed(std::string const&, int, int) [138] 183350579 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [5] 8588826 std::vector, std::allocator > >::_M_fill_insert(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, unsigned int, triple const&) [50] ----------------------------------------------- [139] 0.1 0.11 9.81 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree_impl::_Rb_tree_impl() [139] 5.79 0.66 19302346/2099102434 __gnu_cxx::new_allocator::construct(Contig*, Contig const&) [268] 0.06 3.24 9651173/19302346 triple* std::__copy_move_backward_a2*, triple*>(triple*, triple*, triple*) [158] 0.04 0.02 9651173/38781760 std::_Rb_tree, std::less, std::allocator >::_M_create_node(int const&) [370] ----------------------------------------------- [140] 0.1 0.03 9.82 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [140] 0.02 6.45 9651173/19302346 mar_types* std::__uninitialized_copy::uninitialized_copy<__gnu_cxx::__normal_iterator > >, mar_types*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*) [130] 2.89 0.33 9651173/2099102434 std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [151] 0.03 0.10 9651173/196537847 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] ----------------------------------------------- [141] 0.1 0.06 9.75 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_destroy_node(std::_Rb_tree_node >*) [141] 5.79 0.66 19302346/2099102434 __gnu_cxx::new_allocator::construct(Contig*, Contig const&) [268] 0.06 3.24 9651173/19302346 triple* std::__copy_move_backward_a2*, triple*>(triple*, triple*, triple*) [158] ----------------------------------------------- [142] 0.1 2.94 6.65 std::vector, std::allocator > >::~vector() [142] 3.14 2.13 1180800494/1180800494 std::_Rb_tree, std::less, std::allocator >::begin() const [165] 1.08 0.00 555168922/1180800494 std::vector, std::allocator > >::end() [204] 0.30 0.00 48116890/625631572 std::_Rb_tree, std::less, std::allocator >::end() const [178] ----------------------------------------------- [143] 0.1 0.05 9.36 int* std::vector >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator > > >(unsigned int, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [143] 4.78 0.55 15926951/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 3.61 0.41 12038352/2099102434 void std::__push_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [147] 0.01 0.00 7948176/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [240] ----------------------------------------------- [144] 0.1 0.09 9.18 std::vector >::operator[](unsigned int) [144] 8.24 0.94 27469656/2099102434 Contig::~Contig() [53] ----------------------------------------------- 7737 Cluster::Cluster() [812] 960143 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::~_Rb_tree() [237] 42219518 std::vector >::~vector() [208] 0.00 0.00 5786/2099102434 ShortyString::size() const [580] 0.00 0.00 7343/2099102434 Cluster::AddIndex(int, int, mar_types) [421] 0.01 0.00 20853/2099102434 ReadProcessor::NumUsed(int) [515] 0.01 0.00 49336/2099102434 __gnu_cxx::__normal_iterator > > std::__copy_move_a2 > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [486] 0.29 0.03 960143/2099102434 std::vector >::end() const [353] 14.43 1.65 48116890/2099102434 void std::swap >(triple&, triple&) [83] 20.69 2.37 68975489/2099102434 Assembler::MakeContigs(bool, Cluster const&, SeededRead const&) [21] [145] 0.1 8.13 0.00 161323238 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [145] 0.00 0.00 15474/64810 void std::_Destroy(int*, int*) [722] 0.00 0.00 7737/7737 Vote* std::uninitialized_copy<__gnu_cxx::__normal_iterator > >, Vote*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, Vote*) [757] 91296551 Contig::~Contig() [53] 22989953 std::_Vector_base >::_Vector_impl::_Vector_impl(std::allocator const&) [404] 11504238 Vote* std::uninitialized_copy(Vote*, Vote*, Vote*) [364] 26260 Vote* std::__copy_move_a2(Vote*, Vote*, Vote*) [714] 13130 __gnu_cxx::__normal_iterator > > std::__copy_move_a2 > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [712] 13129 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Rb_tree_impl, false>::_Rb_tree_impl() [750] ----------------------------------------------- 236425176 __static_initialization_and_destruction_0(int, int) [100] [146] 0.1 8.05 0.00 236425176 __gnu_cxx::__enable_if::__value, void>::__type std::__fill_a(char*, char*, int const&) [146] 474169314 __static_initialization_and_destruction_0(int, int) [100] ----------------------------------------------- 3403951 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [177] 9330801 __gnu_cxx::__normal_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [346] 1.17 0.13 3888599/2099102434 std::vector >::capacity() const [241] 3.61 0.41 12038352/2099102434 int* std::vector >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator > > >(unsigned int, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [143] 4.86 0.56 16201587/2099102434 __gnu_cxx::__normal_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [136] 5.09 0.58 16982099/2099102434 mar_types* std::copy<__gnu_cxx::__normal_iterator > >, mar_types*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*) [155] 10.76 1.23 35883263/2099102434 int* std::__copy_move_a2 > >, int*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int*) [98] [147] 0.1 7.67 0.27 97728652 void std::__push_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [147] 0.27 0.00 10628041/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [240] 3441556 ReadProcessor::ReadProcessor(std::string const&) [59] ----------------------------------------------- [148] 0.1 0.12 7.63 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [148] 0.04 4.42 9412154/28236462 std::_Vector_base >::_Vector_base(unsigned int, std::allocator const&) [128] 2.82 0.32 9412154/2099102434 Contig::Contig(Contig const&) [214] 0.02 0.00 9412154/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [240] ----------------------------------------------- [149] 0.1 0.03 7.67 std::_Vector_base >::_Vector_impl::_Vector_impl() [149] 6.88 0.79 22955956/2099102434 std::vector, std::allocator > >::_M_fill_insert(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, unsigned int, triple const&) [50] ----------------------------------------------- [150] 0.1 0.04 7.61 std::_Vector_base, std::allocator > >::_M_allocate(unsigned int) [150] 0.04 4.42 9412154/28236462 std::_Vector_base >::_Vector_base(unsigned int, std::allocator const&) [128] 2.82 0.32 9412154/2099102434 Contig::Contig(Contig const&) [214] ----------------------------------------------- 4 std::deque >::_M_pop_back_aux() [786] 22 ShortyString::Print() const [764] 22 ShortyString::ReverseComplement() const [763] 13130 Contig::PrintContigFormat(std::basic_fstream >*) const [408] 1920286 std::_Deque_base >::_M_initialize_map(unsigned int) [242] 385741013 std::_Vector_base >::~_Vector_base() [46] 0.00 0.00 1/2099102434 std::list, std::allocator > >::push_back(std::pair const&) [659] 0.00 0.00 2/2099102434 Vote* std::__uninitialized_copy::uninitialized_copy<__gnu_cxx::__normal_iterator > >, Vote*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, Vote*) [612] 0.00 0.00 10/2099102434 TrieNode::addPairReadToTrie(int) [611] 0.00 0.00 12334/2099102434 __gnu_cxx::__normal_iterator > > std::__copy_move_a2 > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [486] 0.02 0.00 70208/2099102434 void std::_Destroy<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [465] 0.14 0.02 480071/2099102434 std::deque >::_M_destroy_data_aux(std::_Deque_iterator, std::_Deque_iterator) [397] 0.29 0.03 960143/2099102434 std::_Deque_base >::_Deque_impl::_Deque_impl() [356] 2.82 0.32 9412154/2099102434 void std::__unguarded_linear_insert<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj) [131] 2.89 0.33 9651173/2099102434 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [140] [151] 0.1 7.52 0.00 408260573 std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [151] 0.00 0.00 1920286/1965076 SeededRead** std::copy(SeededRead**, SeededRead**, SeededRead**) [690] 1920286 SeededRead** std::copy_backward(SeededRead**, SeededRead**, SeededRead**) [680] ----------------------------------------------- [152] 0.1 0.04 7.20 mar_types* std::vector >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator > > >(unsigned int, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [152] 4.86 0.56 16201587/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 0.01 1.76 2623439/2623439 int* std::copy<__gnu_cxx::__normal_iterator > >, int*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int*) [225] 0.02 0.00 2623439/6612552 int* std::__uninitialized_copy_a<__gnu_cxx::__normal_iterator > >, int*, int>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int*, std::allocator&) [378] 0.00 0.00 2623439/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [240] ----------------------------------------------- 5.83 1.09 48116890/48116890 ReadProcessor::ReadProcessor(std::string const&) [59] [153] 0.1 5.83 1.09 48116890 std::vector >::push_back(RawRead const&) [153] 1.09 0.00 48116890/362166824 __gnu_cxx::new_allocator::construct(std::string*, std::string const&) [191] ----------------------------------------------- [154] 0.1 0.40 6.40 void std::_Destroy(UtilsMath::median_event_point*, UtilsMath::median_event_point*, std::allocator&) [154] 1.30 4.09 385741013/2635651173 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, UtilsMath::median_event_point const&) [22] 0.89 0.12 385741013/2323744019 std::_Deque_base >::~_Deque_base() [80] ----------------------------------------------- 0.02 1.31 3403951/16982099 std::vector >::max_size() const [239] 0.08 5.24 13578148/16982099 __gnu_cxx::__normal_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [136] [155] 0.1 0.10 6.55 16982099 mar_types* std::copy<__gnu_cxx::__normal_iterator > >, mar_types*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*) [155] 5.09 0.58 16982099/2099102434 void std::__push_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [147] 0.79 0.09 2623439/2099102434 ReadProcessor::ReadProcessor(std::string const&) [59] ----------------------------------------------- 0.02 6.60 9651173/9651173 std::_Rb_tree, std::less, std::allocator >::_Rb_tree_impl, false>::_Rb_tree_impl() [157] [156] 0.1 0.02 6.60 9651173 std::pair* std::__copy_move_backward_a2*, std::pair*>(std::pair*, std::pair*, std::pair*) [156] 0.02 6.45 9651173/19302346 mar_types* std::__uninitialized_copy::uninitialized_copy<__gnu_cxx::__normal_iterator > >, mar_types*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*) [130] 0.03 0.10 9651173/196537847 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] ----------------------------------------------- [157] 0.1 0.00 6.62 std::_Rb_tree, std::less, std::allocator >::_Rb_tree_impl, false>::_Rb_tree_impl() [157] 0.02 6.60 9651173/9651173 std::pair* std::__copy_move_backward_a2*, std::pair*>(std::pair*, std::pair*, std::pair*) [156] ----------------------------------------------- 0.06 3.24 9651173/19302346 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree_impl::_Rb_tree_impl() [139] 0.06 3.24 9651173/19302346 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_destroy_node(std::_Rb_tree_node >*) [141] [158] 0.1 0.12 6.48 19302346 triple* std::__copy_move_backward_a2*, triple*>(triple*, triple*, triple*) [158] 5.79 0.66 19302346/2099102434 std::vector >::operator=(std::vector > const&) [60] 0.02 0.01 10310654/4097652014 Contig* std::__copy_move_backward::__copy_move_b(Contig*, Contig*, Contig*) [79] ----------------------------------------------- [159] 0.1 1.07 5.28 __static_initialization_and_destruction_0(int, int) [159] 0.99 3.74 184878960/184878960 std::vector >::push_back(UtilsMath::median_event_point const&) [169] 0.41 0.13 369757920/537187764 std::_Vector_base, std::allocator > >::_Vector_impl::_Vector_impl() [187] ----------------------------------------------- [160] 0.1 6.23 0.00 readPointer::readPointer() [160] ----------------------------------------------- 48124627 std::vector >::operator=(std::vector > const&) [60] [161] 0.0 5.83 0.00 48124627 triple* std::__uninitialized_copy::uninitialized_copy*, triple*>(triple*, triple*, triple*) [161] 144358407 ReadProcessor::ReadProcessor(std::string const&) [59] ----------------------------------------------- [162] 0.0 1.06 4.64 void std::_Destroy(mar_types*, mar_types*, std::allocator&) [162] 2.11 2.53 730437481/3222388240 std::deque >::deque(std::deque > const&) [31] ----------------------------------------------- [163] 0.0 0.07 5.48 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator*() const [163] 5.48 0.00 101771331/101771331 Vote* std::__copy_move::__copy_m(Vote const*, Vote const*, Vote*) [164] ----------------------------------------------- 5.48 0.00 101771331/101771331 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator*() const [163] [164] 0.0 5.48 0.00 101771331 Vote* std::__copy_move::__copy_m(Vote const*, Vote const*, Vote*) [164] ----------------------------------------------- 3.14 2.13 1180800494/1180800494 std::vector, std::allocator > >::~vector() [142] [165] 0.0 3.14 2.13 1180800494 std::_Rb_tree, std::less, std::allocator >::begin() const [165] 1.75 0.38 1180800494/1735969416 OverlapGraph::ContigInfo* std::copy_backward(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [122] ----------------------------------------------- [166] 0.0 5.22 0.00 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::__normal_iterator(triple* const&) [166] ----------------------------------------------- 4.91 0.01 96299604/96299604 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] [167] 0.0 4.91 0.01 96299604 std::vector, std::allocator > >::_M_erase_at_end(std::pair*) [167] 0.00 0.00 32912/48149802 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [307] ----------------------------------------------- [168] 0.0 0.02 4.84 std::vector, std::allocator > >::begin() [168] 0.06 4.78 1069892/12451411 main [78] ----------------------------------------------- 0.99 3.74 184878960/184878960 __static_initialization_and_destruction_0(int, int) [159] [169] 0.0 0.99 3.74 184878960 std::vector >::push_back(UtilsMath::median_event_point const&) [169] 0.62 1.96 184878960/2635651173 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, UtilsMath::median_event_point const&) [22] 0.69 0.47 369757920/1623116001 std::deque >::_M_reserve_map_at_back(unsigned int) [91] ----------------------------------------------- [170] 0.0 0.00 4.66 __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >::__normal_iterator(std::pair const* const&) [170] 4.18 0.48 13931508/2099102434 void std::__adjust_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [121] ----------------------------------------------- 0.00 0.00 502466/463889692 std::deque >::begin() const [434] 4.57 0.00 463387226/463889692 std::_Deque_iterator std::__uninitialized_copy_a, std::_Deque_iterator, SeededRead>(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator, std::allocator&) [51] [171] 0.0 4.57 0.00 463889692 void std::_Destroy_aux::__destroy(Contig*, Contig*) [171] ----------------------------------------------- 0.00 0.00 177068/1755802966 OverlapGraph::ContigInfo* std::__uninitialized_copy::uninitialized_copy(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [583] 0.01 0.00 9828241/1755802966 void std::_Destroy*>(std::pair*, std::pair*) [497] 0.15 0.00 9828241/1755802966 std::vector >::operator=(std::vector > const&) [283] 1.19 0.00 1180800494/1755802966 std::vector >::_M_check_len(unsigned int, char const*) const [3] 3.13 0.00 555168922/1755802966 OverlapGraph::ContigInfo* std::copy_backward(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [122] [172] 0.0 4.48 0.00 1755802966 std::vector, std::allocator > >::max_size() const [172] ----------------------------------------------- [173] 0.0 4.17 0.00 std::vector >::vector() [173] ----------------------------------------------- 2674989 Contig::operator=(Contig const&) [174] 70208 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Contig const&) [428] 2635729 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 1.15 0.13 3827941/2099102434 global constructors keyed to _ZN13ReadProcessor6total_E [246] [174] 0.0 1.07 3.06 6533878+2674989 Contig::operator=(Contig const&) [174] 3.06 0.00 6502930/1397173708 std::vector >::push_back(int const&) [32] 0.00 0.00 13931508/13931508 __gnu_cxx::__normal_iterator > >::__normal_iterator(Contig* const&) [678] 2674989 Contig::~Contig() [53] 2674989 Contig::operator=(Contig const&) [174] ----------------------------------------------- 0.00 0.00 1/13130 Assembler::Assemble() [474] 0.08 3.89 13129/13130 operator new(unsigned int, void*) [176] [175] 0.0 0.08 3.89 13130 Trie::Insert(std::string const&, int, mar_types) [175] 3.48 0.40 11603908/2099102434 _fini [4] 0.01 0.00 11603908/1506635566 std::pair* std::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [115] ----------------------------------------------- [176] 0.0 0.00 3.97 operator new(unsigned int, void*) [176] 0.08 3.89 13129/13130 Trie::Insert(std::string const&, int, mar_types) [175] ----------------------------------------------- 48116890 std::vector >::operator=(std::vector > const&) [60] 14.43 1.65 48116890/2099102434 void std::swap >(triple&, triple&) [83] [177] 0.0 3.53 0.40 96233780 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [177] 0.29 0.11 3850353/77934596 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair const&) [253] 3403951 void std::__push_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [147] ----------------------------------------------- 0.30 0.00 48116890/625631572 std::vector, std::allocator > >::~vector() [142] 3.62 0.00 577514682/625631572 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::~_Rb_tree() [8] [178] 0.0 3.92 0.00 625631572 std::_Rb_tree, std::less, std::allocator >::end() const [178] ----------------------------------------------- [179] 0.0 0.05 3.86 Contig::Add(Contig const&) [179] 0.02 3.84 11477978/11477978 Contig::GetMt(int) const [181] ----------------------------------------------- [180] 0.0 0.03 3.84 std::_Vector_base >::_M_deallocate(readPointer*, unsigned int) [180] 3.44 0.39 11477978/2099102434 std::vector, std::allocator > >::_M_fill_insert(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, unsigned int, triple const&) [50] ----------------------------------------------- 0.02 3.84 11477978/11477978 Contig::Add(Contig const&) [179] [181] 0.0 0.02 3.84 11477978 Contig::GetMt(int) const [181] 3.44 0.39 11477978/2099102434 Contig::~Contig() [53] ----------------------------------------------- [182] 0.0 0.05 3.72 __gnu_cxx::new_allocator::new_allocator() [182] 3.72 0.00 1937320110/3971005539 SeededRead** std::__copy_move_backward_a2(SeededRead**, SeededRead**, SeededRead**) [72] ----------------------------------------------- 3.53 0.00 9651173/9651173 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] [183] 0.0 3.53 0.00 9651173 std::_Vector_base >::_Vector_impl::_Vector_impl() [183] ----------------------------------------------- [184] 0.0 0.09 3.37 std::_Rb_tree, std::less, std::allocator >::_M_destroy_node(std::_Rb_tree_node*) [184] 2.89 0.33 9651173/2099102434 OverlapGraph::AllocateData() [112] 0.04 0.11 19302346/19961827 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_create_node(std::pair const&) [384] ----------------------------------------------- [185] 0.0 0.81 2.58 std::vector >::begin() [185] 0.62 1.96 184878960/2635651173 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, UtilsMath::median_event_point const&) [22] ----------------------------------------------- [186] 0.0 0.07 3.23 std::_Vector_base, std::allocator > >::_Vector_impl::_Vector_impl() [186] 2.89 0.33 9651173/2099102434 std::vector >::operator=(std::vector > const&) [283] ----------------------------------------------- 0.41 0.13 369757920/537187764 __static_initialization_and_destruction_0(int, int) [159] 2.04 0.66 167429844/537187764 std::deque >::deque(std::deque > const&) [31] [187] 0.0 2.45 0.79 537187764 std::_Vector_base, std::allocator > >::_Vector_impl::_Vector_impl() [187] 0.60 0.19 55809948/111619896 std::_Deque_base >::_M_allocate_node() [262] ----------------------------------------------- 0.00 0.00 3532923/317564878 __gnu_cxx::new_allocator::destroy(Contig*) [562] 0.07 0.00 3532923/317564878 void std::__adjust_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [121] 0.19 0.00 155249516/317564878 std::_List_iterator >::operator*() const [381] 2.96 0.00 155249516/317564878 ReadProcessor::ReadProcessor(std::string const&) [59] [188] 0.0 3.23 0.00 317564878 std::list, std::allocator > >::_M_check_equal_allocators(std::list, std::allocator > >&) [188] ----------------------------------------------- [189] 0.0 0.00 3.23 std::_Rb_tree, std::less, std::allocator >::_S_left(std::_Rb_tree_node_base*) [189] 2.89 0.33 9651173/2099102434 std::vector >::operator=(std::vector > const&) [283] ----------------------------------------------- [190] 0.0 0.07 3.15 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_end() [190] 2.82 0.32 9412154/2099102434 __gnu_cxx::__normal_iterator > >::difference_type __gnu_cxx::operator- > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [297] ----------------------------------------------- 0.35 0.00 236425176/362166824 ReadProcessor::TotalPairs() const [310] 1.09 0.00 48116890/362166824 std::vector >::push_back(RawRead const&) [153] 1.76 0.00 77624758/362166824 void std::fill(char*, char*, int const&) [193] [191] 0.0 3.20 0.00 362166824 __gnu_cxx::new_allocator::construct(std::string*, std::string const&) [191] ----------------------------------------------- [192] 0.0 0.02 3.15 std::pair* std::__uninitialized_move_a*, std::pair*, std::allocator > >(std::pair*, std::pair*, std::pair*, std::allocator >&) [192] 2.82 0.32 9412154/2099102434 Contig::Contig(Contig const&) [214] ----------------------------------------------- 1.38 1.76 77624758/77624758 ReadProcessor::ReadProcessor(std::string const&) [59] [193] 0.0 1.38 1.76 77624758 void std::fill(char*, char*, int const&) [193] 1.76 0.00 77624758/362166824 __gnu_cxx::new_allocator::construct(std::string*, std::string const&) [191] ----------------------------------------------- [194] 0.0 0.01 3.05 std::_Vector_base >::~_Vector_base() [194] 1.36 0.16 4524278/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 1.36 0.16 4524278/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 0.01 0.02 2262139/196537847 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] ----------------------------------------------- [195] 0.0 3.00 0.00 std::vector >::size() const [195] ----------------------------------------------- [196] 0.0 0.02 2.58 triple* std::vector, std::allocator > >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > >(unsigned int, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >) [196] 0.03 1.46 2113286/148011011 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [57] 0.95 0.11 3169929/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] 0.03 0.00 1056643/1397173708 std::vector >::push_back(int const&) [32] ----------------------------------------------- 2.58 0.00 771482026/771482026 std::pair* std::copy_backward*, std::pair*>(std::pair*, std::pair*, std::pair*) [99] [197] 0.0 2.58 0.00 771482026 std::__niter_base::__b(mar_types*) [197] ----------------------------------------------- [198] 0.0 0.02 2.56 std::set, std::allocator >::insert(int const&) [198] 0.01 2.53 2674989/3187563338 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_unique(std::pair const&) [2] 0.00 0.02 2674989/12087143 std::pair >, bool>::pair(std::_Rb_tree_const_iterator > const&, bool const&) [441] ----------------------------------------------- 1077772 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] 0.00 0.00 13249/196537847 void std::sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [270] 0.00 0.00 13249/196537847 std::_Vector_base, std::allocator > >::~_Vector_base() [325] 0.00 0.00 21385/196537847 bool __gnu_cxx::operator!=*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [544] 0.00 0.01 857934/196537847 std::vector, std::allocator > >::operator[](unsigned int) const [516] 0.00 0.01 1069892/196537847 __gnu_cxx::new_allocator::construct(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo const&) [264] 0.00 0.01 1083141/196537847 std::vector, std::allocator > >::end() [513] 0.01 0.02 2139784/196537847 std::vector, std::allocator > >::push_back(triple const&) [345] 0.01 0.02 2262139/196537847 std::_Vector_base >::~_Vector_base() [194] 0.01 0.02 2262139/196537847 std::_Rb_tree, std::less, std::allocator >::_M_erase(std::_Rb_tree_node*) [230] 0.01 0.02 2262139/196537847 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_erase(std::_Rb_tree_node >*) [462] 0.01 0.02 2262139/196537847 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_begin() [478] 0.03 0.10 9651173/196537847 std::pair* std::__copy_move_backward_a2*, std::pair*>(std::pair*, std::pair*, std::pair*) [156] 0.03 0.10 9651173/196537847 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [140] 0.06 0.19 19302346/196537847 std::vector, std::allocator > >::max_size() const [376] 0.06 0.20 19791088/196537847 std::vector, std::allocator > >::operator[](unsigned int) [362] 0.07 0.22 22053227/196537847 std::vector >::push_back(Contig const&) [323] 0.08 0.25 24728216/196537847 std::_Vector_base, std::allocator > >::~_Vector_base() [348] 0.11 0.38 37648616/196537847 void std::__unguarded_linear_insert<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj) [131] 0.12 0.40 39464818/196537847 std::vector, std::allocator > >::operator=(std::vector, std::allocator > > const&) [42] [199] 0.0 0.60 1.97 196537847+1077772 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] 1.32 0.15 4393532/2099102434 std::vector >::operator=(std::vector > const&) [283] 0.45 0.05 1496030/2099102434 __gnu_cxx::new_allocator::construct(Contig*, Contig const&) [268] 0.00 0.00 915/13249 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::__unguarded_partition<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj) [537] 0.00 0.00 177068/9828241 std::allocator >::~allocator() [679] 0.00 0.00 12334/12334 void std::__insertion_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [752] 1077772 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] ----------------------------------------------- 1.00 1.53 77624758/77624758 std::vector >::_M_check_len(unsigned int, char const*) const [43] [200] 0.0 1.00 1.53 77624758 std::list, std::allocator > >::empty() const [200] 1.53 0.00 77624758/77624758 std::list, std::allocator > >::_M_erase(std::_List_iterator >) [231] ----------------------------------------------- [201] 0.0 2.52 0.00 std::vector >::operator[](unsigned int) [201] ----------------------------------------------- [202] 0.0 0.01 2.40 ShortyString::ShortyString() [202] 1.08 0.12 3591444/2099102434 ShortyString::~ShortyString() [34] 1.08 0.12 3591444/2099102434 ShortyString::ShortyString(std::string const&, int) [7] ----------------------------------------------- [203] 0.0 0.01 2.37 SeededRead::SeededRead(SeededRead const&) [203] 2.13 0.24 7092682/2099102434 std::vector >::~vector() [208] ----------------------------------------------- 1.08 0.00 555168922/1180800494 std::vector, std::allocator > >::~vector() [142] 1.21 0.00 625631572/1180800494 std::vector, std::allocator > >::vector() [209] [204] 0.0 2.29 0.00 1180800494 std::vector, std::allocator > >::end() [204] ----------------------------------------------- [205] 0.0 2.23 0.00 myList::myList(readPointer) [205] ----------------------------------------------- [206] 0.0 0.43 1.79 OverlapGraph::IntPairEq::operator()(std::pair const&, std::pair const&) const [206] 0.80 0.09 2674989/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 0.80 0.09 2674989/2099102434 std::vector >::operator=(std::vector > const&) [88] ----------------------------------------------- [207] 0.0 2.20 0.00 std::vector >::~vector() [207] ----------------------------------------------- 1 TrieNode::addToTrie(myList*, int) [330] 1 Hash::LeftShiftHashVal(char, char, int) const [793] 13129 std::_Deque_base >::_M_allocate_map(unsigned int) [731] 11315694 ReadSeededFastaFile(std::string const&, std::vector >*) [26] 0.00 0.00 1/2099102434 Hash::Hash(int) [504] 0.00 0.00 5786/2099102434 Assembler::MakeContigs(bool, Cluster const&, SeededRead const&) [21] 0.00 0.00 5786/2099102434 ShortyString::size() const [580] 0.00 0.00 7343/2099102434 Assembler::ProcessNewSeeds() [38] 0.00 0.00 7343/2099102434 Cluster::AddIndex(int, int, mar_types) [421] 2.13 0.24 7092682/2099102434 SeededRead::SeededRead(SeededRead const&) [203] 7.43 0.85 24771284/2099102434 main [78] [208] 0.0 2.15 0.00 43219050 std::vector >::~vector() [208] 42219518 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [145] 39389 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] ----------------------------------------------- [209] 0.0 0.91 1.21 std::vector, std::allocator > >::vector() [209] 1.21 0.00 625631572/1180800494 std::vector, std::allocator > >::end() [204] ----------------------------------------------- 0.01 0.00 2674989/539451719 OverlapGraph::ContigInfo::~ContigInfo() [517] 0.01 0.00 2674989/539451719 std::vector >::push_back(Contig const&) [323] 0.02 0.00 4703949/539451719 std::vector, std::allocator > >::operator=(std::vector, std::allocator > > const&) [42] 2.05 0.00 529397792/539451719 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::~_Rb_tree() [8] [210] 0.0 2.09 0.00 539451719 std::list, std::allocator > >::operator=(std::list, std::allocator > > const&) [210] ----------------------------------------------- 0.01 0.51 1208491/4833964 void std::_Destroy_aux::__destroy(std::string*, std::string*) [315] 0.04 1.52 3625473/4833964 RawRead* std::__copy_move_backward::__copy_move_b(RawRead*, RawRead*, RawRead*) [229] [211] 0.0 0.05 2.03 4833964 __static_initialization_and_destruction_0(int, int) [211] 1.45 0.17 4833964/2099102434 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [5] 0.37 0.04 1242520/2099102434 ShortyString::ShortyString(std::string const&, int) [366] ----------------------------------------------- 1.58 0.46 529397792/529397792 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_unique(std::pair const&) [2] [212] 0.0 1.58 0.46 529397792 std::_Rb_tree, std::less, std::allocator >::begin() [212] 0.46 0.00 451773034/529397792 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator--() [316] ----------------------------------------------- 48149802 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] [213] 0.0 1.99 0.00 48149802 std::vector, std::allocator > >::end() const [213] 0.00 0.00 70208/96407108 std::_Rb_tree, std::less, std::allocator >::get_allocator() const [447] 48149802 void std::__final_insertion_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [71] ----------------------------------------------- 2674989 Contig::Contig(Contig const&) [214] 3532923 __gnu_cxx::new_allocator::construct(Contig*, Contig const&) [268] 5349978 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [75] 7065846 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 0.80 0.09 2674989/2099102434 std::_Rb_tree_const_iterator::_Rb_tree_const_iterator(std::_Rb_tree_iterator const&) [277] 0.80 0.09 2674989/2099102434 std::pair, bool>::pair(std::_Rb_tree_const_iterator const&, bool const&) [273] 2.82 0.32 9412154/2099102434 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [117] 2.82 0.32 9412154/2099102434 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [148] 2.82 0.32 9412154/2099102434 std::_Vector_base, std::allocator > >::_M_allocate(unsigned int) [150] 2.82 0.32 9412154/2099102434 std::pair* std::__uninitialized_move_a*, std::pair*, std::allocator > >(std::pair*, std::pair*, std::pair*, std::allocator >&) [192] [214] 0.0 1.69 0.31 58947341+2674989 Contig::Contig(Contig const&) [214] 0.31 0.00 3532923/3532923 Contig* std::__uninitialized_move_a >(Contig*, Contig*, Contig*, std::allocator&) [365] 15620066 std::_Vector_base >::_M_allocate(unsigned int) [382] 2674989 std::vector >::begin() [446] 2674989 std::vector >::_M_check_len(unsigned int, char const*) const [43] 2674989 __gnu_cxx::__normal_iterator > >::difference_type __gnu_cxx::operator- > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [297] 2674989 Contig::Contig(Contig const&) [214] ----------------------------------------------- 1.99 0.00 21447747/21447747 ReadProcessor::ReadProcessor(std::string const&) [59] [215] 0.0 1.99 0.00 21447747 std::vector >::push_back(std::string const&) [215] ----------------------------------------------- [216] 0.0 1.99 0.00 NavidIntIntStruct::NavidIntIntStruct() [216] ----------------------------------------------- 0.12 0.00 77624758/155249516 void std::_Destroy_aux::__destroy<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [419] 1.76 0.00 77624758/155249516 std::vector >::_M_check_len(unsigned int, char const*) const [43] [217] 0.0 1.88 0.00 155249516 std::_List_iterator >::operator++() [217] ----------------------------------------------- 0.06 0.00 10409062/304749023 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::get_allocator() const [413] 0.21 0.02 37707828/304749023 std::allocator >::allocator() [363] 0.21 0.02 37740740/304749023 void std::_Destroy<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::allocator >&) [350] 0.27 0.02 48149802/304749023 std::_Vector_base, std::allocator > >::_M_deallocate(std::pair*, unsigned int) [321] 0.28 0.02 48116890/304749023 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [307] 0.70 0.05 122624701/304749023 std::pair* std::vector, std::allocator > >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > >(unsigned int, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >) [89] [218] 0.0 1.74 0.13 304749023 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree_impl::_M_initialize() [218] 0.13 0.00 122624701/518771239 std::_Rb_tree, std::less, std::allocator >::_M_put_node(std::_Rb_tree_node*) [311] ----------------------------------------------- [219] 0.0 0.58 1.26 __gnu_cxx::new_allocator::destroy(OverlapGraph::ContigInfo*) [219] 1.26 0.00 529357842/606974957 void std::iter_swap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [236] ----------------------------------------------- 1 Hash::Insert(std::string const&, int, int, int, int) [220] 1 Hash::LeftShiftHashVal(char, char, int) const [793] 29004034 UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) [9] 0.00 0.00 1/2099102434 std::list, std::allocator > >::_M_insert(std::_List_iterator >, std::pair const&) [643] 0.00 0.00 2502/2099102434 Hash::Insert(std::string const&, int, int, int) [591] 17.40 1.99 58008068/2099102434 bool __gnu_cxx::operator!= > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [116] [220] 0.0 1.84 0.00 87014606+1 Hash::Insert(std::string const&, int, int, int, int) [220] 0.00 0.00 1002/67677006 std::list, std::allocator > >::begin() [255] 0.00 0.00 1/5 __gnu_cxx::new_allocator::destroy(SeededRead*) [777] 2 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::resize(unsigned int, std::list, std::allocator > >) [788] 1 Hash::Insert(std::string const&, int, int, int, int) [220] ----------------------------------------------- 1.84 0.00 237084657/237084657 __static_initialization_and_destruction_0(int, int) [100] [221] 0.0 1.84 0.00 237084657 std::__niter_base::__b(char*) [221] ----------------------------------------------- [222] 0.0 0.01 1.79 std::vector >::~vector() [222] 0.80 0.09 2682726/2099102434 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [75] 0.80 0.09 2674989/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] ----------------------------------------------- 0.08 0.09 9331851/101771331 std::vector >::push_back(mar_types const&) [387] 0.75 0.89 92439480/101771331 ShortyString::Str(std::string const&) [226] [223] 0.0 0.82 0.97 101771331 std::vector, std::allocator > >::push_back(std::pair const&) [223] 0.30 0.17 101771331/1644735383 std::_Vector_base, std::allocator > >::~_Vector_base() [64] 0.23 0.03 101771331/2323744019 std::_Deque_base >::~_Deque_base() [80] 0.18 0.00 101771331/2734359181 std::deque >::_M_destroy_data(std::_Deque_iterator, std::_Deque_iterator, std::allocator const&) [70] 0.06 0.00 101771331/101771331 std::_Vector_base >::_Vector_impl::~_Vector_impl() [454] ----------------------------------------------- [224] 0.0 1.77 0.00 myList::destruct() [224] ----------------------------------------------- 0.01 1.76 2623439/2623439 mar_types* std::vector >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator > > >(unsigned int, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [152] [225] 0.0 0.01 1.76 2623439 int* std::copy<__gnu_cxx::__normal_iterator > >, int*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int*) [225] 1.57 0.18 5246878/2099102434 ReadProcessor::ReadProcessor(std::string const&) [59] 0.00 0.00 2447689/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [240] ----------------------------------------------- [226] 0.0 0.06 1.63 ShortyString::Str(std::string const&) [226] 0.75 0.89 92439480/101771331 std::vector, std::allocator > >::push_back(std::pair const&) [223] ----------------------------------------------- 4833964 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [5] 0.77 0.09 2572727/2099102434 std::vector, std::allocator > >::size() const [274] [227] 0.0 1.69 0.00 7406691 __static_initialization_and_destruction_0(int, int) [227] 50139441 TrieNode::searchWithErrorWholeSeed(std::string const&, int, int) [138] ----------------------------------------------- [228] 0.0 1.60 0.00 myList::~myList() [228] ----------------------------------------------- [229] 0.0 0.03 1.56 RawRead* std::__copy_move_backward::__copy_move_b(RawRead*, RawRead*, RawRead*) [229] 0.04 1.52 3625473/4833964 __static_initialization_and_destruction_0(int, int) [211] ----------------------------------------------- [230] 0.0 0.02 1.54 std::_Rb_tree, std::less, std::allocator >::_M_erase(std::_Rb_tree_node*) [230] 0.68 0.08 2262139/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 0.68 0.08 2262139/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 0.01 0.02 2262139/196537847 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] ----------------------------------------------- 1.53 0.00 77624758/77624758 std::list, std::allocator > >::empty() const [200] [231] 0.0 1.53 0.00 77624758 std::list, std::allocator > >::_M_erase(std::_List_iterator >) [231] ----------------------------------------------- 684149 ReadProcessor::ReadProcessor(std::string const&) [358] [232] 0.0 1.53 0.00 684149 ReadProcessor::GetMarLen(int, mar_types) const [232] 24668 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, RawRead const&) [235] ----------------------------------------------- [233] 0.0 0.02 1.51 std::allocator >::~allocator() [233] 0.68 0.08 2262139/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 0.68 0.08 2262139/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] ----------------------------------------------- [234] 0.0 0.01 1.51 void std::_Destroy(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, std::allocator&) [234] 0.68 0.08 2262139/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 0.68 0.08 2262139/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] ----------------------------------------------- 22395 ReadProcessor::LocateRead(std::string const&) const [709] 24668 ReadProcessor::GetMarLen(int, mar_types) const [232] 201555 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, std::string const&) [706] 11379058 ReadProcessor::ReadProcessor(std::string const&) [59] [235] 0.0 1.23 0.22 11627676 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, RawRead const&) [235] 0.20 0.00 7870317/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [240] 0.02 0.00 67185/3393446 TrieNode::searchWithErrorAllowedNonRecursive(std::string const&, int) [312] 223950 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, std::string const&) [706] 9146 Contig::~Contig() [53] 9146 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator+(int const&) const [410] ----------------------------------------------- 0.18 0.00 77617115/606974957 void std::__heap_select<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [61] 1.26 0.00 529357842/606974957 __gnu_cxx::new_allocator::destroy(OverlapGraph::ContigInfo*) [219] [236] 0.0 1.44 0.00 606974957 void std::iter_swap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [236] ----------------------------------------------- 5657847 ReadSeededFastaFile(std::string const&, std::vector >*) [26] 1.06 0.12 3546341/2099102434 SeededRead::~SeededRead() [251] 3.71 0.43 12385642/2099102434 main [78] [237] 0.0 1.38 0.00 21589830 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::~_Rb_tree() [237] 21109759 Vote* std::copy(Vote*, Vote*, Vote*) [257] 960143 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [145] ----------------------------------------------- 19323731 std::vector >::operator=(std::vector > const&) [60] [238] 0.0 1.38 0.00 19323731 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [238] 19345116 ReadProcessor::ReadProcessor(std::string const&) [59] ----------------------------------------------- [239] 0.0 0.02 1.33 std::vector >::max_size() const [239] 0.02 1.31 3403951/16982099 mar_types* std::copy<__gnu_cxx::__normal_iterator > >, mar_types*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*) [155] ----------------------------------------------- 0.00 0.00 648620/332322227 std::_Rb_tree_const_iterator >::_Rb_tree_const_iterator(std::_Rb_tree_node > const*) [589] 0.00 0.00 648620/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator*() const [588] 0.00 0.00 648620/332322227 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [337] 0.00 0.00 2447689/332322227 int* std::copy<__gnu_cxx::__normal_iterator > >, int*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int*) [225] 0.00 0.00 2623439/332322227 mar_types* std::vector >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator > > >(unsigned int, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [152] 0.01 0.00 3403951/332322227 __gnu_cxx::__normal_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [136] 0.01 0.00 7948176/332322227 int* std::vector >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator > > >(unsigned int, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [143] 0.01 0.00 7978775/332322227 std::vector >::capacity() const [241] 0.02 0.00 9412154/332322227 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [117] 0.02 0.00 9412154/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [148] 0.03 0.00 16201587/332322227 void std::_Destroy<__gnu_cxx::__normal_iterator > >, int>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::allocator&) [414] 0.03 0.00 16201587/332322227 std::vector >::capacity() const [472] 0.03 0.00 16982099/332322227 mar_types* std::__copy_move_a2 > >, mar_types*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*) [394] 0.06 0.00 35883263/332322227 __gnu_cxx::__normal_iterator > >::base() const [445] 0.15 0.00 88748625/332322227 int* std::__copy_move_a2 > >, int*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int*) [98] 0.18 0.00 6883112/332322227 ReadProcessor::ReadProcessor(std::string const&) [59] 0.20 0.00 7870317/332322227 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, RawRead const&) [235] 0.27 0.00 10628041/332322227 void std::__push_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [147] 0.32 0.00 87751398/332322227 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair const&) [253] [240] 0.0 1.35 0.00 332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [240] ----------------------------------------------- [241] 0.0 0.02 1.31 std::vector >::capacity() const [241] 1.17 0.13 3888599/2099102434 void std::__push_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [147] 0.01 0.00 7978775/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [240] ----------------------------------------------- 960143 std::_Deque_base >::_M_initialize_map(unsigned int) [242] 44790 ReadProcessor::ReadProcessor(std::string const&) [358] 48116890 std::vector >::operator=(std::vector > const&) [60] 0.05 0.01 176329/2099102434 __gnu_cxx::new_allocator >::construct(std::pair*, std::pair const&) [425] 0.29 0.03 960143/2099102434 std::vector >::begin() const [360] 0.29 0.03 960143/2099102434 std::_Vector_base >::_M_deallocate(Vote*, unsigned int) [354] 0.29 0.03 960143/2099102434 void std::_Destroy<__gnu_cxx::__normal_iterator > >, Vote>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::allocator&) [361] 0.58 0.07 1920286/2099102434 std::vector >::capacity() const [303] 0.58 0.07 1920286/2099102434 Vote* std::vector >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator > > >(unsigned int, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [243] [242] 0.0 1.07 0.24 55059010+960143 std::_Deque_base >::_M_initialize_map(unsigned int) [242] 0.14 0.11 1920286/116345246 std::deque >::~deque() [134] 0.00 0.00 1920286/1920286 std::allocator::allocator() [692] 0.00 0.00 1004933/2925217 std::pair* std::__copy_move_backward_a2*, std::pair*>(std::pair*, std::pair*, std::pair*) [684] 1920286 std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [151] 1920286 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_destroy_node(std::_Rb_tree_node >*) [406] 1004933 __gnu_cxx::new_allocator >::deallocate(std::pair*, unsigned int) [697] 960143 std::_Deque_base >::_M_initialize_map(unsigned int) [242] ----------------------------------------------- [243] 0.0 0.02 1.28 Vote* std::vector >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator > > >(unsigned int, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [243] 0.58 0.07 1920286/2099102434 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_destroy_node(std::_Rb_tree_node >*) [406] 0.58 0.07 1920286/2099102434 std::_Deque_base >::_M_initialize_map(unsigned int) [242] 0.00 0.00 2880429/4238020 std::pair::operator=(std::pair const&) [681] ----------------------------------------------- 1.30 0.00 279401951/279401951 OverlapGraph::ContigInfo* std::__uninitialized_move_a >(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, std::allocator&) [113] [244] 0.0 1.30 0.00 279401951 bool __gnu_cxx::operator< *, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [244] ----------------------------------------------- 7737 Cluster::Cluster() [812] 0.00 0.00 7737/2099102434 std::vector, std::allocator > >::push_back(std::pair const&) [265] [245] 0.0 1.23 0.07 15474 OverlapGraph::Traverse(int, int, int, int) [245] 0.07 0.00 2674989/158981148 operator<<(std::ostream&, ShortyString const&) [359] 5419611 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [75] 5357715 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] ----------------------------------------------- [246] 0.0 0.00 1.28 global constructors keyed to _ZN13ReadProcessor6total_E [246] 1.15 0.13 3827941/2099102434 Contig::operator=(Contig const&) [174] ----------------------------------------------- [247] 0.0 0.29 0.97 std::basic_string, std::allocator > std::operator+, std::allocator >(std::basic_string, std::allocator > const&, char const*) [247] 0.24 0.45 25559691/25559691 std::deque >::end() [296] 0.07 0.09 25559691/3222388240 std::deque >::deque(std::deque > const&) [31] 0.06 0.01 25559691/2323744019 std::_Deque_base >::~_Deque_base() [80] 0.05 0.00 25559691/2734359181 std::deque >::_M_destroy_data(std::_Deque_iterator, std::_Deque_iterator, std::allocator const&) [70] ----------------------------------------------- [248] 0.0 1.24 0.00 __gnu_cxx::__normal_iterator > >::base() const [248] ----------------------------------------------- [249] 0.0 0.01 1.21 RawRead* std::__uninitialized_copy::uninitialized_copy(RawRead*, RawRead*, RawRead*) [249] 0.72 0.08 2416982/2099102434 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [5] 0.36 0.04 1208491/2099102434 ShortyString::ShortyString(std::string const&, int) [7] 0.00 0.00 1208491/1208491 ShortyString::operator==(std::string const&) const [696] ----------------------------------------------- [250] 0.0 1.22 0.00 __gnu_cxx::new_allocator > >::new_allocator() [250] ----------------------------------------------- 0.00 0.00 4/52520 Assembler::Assemble() [474] 0.00 0.52 23144/52520 Assembler::MakeCluster(bool, std::vector, std::allocator > > const&, Cluster*, Cluster*, Contig*, Contig*) [27] 0.00 0.66 29372/52520 Assembler::ProcessNewSeeds() [38] [251] 0.0 0.00 1.19 52520 SeededRead::~SeededRead() [251] 1.06 0.12 3546341/2099102434 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::~_Rb_tree() [237] ----------------------------------------------- 0.00 0.00 1/271331188 __gnu_cxx::__enable_if::__value, void>::__type std::__fill_a(short*, short*, int const&) [675] 0.00 0.00 2/271331188 UtilsString::PrintContig(std::string const&, std::string const&) [670] 0.00 0.00 1056643/271331188 std::vector, std::allocator > >::operator=(std::vector, std::allocator > > const&) [389] 0.08 0.00 66875224/271331188 UtilsString::OverlapFromCommonReadMapping(ShortyString const&, ShortyString const&, std::vector, std::allocator > > const&, std::vector, std::allocator > > const&, ReadProcessor const*, int*, int*, ShortyString*) [388] 0.09 0.00 77624758/271331188 void std::_Destroy<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::allocator >&) [430] 0.09 0.00 77624758/271331188 Vote::operator+=(Vote const&) [267] 0.90 0.00 48149802/271331188 _fini [4] [252] 0.0 1.17 0.00 271331188 __static_initialization_and_destruction_0(int, int) [252] ----------------------------------------------- 0.00 0.00 648620/77934596 triple* std::copy_backward*, triple*>(triple*, triple*, triple*) [498] 0.01 0.00 2447689/77934596 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::end() const [282] 0.01 0.00 2447689/77934596 triple* std::__uninitialized_move_a*, triple*, std::allocator > >(triple*, triple*, triple*, std::allocator >&) [502] 0.01 0.01 2674989/77934596 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::begin() const [499] 0.02 0.01 3744929/77934596 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [337] 0.04 0.01 7261172/77934596 std::_Vector_base >::_Vector_base(unsigned int, std::allocator const&) [437] 0.05 0.02 9412154/77934596 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [117] 0.06 0.02 12087143/77934596 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_unique(std::pair const&) [2] 0.06 0.02 12087143/77934596 std::pair >, bool>::pair(std::_Rb_tree_const_iterator > const&, bool const&) [441] 0.09 0.04 18649276/77934596 __gnu_cxx::__normal_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [136] 0.20 0.08 2623439/77934596 ReadProcessor::ReadProcessor(std::string const&) [59] 0.29 0.11 3850353/77934596 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [177] [253] 0.0 0.83 0.32 77934596 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair const&) [253] 0.32 0.00 87751398/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [240] ----------------------------------------------- [254] 0.0 0.02 1.10 std::vector >::_M_erase_at_end(Vote*) [254] 0.01 0.73 1056643/148011011 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [57] 0.32 0.04 1056643/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] ----------------------------------------------- 0.00 0.00 1/67677006 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::~vector() [674] 0.00 0.00 1/67677006 std::list, std::allocator > >::list() [673] 0.00 0.00 2/67677006 std::_Vector_base, std::allocator > >, std::allocator, std::allocator > > > >::~_Vector_base() [669] 0.00 0.00 1002/67677006 Hash::Insert(std::string const&, int, int, int, int) [220] 1.09 0.00 67676000/67677006 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, UtilsMath::median_event_point const&) [22] [255] 0.0 1.09 0.00 67677006 std::list, std::allocator > >::begin() [255] ----------------------------------------------- 0.30 0.13 960142/2422750 __gnu_cxx::new_allocator::deallocate(Contig*, unsigned int) [339] 0.46 0.19 1462608/2422750 std::pair* std::__uninitialized_copy_a*, std::pair*, std::pair >(std::pair*, std::pair*, std::pair*, std::allocator >&) [301] [256] 0.0 0.76 0.32 2422750 mar_types* std::copy(mar_types*, mar_types*, mar_types*) [256] 0.29 0.03 960142/2099102434 TrieNode::searchWithErrorAllowed(std::string const&, int, int) [367] ----------------------------------------------- 21109759 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::~_Rb_tree() [237] 0.14 0.02 480071/2099102434 Vote* std::__uninitialized_copy_a<__gnu_cxx::__normal_iterator > >, Vote*, Vote>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, Vote*, std::allocator&) [402] [257] 0.0 1.07 0.00 21589830 Vote* std::copy(Vote*, Vote*, Vote*) [257] 21589830 Contig::~Contig() [53] ----------------------------------------------- 6502930 ReadProcessor::ReadProcessor(std::string const&) [59] 0.80 0.09 2674989/2099102434 OverlapGraph::MergeReads(std::vector, std::allocator > > const&) [40] [258] 0.0 1.07 0.00 9177919 std::vector >::end() [258] 9177919 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] 7737 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [75] ----------------------------------------------- [259] 0.0 0.00 1.06 OverlapGraph::ContigInfo::ContigInfo(OverlapGraph::ContigInfo const&) [259] 0.63 0.07 2113286/2099102434 void std::__introsort_loop<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj) [86] 0.32 0.04 1056643/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] ----------------------------------------------- [260] 0.0 1.02 0.00 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_get_Node_allocator() const [260] ----------------------------------------------- [261] 0.0 1.00 0.00 std::pair::pair() [261] ----------------------------------------------- 0.14 0.05 55809948/111619896 std::_Vector_base, std::allocator > >::_M_deallocate(std::pair*, unsigned int) [319] 0.60 0.19 55809948/111619896 std::_Vector_base, std::allocator > >::_Vector_impl::_Vector_impl() [187] [262] 0.0 0.75 0.24 111619896 std::_Deque_base >::_M_allocate_node() [262] 0.24 0.00 55809948/1914486784 bool std::operator==(std::_Deque_iterator const&, std::_Deque_iterator const&) [81] ----------------------------------------------- [263] 0.0 0.79 0.18 __static_initialization_and_destruction_0(int, int) [263] 0.18 0.00 158981148/1506635566 std::pair* std::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [115] ----------------------------------------------- [264] 0.0 0.04 0.93 __gnu_cxx::new_allocator::construct(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo const&) [264] 0.32 0.04 1056643/2099102434 std::vector >::operator=(std::vector > const&) [88] 0.32 0.04 1056643/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] 0.21 0.00 1056643/1056643 std::vector, std::allocator > >::operator=(std::vector, std::allocator > > const&) [389] 0.00 0.01 1069892/196537847 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] ----------------------------------------------- 0.03 0.92 7737/7737 Assembler::MakeContigs(bool, Cluster const&, SeededRead const&) [21] [265] 0.0 0.03 0.92 7737 std::vector, std::allocator > >::push_back(std::pair const&) [265] 0.80 0.09 2682726/2099102434 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [75] 0.00 0.02 2674989/2674989 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::begin() const [499] 0.00 0.00 7737/2099102434 OverlapGraph::Traverse(int, int, int, int) [245] 0.00 0.00 7737/7737 __static_initialization_and_destruction_0(int, int) [755] ----------------------------------------------- [266] 0.0 0.33 0.60 std::vector, std::allocator > >::~vector() [266] 0.16 0.19 55809948/3222388240 std::deque >::deque(std::deque > const&) [31] 0.13 0.02 55809948/2323744019 std::_Deque_base >::~_Deque_base() [80] 0.10 0.00 55809948/2734359181 std::deque >::_M_destroy_data(std::_Deque_iterator, std::_Deque_iterator, std::allocator const&) [70] ----------------------------------------------- 0.72 0.21 77624758/77624758 std::vector >::swap(std::vector >&) [85] [267] 0.0 0.72 0.21 77624758 Vote::operator+=(Vote const&) [267] 0.02 0.09 77624758/77624758 void std::_Destroy<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::allocator >&) [430] 0.09 0.00 77624758/271331188 __static_initialization_and_destruction_0(int, int) [252] ----------------------------------------------- 175862 std::vector >::operator=(std::vector > const&) [60] 659481 std::vector >::operator=(std::vector > const&) [283] 7065846 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 0.01 0.00 21385/2099102434 bool __gnu_cxx::operator!=*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [544] 0.45 0.05 1496030/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] 5.79 0.66 19302346/2099102434 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree_impl::_Rb_tree_impl() [139] 5.79 0.66 19302346/2099102434 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_destroy_node(std::_Rb_tree_node >*) [141] [268] 0.0 0.92 0.00 48023296 __gnu_cxx::new_allocator::construct(Contig*, Contig const&) [268] 3532923 std::vector >::operator=(std::vector > const&) [283] 3532923 Contig::Contig(Contig const&) [214] ----------------------------------------------- [269] 0.0 0.02 0.90 std::set, OverlapGraph::IntPairEq, std::allocator > >::insert(std::pair const&) [269] 0.80 0.09 2682726/2099102434 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [75] 0.00 0.00 412850/2674989 std::vector, std::allocator > >::size() const [687] ----------------------------------------------- [270] 0.0 0.01 0.90 void std::sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [270] 0.80 0.09 2682726/2099102434 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [75] 0.00 0.00 13249/2099102434 std::vector >::operator=(std::vector > const&) [88] 0.00 0.00 13249/196537847 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] ----------------------------------------------- [271] 0.0 0.01 0.89 Cluster::GetGen(int) const [271] 0.80 0.09 2674989/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] ----------------------------------------------- [272] 0.0 0.01 0.89 Cluster::GetIndex(int) const [272] 0.80 0.09 2674989/2099102434 _fini [4] ----------------------------------------------- [273] 0.0 0.01 0.89 std::pair, bool>::pair(std::_Rb_tree_const_iterator const&, bool const&) [273] 0.80 0.09 2674989/2099102434 Contig::Contig(Contig const&) [214] ----------------------------------------------- [274] 0.0 0.04 0.86 std::vector, std::allocator > >::size() const [274] 0.77 0.09 2572727/2099102434 __static_initialization_and_destruction_0(int, int) [227] ----------------------------------------------- [275] 0.0 0.00 0.90 std::set, std::allocator >::begin() const [275] 0.80 0.09 2682726/2099102434 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [75] ----------------------------------------------- [276] 0.0 0.00 0.89 global constructors keyed to _ZN12OverlapGraphC2EbRK7ClusterPK10SeededReadPK13ReadProcessorPSt13basic_fstreamIcSt11char_traitsIcEESD_ [276] 0.80 0.09 2674989/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] ----------------------------------------------- [277] 0.0 0.00 0.89 std::_Rb_tree_const_iterator::_Rb_tree_const_iterator(std::_Rb_tree_iterator const&) [277] 0.80 0.09 2674989/2099102434 Contig::Contig(Contig const&) [214] ----------------------------------------------- [278] 0.0 0.00 0.89 std::set, OverlapGraph::IntPairEq, std::allocator > >::~set() [278] 0.80 0.09 2674989/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] ----------------------------------------------- [279] 0.0 0.00 0.89 std::set, std::allocator >::~set() [279] 0.80 0.09 2674989/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] ----------------------------------------------- 0.88 0.00 529397792/529397792 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_unique(std::pair const&) [2] [280] 0.0 0.88 0.00 529397792 std::_Rb_tree_iterator::operator==(std::_Rb_tree_iterator const&) const [280] ----------------------------------------------- [281] 0.0 0.32 0.53 std::vector >::~vector() [281] 0.16 0.19 55809948/3222388240 std::deque >::deque(std::deque > const&) [31] 0.18 0.00 55809948/55809948 std::_Vector_base, std::allocator > >::_Vector_impl::~_Vector_impl() [396] ----------------------------------------------- [282] 0.0 0.01 0.83 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::end() const [282] 0.73 0.08 2447689/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] 0.01 0.00 2447689/77934596 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair const&) [253] ----------------------------------------------- 3532923 __gnu_cxx::new_allocator::construct(Contig*, Contig const&) [268] 0.01 0.00 21385/2099102434 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::__normal_iterator(triple* const&) [546] 1.32 0.15 4393532/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] 2.89 0.33 9651173/2099102434 std::_Rb_tree, std::less, std::allocator >::_S_left(std::_Rb_tree_node_base*) [189] 2.89 0.33 9651173/2099102434 std::_Vector_base, std::allocator > >::_Vector_impl::_Vector_impl() [186] [283] 0.0 0.61 0.23 27250186 std::vector >::operator=(std::vector > const&) [283] 0.15 0.00 9828241/1755802966 std::vector, std::allocator > >::max_size() const [172] 0.02 0.06 659481/19961827 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_create_node(std::pair const&) [384] 0.00 0.00 2344913/2357247 std::pair* std::__copy_move::__copy_m*, std::pair*>(std::pair*, std::pair*, std::pair*) [689] 10841858 OverlapGraph::ContigInfo* std::__copy_move_backward::__copy_move_b(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [331] 659481 __gnu_cxx::new_allocator::construct(Contig*, Contig const&) [268] 198453 OverlapGraph::ContigInfo* std::__uninitialized_copy::uninitialized_copy(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [583] ----------------------------------------------- [284] 0.0 0.82 0.00 __gnu_cxx::__normal_iterator > >::operator*() const [284] ----------------------------------------------- [285] 0.0 0.01 0.81 std::string* std::__copy_move_backward::__copy_move_b(std::string*, std::string*, std::string*) [285] 0.72 0.08 2416982/2099102434 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [5] ----------------------------------------------- [286] 0.0 0.00 0.81 __static_initialization_and_destruction_0(int, int) [286] 0.72 0.08 2416982/2099102434 UtilsFile::OpenFile(std::string const&, std::string const&) [54] ----------------------------------------------- [287] 0.0 0.81 0.00 std::_Rb_tree, std::less, std::allocator >::_Rb_tree_impl, false>::~_Rb_tree_impl() [287] ----------------------------------------------- [288] 0.0 0.79 0.00 int* std::uninitialized_copy(int*, int*, int*) [288] ----------------------------------------------- [289] 0.0 0.06 0.73 bool __gnu_cxx::operator== > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [289] 0.73 0.00 23804298/1397173708 std::vector >::push_back(int const&) [32] ----------------------------------------------- [290] 0.0 0.78 0.00 __gnu_cxx::__normal_iterator > >::base() const [290] ----------------------------------------------- [291] 0.0 0.00 0.78 std::vector >::insert(__gnu_cxx::__normal_iterator > >, unsigned int, Vote const&) [291] 0.01 0.73 1056643/148011011 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [57] 0.03 0.00 1056643/1397173708 std::vector >::push_back(int const&) [32] ----------------------------------------------- [292] 0.0 0.76 0.00 std::_Vector_base, std::allocator > >::_M_get_Tp_allocator() [292] ----------------------------------------------- [293] 0.0 0.74 0.00 __gnu_cxx::new_allocator::new_allocator(__gnu_cxx::new_allocator const&) [293] ----------------------------------------------- [294] 0.0 0.74 0.00 std::_Vector_base >::_M_get_Tp_allocator() [294] ----------------------------------------------- [295] 0.0 0.01 0.71 bool __gnu_cxx::operator!= > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [295] 0.63 0.07 2113286/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] ----------------------------------------------- 0.24 0.45 25559691/25559691 std::basic_string, std::allocator > std::operator+, std::allocator >(std::basic_string, std::allocator > const&, char const*) [247] [296] 0.0 0.24 0.45 25559691 std::deque >::end() [296] 0.45 0.00 301140141/1526430335 std::deque >::end() const [111] ----------------------------------------------- 2674989 Contig::Contig(Contig const&) [214] 2.82 0.32 9412154/2099102434 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_end() [190] [297] 0.0 0.69 0.00 12087143 __gnu_cxx::__normal_iterator > >::difference_type __gnu_cxx::operator- > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [297] 9412154 void std::__adjust_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [121] ----------------------------------------------- [298] 0.0 0.22 0.47 TrieNode::Insert(int, mar_types) [298] 0.42 0.05 1405934/2099102434 TrieNode::searchWithErrorWholeSeed(std::string const&, int, int) [138] ----------------------------------------------- 0.06 0.00 25559691/275580450 std::stack > >::stack(std::deque > const&) [395] 0.14 0.00 55809948/275580450 std::vector >::operator[](unsigned int) const [401] 0.23 0.00 92439480/275580450 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [57] 0.25 0.00 101771331/275580450 std::stack > >::empty() const [343] [299] 0.0 0.69 0.00 275580450 std::deque >::begin() [299] ----------------------------------------------- 0.67 0.00 606974957/606974957 bool __gnu_cxx::operator==*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [107] [300] 0.0 0.67 0.00 606974957 std::__niter_base<__gnu_cxx::__normal_iterator > >, true>::__b(__gnu_cxx::__normal_iterator > >) [300] ----------------------------------------------- 0.01 0.65 502466/502466 std::deque >::size() const [302] [301] 0.0 0.01 0.65 502466 std::pair* std::__uninitialized_copy_a*, std::pair*, std::pair >(std::pair*, std::pair*, std::pair*, std::allocator >&) [301] 0.46 0.19 1462608/2422750 mar_types* std::copy(mar_types*, mar_types*, mar_types*) [256] ----------------------------------------------- [302] 0.0 0.00 0.66 std::deque >::size() const [302] 0.01 0.65 502466/502466 std::pair* std::__uninitialized_copy_a*, std::pair*, std::pair >(std::pair*, std::pair*, std::pair*, std::allocator >&) [301] ----------------------------------------------- [303] 0.0 0.01 0.64 std::vector >::capacity() const [303] 0.58 0.07 1920286/2099102434 std::_Deque_base >::_M_initialize_map(unsigned int) [242] ----------------------------------------------- [304] 0.0 0.65 0.00 std::pair* std::__copy_move_backward_a*, std::pair*>(std::pair*, std::pair*, std::pair*) [304] ----------------------------------------------- [305] 0.0 0.41 0.24 void std::reverse<__gnu_cxx::__normal_iterator >(__gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator) [305] 0.24 0.00 66874725/1724816198 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [69] ----------------------------------------------- [306] 0.0 0.00 0.64 void std::_Destroy_aux::__destroy(mar_types*, mar_types*) [306] 0.58 0.07 1920286/2099102434 SeededRead** std::copy_backward(SeededRead**, SeededRead**, SeededRead**) [680] ----------------------------------------------- 0.00 0.00 32912/48149802 std::vector, std::allocator > >::_M_erase_at_end(std::pair*) [167] 0.07 0.06 10409062/48149802 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [109] 0.25 0.23 37707828/48149802 std::pair* std::__uninitialized_copy_a*, std::pair*, std::pair >(std::pair*, std::pair*, std::pair*, std::allocator >&) [322] [307] 0.0 0.32 0.30 48149802 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [307] 0.28 0.02 48116890/304749023 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree_impl::_M_initialize() [218] ----------------------------------------------- 4833964 std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [5] 0.00 0.00 13130/2099102434 std::vector, std::allocator > >::end() [511] [308] 0.0 0.61 0.00 4847094 std::_Vector_base, std::allocator > >::_Vector_impl::_Vector_impl() [308] 13130 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [368] ----------------------------------------------- [309] 0.0 0.60 0.00 std::allocator >::allocator() [309] ----------------------------------------------- [310] 0.0 0.23 0.35 ReadProcessor::TotalPairs() const [310] 0.35 0.00 236425176/362166824 __gnu_cxx::new_allocator::construct(std::string*, std::string const&) [191] ----------------------------------------------- 0.04 0.00 37707828/518771239 std::allocator >::allocator() [363] 0.04 0.00 37740740/518771239 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [109] 0.10 0.00 75448568/518771239 std::_Rb_tree, std::less, std::allocator >::_M_create_node(int const&) [370] 0.13 0.00 122624701/518771239 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree_impl::_M_initialize() [218] 0.26 0.00 245249402/518771239 std::pair* std::vector, std::allocator > >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > >(unsigned int, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >) [89] [311] 0.0 0.57 0.00 518771239 std::_Rb_tree, std::less, std::allocator >::_M_put_node(std::_Rb_tree_node*) [311] ----------------------------------------------- 3840580 TrieNode::searchWithErrorAllowedNonRecursive(std::string const&, int) [312] 0.00 0.00 1/3393446 RawRead* std::__copy_move_backward_a2(RawRead*, RawRead*, RawRead*) [668] 0.00 0.00 10/3393446 TrieNode::addToTrie(myList*, int) [330] 0.02 0.00 67185/3393446 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, RawRead const&) [235] 0.02 0.00 1405934/3393446 TrieNode::Search(std::string const&) [320] 0.52 0.00 1920316/3393446 TrieNode::traceTrie() [317] [312] 0.0 0.56 0.00 3393446+3840580 TrieNode::searchWithErrorAllowedNonRecursive(std::string const&, int) [312] 0.00 0.00 960142/2902821 __gnu_cxx::new_allocator::max_size() const [686] 3840580 TrieNode::searchWithErrorAllowedNonRecursive(std::string const&, int) [312] ----------------------------------------------- [313] 0.0 0.00 0.56 std::allocator > >::~allocator() [313] 0.50 0.06 1683262/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] ----------------------------------------------- [314] 0.0 0.00 0.56 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree() [314] 0.50 0.06 1683262/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] ----------------------------------------------- [315] 0.0 0.02 0.52 void std::_Destroy_aux::__destroy(std::string*, std::string*) [315] 0.01 0.51 1208491/4833964 __static_initialization_and_destruction_0(int, int) [211] ----------------------------------------------- 0.00 0.00 39950/529397792 OverlapGraph::ContigInfo* std::__uninitialized_move_a >(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, std::allocator&) [113] 0.08 0.00 77584808/529397792 std::less::operator()(int const&, int const&) const [377] 0.46 0.00 451773034/529397792 std::_Rb_tree, std::less, std::allocator >::begin() [212] [316] 0.0 0.54 0.00 529397792 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator--() [316] ----------------------------------------------- 2880428 TrieNode::addToTrie(myList*, int) [330] [317] 0.0 0.00 0.52 2880428 TrieNode::traceTrie() [317] 0.52 0.00 1920316/3393446 TrieNode::searchWithErrorAllowedNonRecursive(std::string const&, int) [312] 0.00 0.00 1920284/2902821 __gnu_cxx::new_allocator::max_size() const [686] 5760858 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [405] ----------------------------------------------- [318] 0.0 0.52 0.00 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::base() const [318] ----------------------------------------------- [319] 0.0 0.07 0.44 std::_Vector_base, std::allocator > >::_M_deallocate(std::pair*, unsigned int) [319] 0.16 0.09 55809948/2544037281 std::_Deque_iterator std::__uninitialized_copy_a, std::_Deque_iterator, SeededRead>(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator, std::allocator&) [51] 0.14 0.05 55809948/111619896 std::_Deque_base >::_M_allocate_node() [262] ----------------------------------------------- [320] 0.0 0.01 0.49 TrieNode::Search(std::string const&) [320] 0.42 0.05 1405934/2099102434 TrieNode::searchWithErrorWholeSeed(std::string const&, int, int) [138] 0.02 0.00 1405934/3393446 TrieNode::searchWithErrorAllowedNonRecursive(std::string const&, int) [312] ----------------------------------------------- [321] 0.0 0.06 0.44 std::_Vector_base, std::allocator > >::_M_deallocate(std::pair*, unsigned int) [321] 0.27 0.02 48149802/304749023 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree_impl::_M_initialize() [218] 0.09 0.06 10409062/10409062 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::get_allocator() const [413] ----------------------------------------------- [322] 0.0 0.01 0.48 std::pair* std::__uninitialized_copy_a*, std::pair*, std::pair >(std::pair*, std::pair*, std::pair*, std::allocator >&) [322] 0.25 0.23 37707828/48149802 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [307] ----------------------------------------------- [323] 0.0 0.19 0.30 std::vector >::push_back(Contig const&) [323] 0.07 0.22 22053227/196537847 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] 0.01 0.00 2674989/539451719 std::list, std::allocator > >::operator=(std::list, std::allocator > > const&) [210] ----------------------------------------------- [324] 0.0 0.01 0.47 std::_Vector_base >::_Vector_impl::_Vector_impl() [324] 0.14 0.33 55809948/55809948 int* std::__copy_move_backward_a(int*, int*, int*) [328] ----------------------------------------------- 0.02 0.46 13249/13249 std::set, OverlapGraph::IntPairEq, std::allocator > >::end() const [326] [325] 0.0 0.02 0.46 13249 std::_Vector_base, std::allocator > >::~_Vector_base() [325] 0.41 0.05 1368147/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 0.00 0.00 13249/196537847 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] ----------------------------------------------- [326] 0.0 0.00 0.48 std::set, OverlapGraph::IntPairEq, std::allocator > >::end() const [326] 0.02 0.46 13249/13249 std::_Vector_base, std::allocator > >::~_Vector_base() [325] ----------------------------------------------- [327] 0.0 0.47 0.00 std::_Rb_tree_iterator::_Rb_tree_iterator(std::_Rb_tree_node*) [327] ----------------------------------------------- 0.14 0.33 55809948/55809948 std::_Vector_base >::_Vector_impl::_Vector_impl() [324] [328] 0.0 0.14 0.33 55809948 int* std::__copy_move_backward_a(int*, int*, int*) [328] 0.33 0.00 55809948/55809948 std::_Deque_iterator::_M_set_node(SeededRead**) [355] ----------------------------------------------- [329] 0.0 0.10 0.36 std::_Vector_base >::_Vector_base() [329] 0.33 0.03 101771331/873253357 std::pair* std::copy_backward*, std::pair*>(std::pair*, std::pair*, std::pair*) [99] ----------------------------------------------- 30 TrieNode::addToTrie(myList*, int) [330] 2 std::_List_base, std::allocator > >::_M_clear() [783] 960145 TrieNode::searchWithErrorAllowed(std::string const&, int, int) [367] 1920887 TrieNode::searchWithError(std::string const&, int) [691] 0.00 0.00 10/2099102434 TrieNode::constructTrie() [609] [330] 0.0 0.46 0.00 2881044+30 TrieNode::addToTrie(myList*, int) [330] 0.00 0.00 10/3393446 TrieNode::searchWithErrorAllowedNonRecursive(std::string const&, int) [312] 0.00 0.00 3840572/3840572 std::_Deque_iterator::_Deque_iterator(std::_Deque_iterator const&) [682] 0.00 0.00 1920284/2925217 std::pair* std::__copy_move_backward_a2*, std::pair*>(std::pair*, std::pair*, std::pair*) [684] 2880428 TrieNode::traceTrie() [317] 1 std::vector >::~vector() [208] 30 TrieNode::addToTrie(myList*, int) [330] ----------------------------------------------- 10841858 std::vector >::operator=(std::vector > const&) [283] [331] 0.0 0.46 0.00 10841858 OverlapGraph::ContigInfo* std::__copy_move_backward::__copy_move_b(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [331] 659481 ReadProcessor::ReadProcessor(std::string const&) [358] ----------------------------------------------- 22 ShortyString::GetConfidentClone() const [332] 22 ShortyString::ShortyString(std::string const&, int) [7] 44 ShortyString::~ShortyString() [34] 1242502 ShortyString::ShortyString(std::string const&, int) [366] [332] 0.0 0.46 0.00 1242568+22 ShortyString::GetConfidentClone() const [332] 1242520 Contig::~Contig() [53] 176 ShortyString::operator+(ShortyString const&) [761] 132 ShortyString::ReverseComplement() const [763] 22 ShortyString::RepresentativeVotes() const [768] 22 ShortyString::GetConfidentClone() const [332] ----------------------------------------------- 44 ShortyString::operator+=(ShortyString const&) [334] [333] 0.0 0.46 0.00 44 ShortyString::operator+=(std::string const&) [333] 2097151 Contig::~Contig() [53] ----------------------------------------------- 111 ShortyString::operator+(std::string const&) [762] [334] 0.0 0.31 0.15 111 ShortyString::operator+=(ShortyString const&) [334] 0.15 0.00 3339671/3339671 ShortyString::operator=(std::string const&) [407] 2097151 Contig::~Contig() [53] 44 ShortyString::operator+=(std::string const&) [333] ----------------------------------------------- [335] 0.0 0.02 0.44 std::vector >::vector() [335] 0.11 0.33 31421017/2635651173 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, UtilsMath::median_event_point const&) [22] ----------------------------------------------- [336] 0.0 0.10 0.35 std::allocator >::~allocator() [336] 0.21 0.14 111619896/1623116001 std::deque >::_M_reserve_map_at_back(unsigned int) [91] ----------------------------------------------- [337] 0.0 0.00 0.45 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [337] 0.00 0.22 648620/648620 std::vector >::begin() const [386] 0.00 0.21 648620/648620 Contig* std::__copy_move_backward_a2(Contig*, Contig*, Contig*) [390] 0.02 0.01 3744929/77934596 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair const&) [253] 0.00 0.00 648620/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [240] 0.00 0.00 648620/3096309 std::pair >, bool>::pair(std::_Rb_tree_iterator > const&, bool const&) [683] ----------------------------------------------- [338] 0.0 0.43 0.00 std::_Vector_base >::_M_get_Tp_allocator() const [338] ----------------------------------------------- [339] 0.0 0.00 0.43 __gnu_cxx::new_allocator::deallocate(Contig*, unsigned int) [339] 0.30 0.13 960142/2422750 mar_types* std::copy(mar_types*, mar_types*, mar_types*) [256] ----------------------------------------------- [340] 0.0 0.02 0.41 UtilsMath::median_event_point::operator<(UtilsMath::median_event_point const&) const [340] 0.10 0.31 29004034/2635651173 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, UtilsMath::median_event_point const&) [22] ----------------------------------------------- [341] 0.0 0.01 0.42 global constructors keyed to _ZN7RawReadC2Eiiiii [341] 0.37 0.04 1242520/2099102434 ShortyString::ShortyString(std::string const&, int) [366] ----------------------------------------------- [342] 0.0 0.07 0.35 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [342] 0.32 0.04 1056643/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] ----------------------------------------------- [343] 0.0 0.15 0.25 std::stack > >::empty() const [343] 0.25 0.00 101771331/275580450 std::deque >::begin() [299] ----------------------------------------------- [344] 0.0 0.04 0.35 std::vector >::operator[](unsigned int) [344] 0.16 0.19 55809948/3222388240 std::deque >::deque(std::deque > const&) [31] ----------------------------------------------- [345] 0.0 0.00 0.39 std::vector, std::allocator > >::push_back(triple const&) [345] 0.32 0.04 1069892/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 0.01 0.02 2139784/196537847 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] ----------------------------------------------- 2001287 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator+(int const&) const [410] 0.13 0.02 446402/2099102434 void std::partial_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [135] [346] 0.0 0.15 0.23 2447689 __gnu_cxx::__normal_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [346] 0.23 0.00 2447689/6612552 int* std::__uninitialized_copy_a<__gnu_cxx::__normal_iterator > >, int*, int>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int*, std::allocator&) [378] 9330801 void std::__push_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [147] ----------------------------------------------- [347] 0.0 0.38 0.00 __gnu_cxx::__normal_iterator > >::base() const [347] ----------------------------------------------- [348] 0.0 0.05 0.32 std::_Vector_base, std::allocator > >::~_Vector_base() [348] 0.08 0.25 24728216/196537847 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] ----------------------------------------------- [349] 0.0 0.02 0.35 std::vector, std::allocator > >::capacity() const [349] 0.32 0.04 1056643/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] ----------------------------------------------- [350] 0.0 0.14 0.23 void std::_Destroy<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::allocator >&) [350] 0.21 0.02 37740740/304749023 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree_impl::_M_initialize() [218] ----------------------------------------------- [351] 0.0 0.10 0.27 std::stack > >::top() [351] 0.23 0.03 101771331/2323744019 std::_Deque_base >::~_Deque_base() [80] ----------------------------------------------- [352] 0.0 0.34 0.00 TrieNode::~TrieNode() [352] ----------------------------------------------- [353] 0.0 0.01 0.32 std::vector >::end() const [353] 0.29 0.03 960143/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [145] 0.00 0.00 960143/4238020 std::pair::operator=(std::pair const&) [681] ----------------------------------------------- [354] 0.0 0.01 0.32 std::_Vector_base >::_M_deallocate(Vote*, unsigned int) [354] 0.29 0.03 960143/2099102434 std::_Deque_base >::_M_initialize_map(unsigned int) [242] ----------------------------------------------- 0.33 0.00 55809948/55809948 int* std::__copy_move_backward_a(int*, int*, int*) [328] [355] 0.0 0.33 0.00 55809948 std::_Deque_iterator::_M_set_node(SeededRead**) [355] ----------------------------------------------- 0.00 0.33 960143/960143 std::vector >::size() const [357] [356] 0.0 0.00 0.33 960143 std::_Deque_base >::_Deque_impl::_Deque_impl() [356] 0.29 0.03 960143/2099102434 std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [151] 0.00 0.00 960143/116345246 std::deque >::~deque() [134] ----------------------------------------------- [357] 0.0 0.00 0.33 std::vector >::size() const [357] 0.00 0.33 960143/960143 std::_Deque_base >::_Deque_impl::_Deque_impl() [356] ----------------------------------------------- 659481 OverlapGraph::ContigInfo* std::__copy_move_backward::__copy_move_b(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [331] 949495 OverlapGraph::ContigInfo* std::__uninitialized_copy::uninitialized_copy(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [583] 0.00 0.00 12334/2099102434 std::__miter_base<__gnu_cxx::__normal_iterator > >, false>::__b(__gnu_cxx::__normal_iterator > >) [578] 0.00 0.00 12334/2099102434 void std::_Destroy<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [579] 0.00 0.00 12334/2099102434 std::pair* std::__uninitialized_copy::uninitialized_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*>(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*) [576] 0.01 0.00 22395/2099102434 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [542] 0.01 0.00 22395/2099102434 std::allocator::allocator >(std::allocator > const&) [543] 0.01 0.00 24668/2099102434 std::pair* std::__copy_move::__copy_m const*, std::pair*>(std::pair const*, std::pair const*, std::pair*) [540] 0.01 0.00 44790/2099102434 std::__niter_base<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, true>::__b(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [508] 0.01 0.00 44790/2099102434 std::pair* std::__copy_move_a const*, std::pair*>(std::pair const*, std::pair const*, std::pair*) [509] 0.01 0.00 44790/2099102434 void std::_Destroy_aux::__destroy<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [507] 0.01 0.00 44790/2099102434 void std::_Destroy(OverlapGraph::ContigInfo*) [510] [358] 0.0 0.31 0.02 1894596 ReadProcessor::ReadProcessor(std::string const&) [358] 0.01 0.01 177068/38781760 std::_Rb_tree, std::less, std::allocator >::_M_create_node(int const&) [370] 0.00 0.00 61670/61670 ReadProcessor::GetMar(int, mar_types) const [723] 0.00 0.00 22395/502466 std::_Deque_base >::_M_get_Tp_allocator() const [702] 684149 ReadProcessor::GetMarLen(int, mar_types) const [232] 531204 __static_initialization_and_destruction_0(int, int) [100] 156765 ReadProcessor::ReadProcessor(std::string const&) [59] 67185 ReadProcessor::LocateRead(std::string const&) const [709] 44790 std::_Deque_base >::_M_initialize_map(unsigned int) [242] ----------------------------------------------- 0.00 0.00 1056643/158981148 triple::triple(int, int, mar_types) [587] 0.07 0.00 2674989/158981148 OverlapGraph::Traverse(int, int, int, int) [245] 0.13 0.00 77624758/158981148 std::vector, std::allocator > >::~vector() [41] 0.13 0.00 77624758/158981148 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [12] [359] 0.0 0.32 0.00 158981148 operator<<(std::ostream&, ShortyString const&) [359] ----------------------------------------------- [360] 0.0 0.00 0.32 std::vector >::begin() const [360] 0.29 0.03 960143/2099102434 std::_Deque_base >::_M_initialize_map(unsigned int) [242] ----------------------------------------------- [361] 0.0 0.00 0.32 void std::_Destroy<__gnu_cxx::__normal_iterator > >, Vote>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::allocator&) [361] 0.29 0.03 960143/2099102434 std::_Deque_base >::_M_initialize_map(unsigned int) [242] ----------------------------------------------- [362] 0.0 0.06 0.26 std::vector, std::allocator > >::operator[](unsigned int) [362] 0.06 0.20 19791088/196537847 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] ----------------------------------------------- [363] 0.0 0.04 0.27 std::allocator >::allocator() [363] 0.21 0.02 37707828/304749023 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree_impl::_M_initialize() [218] 0.04 0.00 37707828/518771239 std::_Rb_tree, std::less, std::allocator >::_M_put_node(std::_Rb_tree_node*) [311] ----------------------------------------------- 11504238 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [145] [364] 0.0 0.31 0.00 11504238 Vote* std::uninitialized_copy(Vote*, Vote*, Vote*) [364] 26260 std::_Deque_iterator::_M_set_node(SeededRead**) [729] ----------------------------------------------- 0.31 0.00 3532923/3532923 Contig::Contig(Contig const&) [214] [365] 0.0 0.31 0.00 3532923 Contig* std::__uninitialized_move_a >(Contig*, Contig*, Contig*, std::allocator&) [365] ----------------------------------------------- 88 ShortyString::ReverseComplement() const [763] 0.00 0.00 1/2099102434 std::vector >::~vector() [661] 0.00 0.00 2/2099102434 std::vector >::~vector() [645] 0.37 0.04 1242520/2099102434 __static_initialization_and_destruction_0(int, int) [211] 0.37 0.04 1242520/2099102434 global constructors keyed to _ZN7RawReadC2Eiiiii [341] [366] 0.0 0.31 0.00 2485131 ShortyString::ShortyString(std::string const&, int) [366] 1242502 ShortyString::GetConfidentClone() const [332] 22 ShortyString::reverse() [769] 2 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [405] ----------------------------------------------- 2 int* std::__copy_move_a(int*, int*, int*) [809] 4 TrieNode::TrieNode() [773] 6 SeededRead** std::__copy_move_backward_a(SeededRead**, SeededRead**, SeededRead**) [776] 14 mar_types* std::__copy_move_a2(mar_types*, mar_types*, mar_types*) [771] 28 SeededRead** std::__copy_move_a(SeededRead**, SeededRead**, SeededRead**) [765] 0.00 0.00 2/2099102434 SeededRead** std::__copy_move_backward::__copy_move_b(SeededRead* const*, SeededRead* const*, SeededRead**) [641] 0.29 0.03 960142/2099102434 mar_types* std::copy(mar_types*, mar_types*, mar_types*) [256] [367] 0.0 0.31 0.00 960198 TrieNode::searchWithErrorAllowed(std::string const&, int, int) [367] 960145 TrieNode::addToTrie(myList*, int) [330] ----------------------------------------------- 13130 std::_Vector_base, std::allocator > >::_Vector_impl::_Vector_impl() [308] [368] 0.0 0.31 0.00 13130 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [368] 0.00 0.00 13130/13130 readPointer* std::__copy_move_backward::__copy_move_b(readPointer*, readPointer*, readPointer*) [745] 13130 Contig::Contig(bool, int, int, ShortyString const&, int, ReadProcessor const*) [734] ----------------------------------------------- [369] 0.0 0.30 0.00 __gnu_cxx::new_allocator >::~new_allocator() [369] ----------------------------------------------- 0.01 0.01 177068/38781760 ReadProcessor::ReadProcessor(std::string const&) [358] 0.04 0.02 9651173/38781760 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree_impl::_Rb_tree_impl() [139] 0.04 0.02 9651173/38781760 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_S_right(std::_Rb_tree_node_base*) [458] 0.11 0.06 19302346/38781760 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_create_node(std::pair const&) [384] [370] 0.0 0.20 0.10 38781760 std::_Rb_tree, std::less, std::allocator >::_M_create_node(int const&) [370] 0.10 0.00 75448568/518771239 std::_Rb_tree, std::less, std::allocator >::_M_put_node(std::_Rb_tree_node*) [311] ----------------------------------------------- [371] 0.0 0.00 0.29 std::_Vector_base >::_Vector_impl::~_Vector_impl() [371] 0.26 0.03 857934/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] ----------------------------------------------- [372] 0.0 0.21 0.07 std::pair* std::copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [372] 0.07 0.00 37707828/58525952 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_put_node(std::_Rb_tree_node >*) [429] ----------------------------------------------- [373] 0.0 0.28 0.00 std::vector >::max_size() const [373] ----------------------------------------------- [374] 0.0 0.00 0.28 std::_Rb_tree_const_iterator::operator++() [374] 0.12 0.01 412850/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 0.12 0.01 412850/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] ----------------------------------------------- [375] 0.0 0.11 0.16 std::vector, std::allocator > >::vector() [375] 0.07 0.09 25559691/3222388240 std::deque >::deque(std::deque > const&) [31] ----------------------------------------------- [376] 0.0 0.02 0.25 std::vector, std::allocator > >::max_size() const [376] 0.06 0.19 19302346/196537847 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] ----------------------------------------------- [377] 0.0 0.19 0.08 std::less::operator()(int const&, int const&) const [377] 0.08 0.00 77584808/529397792 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator--() [316] ----------------------------------------------- 0.00 0.00 446402/6612552 __gnu_cxx::new_allocator >::destroy(triple*) [584] 0.00 0.00 446402/6612552 void std::partial_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [135] 0.00 0.00 648620/6612552 triple* std::copy_backward*, triple*>(triple*, triple*, triple*) [498] 0.02 0.00 2623439/6612552 mar_types* std::vector >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator > > >(unsigned int, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [152] 0.23 0.00 2447689/6612552 __gnu_cxx::__normal_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [346] [378] 0.0 0.25 0.00 6612552 int* std::__uninitialized_copy_a<__gnu_cxx::__normal_iterator > >, int*, int>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int*, std::allocator&) [378] ----------------------------------------------- [379] 0.0 0.24 0.00 std::_Vector_base >::_M_get_Tp_allocator() [379] ----------------------------------------------- [380] 0.0 0.00 0.24 triple const& std::__median, OverlapGraph::SortAdj>(triple const&, triple const&, triple const&, OverlapGraph::SortAdj) [380] 0.11 0.12 44790/44790 Contig* std::__uninitialized_copy_a(Contig*, Contig*, Contig*, std::allocator&) [383] 0.00 0.01 22395/22395 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [542] 0.00 0.00 22395/1397173708 std::vector >::push_back(int const&) [32] ----------------------------------------------- [381] 0.0 0.04 0.19 std::_List_iterator >::operator*() const [381] 0.19 0.00 155249516/317564878 std::list, std::allocator > >::_M_check_equal_allocators(std::list, std::allocator > >&) [188] ----------------------------------------------- 15620066 Contig::Contig(Contig const&) [214] [382] 0.0 0.23 0.00 15620066 std::_Vector_base >::_M_allocate(unsigned int) [382] 15620066 void std::__adjust_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [121] ----------------------------------------------- 0.11 0.12 44790/44790 triple const& std::__median, OverlapGraph::SortAdj>(triple const&, triple const&, triple const&, OverlapGraph::SortAdj) [380] [383] 0.0 0.11 0.12 44790 Contig* std::__uninitialized_copy_a(Contig*, Contig*, Contig*, std::allocator&) [383] 0.12 0.00 96233780/97678121 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [415] 0.00 0.00 44790/1965076 SeededRead** std::copy(SeededRead**, SeededRead**, SeededRead**) [690] ----------------------------------------------- 0.02 0.06 659481/19961827 std::vector >::operator=(std::vector > const&) [283] 0.04 0.11 19302346/19961827 std::_Rb_tree, std::less, std::allocator >::_M_destroy_node(std::_Rb_tree_node*) [184] [384] 0.0 0.06 0.17 19961827 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_create_node(std::pair const&) [384] 0.11 0.06 19302346/38781760 std::_Rb_tree, std::less, std::allocator >::_M_create_node(int const&) [370] ----------------------------------------------- 114424 std::vector >::operator=(std::vector > const&) [88] 0.00 0.00 8/2099102434 Vote* std::__uninitialized_copy::uninitialized_copy<__gnu_cxx::__normal_iterator > >, Vote*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, Vote*) [612] 0.00 0.00 10/2099102434 Assembler::Assemble() [474] 0.00 0.00 5786/2099102434 Assembler::MakeCluster(bool, std::vector, std::allocator > > const&, Cluster*, Cluster*, Contig*, Contig*) [27] 0.01 0.00 39509/2099102434 main [78] 0.02 0.00 67208/2099102434 Assembler::ProcessNewSeeds() [38] 0.03 0.00 84568/2099102434 Assembler::MakeContigs(bool, Cluster const&, SeededRead const&) [21] [385] 0.0 0.15 0.07 311513 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] 0.00 0.04 65769/65769 void std::_Destroy*, triple >(triple*, triple*, std::allocator >&) [471] 0.00 0.02 189458/2132137 std::_Vector_base >::~_Vector_base() [473] 0.01 0.00 13130/1397173708 std::vector >::push_back(int const&) [32] 0.00 0.00 88164/88164 __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >::base() const [715] 0.00 0.00 13137/13137 std::_Vector_base >::_M_deallocate(mar_types*, unsigned int) [741] 0.00 0.00 13129/13129 __gnu_cxx::__normal_iterator > >::__normal_iterator(Vote const* const&) [748] 0.00 0.00 13129/13129 void std::_Destroy(Vote*, Vote*) [751] 0.00 0.00 2/2 __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >::__normal_iterator(std::pair const* const&) [797] 0.00 0.00 2/2 mar_types* std::__uninitialized_move_a >(mar_types*, mar_types*, mar_types*, std::allocator&) [810] 0.00 0.00 2/2 std::vector >::_M_check_len(unsigned int, char const*) const [799] 65650 __gnu_cxx::__normal_iterator > > std::__copy_move_a2 > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [712] 13128 std::deque >::push_back(SeededRead const&) [549] 2 std::_Vector_base, std::allocator > >::~_Vector_base() [732] ----------------------------------------------- 0.00 0.22 648620/648620 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [337] [386] 0.0 0.00 0.22 648620 std::vector >::begin() const [386] 0.19 0.02 648620/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] ----------------------------------------------- 0.00 0.00 1/13130 Hash::Hash(int) [504] 0.02 0.07 5786/13130 ShortyString::Str() const [440] 0.03 0.09 7343/13130 Cluster::AddIndex(int, int, mar_types) [421] [387] 0.0 0.05 0.17 13130 std::vector >::push_back(mar_types const&) [387] 0.08 0.09 9331851/101771331 std::vector, std::allocator > >::push_back(std::pair const&) [223] 0.00 0.00 13130/1397173708 std::vector >::push_back(int const&) [32] ----------------------------------------------- 0.00 0.00 499/66875224 bool std::operator!=, std::allocator >(std::basic_string, std::allocator > const&, std::basic_string, std::allocator > const&) [597] 0.13 0.08 66874725/66875224 std::vector >::swap(std::vector >&) [87] [388] 0.0 0.13 0.08 66875224 UtilsString::OverlapFromCommonReadMapping(ShortyString const&, ShortyString const&, std::vector, std::allocator > > const&, std::vector, std::allocator > > const&, ReadProcessor const*, int*, int*, ShortyString*) [388] 0.08 0.00 66875224/271331188 __static_initialization_and_destruction_0(int, int) [252] ----------------------------------------------- 0.21 0.00 1056643/1056643 __gnu_cxx::new_allocator::construct(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo const&) [264] [389] 0.0 0.21 0.00 1056643 std::vector, std::allocator > >::operator=(std::vector, std::allocator > > const&) [389] 0.00 0.00 1056643/271331188 __static_initialization_and_destruction_0(int, int) [252] ----------------------------------------------- 0.00 0.21 648620/648620 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [337] [390] 0.0 0.00 0.21 648620 Contig* std::__copy_move_backward_a2(Contig*, Contig*, Contig*) [390] 0.19 0.02 619831/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] ----------------------------------------------- 0.20 0.00 92439480/92439480 std::back_insert_iterator > > std::__copy_move_a2 > >, std::back_insert_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::back_insert_iterator > >) [95] [391] 0.0 0.20 0.00 92439480 global constructors keyed to _ZN12ShortyStringC2Ev [391] ----------------------------------------------- [392] 0.0 0.05 0.15 std::vector >::vector() [392] 0.13 0.02 55809948/2323744019 std::_Deque_base >::~_Deque_base() [80] ----------------------------------------------- [393] 0.0 0.00 0.19 std::pair* std::uninitialized_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*>(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*) [393] 0.15 0.04 44790/44790 mar_types* std::__copy_move_a2 > >, mar_types*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*) [394] 0.00 0.00 44790/116345246 std::deque >::~deque() [134] ----------------------------------------------- 0.15 0.04 44790/44790 std::pair* std::uninitialized_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*>(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*) [393] [394] 0.0 0.15 0.04 44790 mar_types* std::__copy_move_a2 > >, mar_types*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*) [394] 0.03 0.00 16982099/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [240] 0.01 0.00 44790/2099102434 ReadProcessor::ReadProcessor(std::string const&) [59] ----------------------------------------------- [395] 0.0 0.12 0.06 std::stack > >::stack(std::deque > const&) [395] 0.06 0.00 25559691/275580450 std::deque >::begin() [299] ----------------------------------------------- 0.18 0.00 55809948/55809948 std::vector >::~vector() [281] [396] 0.0 0.18 0.00 55809948 std::_Vector_base, std::allocator > >::_Vector_impl::~_Vector_impl() [396] ----------------------------------------------- 0.01 0.17 960142/960142 std::_Vector_base >::~_Vector_base() [398] [397] 0.0 0.01 0.17 960142 std::deque >::_M_destroy_data_aux(std::_Deque_iterator, std::_Deque_iterator) [397] 0.14 0.02 480071/2099102434 std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [151] 0.01 0.00 480071/960142 std::deque >::begin() const [434] 0.00 0.00 1920284/2902821 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [685] 0.00 0.00 960142/1920284 std::_Deque_base >::_M_destroy_nodes(SeededRead**, SeededRead**) [693] ----------------------------------------------- [398] 0.0 0.00 0.18 std::_Vector_base >::~_Vector_base() [398] 0.01 0.17 960142/960142 std::deque >::_M_destroy_data_aux(std::_Deque_iterator, std::_Deque_iterator) [397] 0.00 0.00 480071/502466 std::_Deque_base >::_M_get_Tp_allocator() const [702] ----------------------------------------------- [399] 0.0 0.17 0.00 __gnu_cxx::__normal_iterator > >::difference_type __gnu_cxx::operator- > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [399] ----------------------------------------------- [400] 0.0 0.17 0.00 __gnu_cxx::__enable_if::__value, void>::__type std::__fill_a(int*, int*, int const&) [400] ----------------------------------------------- [401] 0.0 0.03 0.14 std::vector >::operator[](unsigned int) const [401] 0.14 0.00 55809948/275580450 std::deque >::begin() [299] ----------------------------------------------- [402] 0.0 0.00 0.16 Vote* std::__uninitialized_copy_a<__gnu_cxx::__normal_iterator > >, Vote*, Vote>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, Vote*, std::allocator&) [402] 0.14 0.02 480071/2099102434 Vote* std::copy(Vote*, Vote*, Vote*) [257] ----------------------------------------------- [403] 0.0 0.16 0.00 void std::_Destroy_aux::__destroy >(std::_Deque_iterator, std::_Deque_iterator) [403] ----------------------------------------------- 22989953 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [145] 0.00 0.00 7737/2099102434 std::_Vector_base >::_Vector_impl::_Vector_impl() [575] [404] 0.0 0.15 0.00 22997690 std::_Vector_base >::_Vector_impl::_Vector_impl(std::allocator const&) [404] 7737 std::_Deque_base >::_M_deallocate_node(SeededRead*) [756] 7737 std::_Deque_iterator::_M_set_node(SeededRead**) [729] ----------------------------------------------- 2 ShortyString::ShortyString(std::string const&, int) [366] 1192 std::_Deque_iterator::difference_type std::operator-(std::_Deque_iterator const&, std::_Deque_iterator const&) [760] 44790 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, std::string const&) [706] 5760858 TrieNode::traceTrie() [317] 0.00 0.00 4/2099102434 std::pair* std::__copy_move_backward_a*, std::pair*>(std::pair*, std::pair*, std::pair*) [627] [405] 0.0 0.15 0.00 5806846 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [405] 600 Contig::~Contig() [53] 600 TrieNode::searchWithError(std::string const&, int) [691] 10 TrieNode::destructNode() [730] ----------------------------------------------- 1920286 std::_Deque_base >::_M_initialize_map(unsigned int) [242] 0.58 0.07 1920286/2099102434 Vote* std::vector >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator > > >(unsigned int, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [243] [406] 0.0 0.15 0.00 3840572 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_destroy_node(std::_Rb_tree_node >*) [406] 596 std::_Deque_iterator::difference_type std::operator-(std::_Deque_iterator const&, std::_Deque_iterator const&) [760] ----------------------------------------------- 0.15 0.00 3339671/3339671 ShortyString::operator+=(ShortyString const&) [334] [407] 0.0 0.15 0.00 3339671 ShortyString::operator=(std::string const&) [407] ----------------------------------------------- 39390 Contig::PrintContigFormat(std::basic_fstream >*) const [408] 26260 Contig::Contig(bool, int, int, ShortyString const&, int, ReadProcessor const*) [734] 0.00 0.00 13130/2099102434 Contig::Contig(bool, int, int, ShortyString const&, int, ReadProcessor const*) [500] 0.00 0.00 13130/2099102434 Contig::AddRead(int, int, int, mar_types) [564] 0.02 0.00 78780/2099102434 Contig::Contig(bool, int, int, ShortyString const&, ReadProcessor const*) [463] [408] 0.0 0.00 0.15 131300+39390 Contig::PrintContigFormat(std::basic_fstream >*) const [408] 0.00 0.15 65650/65650 Contig::PrintGeoFormat(std::basic_fstream >*) const [409] 0.00 0.00 52520/91910 std::vector >::_M_check_len(unsigned int, char const*) const [713] 0.00 0.00 26260/26260 Contig::PrintFastaFormat(std::basic_fstream >*) const [737] 0.00 0.00 13130/26260 readPointer* std::__uninitialized_copy::uninitialized_copy(readPointer*, readPointer*, readPointer*) [738] 13130 std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [151] 39390 Contig::PrintContigFormat(std::basic_fstream >*) const [408] ----------------------------------------------- 26260 Contig::PrintGeoFormat(std::basic_fstream >*) const [409] 0.00 0.15 65650/65650 Contig::PrintContigFormat(std::basic_fstream >*) const [408] [409] 0.0 0.00 0.15 65650+26260 Contig::PrintGeoFormat(std::basic_fstream >*) const [409] 0.15 0.00 13130/13130 Contig::IsGoodSeed(std::basic_fstream >*, Contig const&) const [412] 0.00 0.00 26260/26260 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [736] 26260 Contig::PrintGeoFormat(std::basic_fstream >*) const [409] ----------------------------------------------- 9146 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, RawRead const&) [235] 0.00 0.00 13249/2099102434 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::__unguarded_partition<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj) [537] [410] 0.0 0.15 0.00 22395 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator+(int const&) const [410] 2001287 __gnu_cxx::__normal_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [346] ----------------------------------------------- 2 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [795] 2 Vote* std::__copy_move_a(Vote const*, Vote const*, Vote*) [789] 13134 Vote* std::__copy_move_a(Vote*, Vote*, Vote*) [742] 0.00 0.00 2/2099102434 std::__niter_base::__b(Vote*) [640] [411] 0.0 0.15 0.00 13140 mar_types* std::__copy_move_backward::__copy_move_b(mar_types const*, mar_types const*, mar_types*) [411] 2 mar_types* std::__copy_move::__copy_m(mar_types const*, mar_types const*, mar_types*) [717] ----------------------------------------------- 0.15 0.00 13130/13130 Contig::PrintGeoFormat(std::basic_fstream >*) const [409] [412] 0.0 0.15 0.00 13130 Contig::IsGoodSeed(std::basic_fstream >*, Contig const&) const [412] ----------------------------------------------- 0.09 0.06 10409062/10409062 std::_Vector_base, std::allocator > >::_M_deallocate(std::pair*, unsigned int) [321] [413] 0.0 0.09 0.06 10409062 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::get_allocator() const [413] 0.06 0.00 10409062/304749023 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree_impl::_M_initialize() [218] ----------------------------------------------- [414] 0.0 0.12 0.03 void std::_Destroy<__gnu_cxx::__normal_iterator > >, int>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::allocator&) [414] 0.03 0.00 16201587/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [240] ----------------------------------------------- 0.00 0.00 1/97678121 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [667] 0.01 0.00 307868/97678121 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [92] 0.02 0.00 1136472/97678121 std::vector, std::allocator > >::begin() [485] 0.12 0.00 96233780/97678121 Contig* std::__uninitialized_copy_a(Contig*, Contig*, Contig*, std::allocator&) [383] [415] 0.0 0.15 0.00 97678121 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [415] 0.00 0.00 131539/3971005539 SeededRead** std::__copy_move_backward_a2(SeededRead**, SeededRead**, SeededRead**) [72] ----------------------------------------------- [416] 0.0 0.14 0.00 __gnu_cxx::__normal_iterator > >::operator*() const [416] ----------------------------------------------- [417] 0.0 0.14 0.00 ShortyString::Votes(std::vector > const&) [417] ----------------------------------------------- [418] 0.0 0.14 0.00 OverlapGraph::ContigInfo::size() const [418] ----------------------------------------------- [419] 0.0 0.02 0.12 void std::_Destroy_aux::__destroy<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [419] 0.12 0.00 77624758/155249516 std::_List_iterator >::operator++() [217] ----------------------------------------------- [420] 0.0 0.14 0.00 std::_Rb_tree, std::less, std::allocator >::_M_end() [420] ----------------------------------------------- [421] 0.0 0.00 0.13 Cluster::AddIndex(int, int, mar_types) [421] 0.03 0.09 7343/13130 std::vector >::push_back(mar_types const&) [387] 0.00 0.00 7343/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [145] 0.00 0.00 7343/2099102434 std::vector >::~vector() [208] ----------------------------------------------- [422] 0.0 0.03 0.09 GetFirstLine(std::basic_fstream >&, char*) [422] 0.05 0.04 11328880/116345246 std::deque >::~deque() [134] ----------------------------------------------- [423] 0.0 0.12 0.00 std::vector >::size() const [423] ----------------------------------------------- [424] 0.0 0.12 0.00 std::_Vector_base >::_Vector_base() [424] ----------------------------------------------- 0.00 0.12 176329/176329 bool __gnu_cxx::operator!= const*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > const&) [426] [425] 0.0 0.00 0.12 176329 __gnu_cxx::new_allocator >::construct(std::pair*, std::pair const&) [425] 0.05 0.01 176329/2099102434 std::_Deque_base >::_M_initialize_map(unsigned int) [242] 0.05 0.01 176329/2099102434 std::pair::pair(std::pair const&) [705] ----------------------------------------------- [426] 0.0 0.00 0.12 bool __gnu_cxx::operator!= const*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > const&) [426] 0.00 0.12 176329/176329 __gnu_cxx::new_allocator >::construct(std::pair*, std::pair const&) [425] ----------------------------------------------- 0.00 0.00 70208/280832 __gnu_cxx::new_allocator::deallocate(OverlapGraph::ContigInfo*, unsigned int) [585] 0.04 0.00 70208/280832 std::allocator::allocator() [470] 0.08 0.00 140416/280832 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Contig const&) [428] [427] 0.0 0.12 0.00 280832 std::pair* std::__uninitialized_copy_a<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*, std::pair >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*, std::allocator >&) [427] ----------------------------------------------- 70208 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] [428] 0.0 0.00 0.12 70208 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Contig const&) [428] 0.08 0.00 140416/280832 std::pair* std::__uninitialized_copy_a<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*, std::pair >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*, std::allocator >&) [427] 0.00 0.04 70208/70208 std::allocator::allocator() [470] 0.00 0.00 70208/70208 std::pair* std::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [590] 0.00 0.00 70208/70208 void std::_Destroy_aux::__destroy(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [719] 280832 void std::__introsort_loop<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj) [86] 140416 std::_Rb_tree, std::less, std::allocator >::_Rb_tree_impl, false>::_M_initialize() [710] 70208 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::__copy_move_a2 const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [720] 70208 Contig::operator=(Contig const&) [174] 70208 std::vector >::operator=(std::vector > const&) [60] ----------------------------------------------- 0.02 0.00 10409062/58525952 std::vector, std::allocator > >::begin() [487] 0.02 0.00 10409062/58525952 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [109] 0.07 0.00 37707828/58525952 std::pair* std::copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [372] [429] 0.0 0.12 0.00 58525952 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_put_node(std::_Rb_tree_node >*) [429] ----------------------------------------------- 0.02 0.09 77624758/77624758 Vote::operator+=(Vote const&) [267] [430] 0.0 0.02 0.09 77624758 void std::_Destroy<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::allocator >&) [430] 0.09 0.00 77624758/271331188 __static_initialization_and_destruction_0(int, int) [252] ----------------------------------------------- [431] 0.0 0.04 0.07 std::_Vector_base, std::allocator > >::_Vector_base() [431] 0.07 0.00 55809948/55809948 void std::_Destroy*>(std::pair*, std::pair*) [450] ----------------------------------------------- 0.11 0.00 29004034/29004034 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, UtilsMath::median_event_point const&) [22] [432] 0.0 0.11 0.00 29004034 __gnu_cxx::__normal_iterator > >::__normal_iterator(UtilsMath::median_event_point* const&) [432] ----------------------------------------------- 0.10 0.00 184878960/184878960 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [57] [433] 0.0 0.10 0.00 184878960 __gnu_cxx::new_allocator >::max_size() const [433] ----------------------------------------------- 0.01 0.00 480071/960142 std::deque >::_M_destroy_data_aux(std::_Deque_iterator, std::_Deque_iterator) [397] 0.09 0.00 480071/960142 std::_Deque_base >::~_Deque_base() [80] [434] 0.0 0.10 0.00 960142 std::deque >::begin() const [434] 0.00 0.00 502466/463889692 void std::_Destroy_aux::__destroy(Contig*, Contig*) [171] ----------------------------------------------- [435] 0.0 0.10 0.00 __gnu_cxx::new_allocator >::new_allocator() [435] ----------------------------------------------- [436] 0.0 0.10 0.00 OverlapGraph::ContigInfo* std::__uninitialized_copy_a(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, std::allocator&) [436] ----------------------------------------------- 0.05 0.05 648620/648620 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_S_key(std::_Rb_tree_node_base const*) [438] [437] 0.0 0.05 0.05 648620 std::_Vector_base >::_Vector_base(unsigned int, std::allocator const&) [437] 0.04 0.01 7261172/77934596 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair const&) [253] ----------------------------------------------- [438] 0.0 0.00 0.10 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_S_key(std::_Rb_tree_node_base const*) [438] 0.05 0.05 648620/648620 std::_Vector_base >::_Vector_base(unsigned int, std::allocator const&) [437] ----------------------------------------------- [439] 0.0 0.00 0.10 std::vector >::end() const [439] 0.09 0.01 288962/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] ----------------------------------------------- [440] 0.0 0.00 0.09 ShortyString::Str() const [440] 0.02 0.07 5786/13130 std::vector >::push_back(mar_types const&) [387] ----------------------------------------------- 0.00 0.02 2674989/12087143 std::set, std::allocator >::insert(int const&) [198] 0.01 0.06 9412154/12087143 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_unique(std::pair const&) [2] [441] 0.0 0.01 0.08 12087143 std::pair >, bool>::pair(std::_Rb_tree_const_iterator > const&, bool const&) [441] 0.06 0.02 12087143/77934596 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair const&) [253] ----------------------------------------------- [442] 0.0 0.05 0.04 std::allocator >::allocator() [442] 0.04 0.00 48116890/96407108 std::_Rb_tree, std::less, std::allocator >::get_allocator() const [447] ----------------------------------------------- [443] 0.0 0.09 0.00 std::vector >::size() const [443] ----------------------------------------------- [444] 0.0 0.00 0.08 std::__lg(int) [444] 0.08 0.00 2674989/1397173708 std::vector >::push_back(int const&) [32] ----------------------------------------------- [445] 0.0 0.02 0.06 __gnu_cxx::__normal_iterator > >::base() const [445] 0.06 0.00 35883263/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [240] ----------------------------------------------- 2674989 Contig::Contig(Contig const&) [214] [446] 0.0 0.08 0.00 2674989 std::vector >::begin() [446] 2674989 void std::__adjust_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [121] ----------------------------------------------- 0.00 0.00 70208/96407108 std::vector, std::allocator > >::end() const [213] 0.00 0.00 70208/96407108 std::pair* std::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [590] 0.04 0.00 48116890/96407108 std::allocator >::allocator() [442] 0.04 0.00 48149802/96407108 std::pair* std::vector, std::allocator > >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > >(unsigned int, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >) [89] [447] 0.0 0.08 0.00 96407108 std::_Rb_tree, std::less, std::allocator >::get_allocator() const [447] ----------------------------------------------- 0.00 0.00 2/722176 mar_types* std::copy_backward(mar_types*, mar_types*, mar_types*) [664] 0.00 0.00 2/722176 std::vector >::_M_check_len(unsigned int, char const*) const [615] 0.00 0.00 2/722176 __gnu_cxx::new_allocator::~new_allocator() [665] 0.00 0.00 2/722176 std::allocator > >::allocator() [666] 0.00 0.00 65769/722176 __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >::__normal_iterator(triple const* const&) [586] 0.04 0.00 568235/722176 std::_Vector_base >::~_Vector_base() [473] 0.04 0.00 88164/722176 void std::_Destroy*, triple >(triple*, triple*, std::allocator >&) [471] [448] 0.0 0.08 0.00 722176 Vote* std::__uninitialized_copy::uninitialized_copy(Vote*, Vote*, Vote*) [448] 0.00 0.00 656399/656399 void std::_Destroy_aux::__destroy(SeededRead*, SeededRead*) [701] 0.00 0.00 65769/65769 __gnu_cxx::new_allocator::max_size() const [721] ----------------------------------------------- [449] 0.0 0.07 0.00 std::set, std::allocator >::set() [449] ----------------------------------------------- 0.07 0.00 55809948/55809948 std::_Vector_base, std::allocator > >::_Vector_base() [431] [450] 0.0 0.07 0.00 55809948 void std::_Destroy*>(std::pair*, std::pair*) [450] ----------------------------------------------- [451] 0.0 0.07 0.00 std::_Vector_base, std::allocator > >::_Vector_base() [451] 0.00 0.00 2262139/2674989 std::vector, std::allocator > >::size() const [687] ----------------------------------------------- [452] 0.0 0.00 0.07 mar_types* std::__uninitialized_copy_a<__gnu_cxx::__normal_iterator > >, mar_types*, mar_types>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*, std::allocator&) [452] 0.06 0.01 207871/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [6] ----------------------------------------------- [453] 0.0 0.07 0.00 std::stack > >::pop() [453] ----------------------------------------------- 0.06 0.00 101771331/101771331 std::vector, std::allocator > >::push_back(std::pair const&) [223] [454] 0.0 0.06 0.00 101771331 std::_Vector_base >::_Vector_impl::~_Vector_impl() [454] ----------------------------------------------- 0.00 0.00 2674989/58246520 OverlapGraph::BuildGraph() [23] 0.06 0.00 55571531/58246520 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [57] [455] 0.0 0.06 0.00 58246520 std::vector >::push_back(Vote const&) [455] ----------------------------------------------- [456] 0.0 0.06 0.00 void std::swap(Vote*&, Vote*&) [456] ----------------------------------------------- [457] 0.0 0.00 0.06 triple::triple(int, int, int) [457] 0.00 0.06 13249/12451411 main [78] ----------------------------------------------- [458] 0.0 0.00 0.06 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_S_right(std::_Rb_tree_node_base*) [458] 0.04 0.02 9651173/38781760 std::_Rb_tree, std::less, std::allocator >::_M_create_node(int const&) [370] ----------------------------------------------- [459] 0.0 0.06 0.00 std::vector >::operator[](unsigned int) [459] ----------------------------------------------- [460] 0.0 0.05 0.00 myList::addToList(myList*) [460] ----------------------------------------------- [461] 0.0 0.05 0.00 std::vector >::size() const [461] ----------------------------------------------- [462] 0.0 0.02 0.03 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_erase(std::_Rb_tree_node >*) [462] 0.01 0.02 2262139/196537847 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] ----------------------------------------------- [463] 0.0 0.00 0.05 Contig::Contig(bool, int, int, ShortyString const&, ReadProcessor const*) [463] 0.02 0.00 78780/2099102434 Contig::PrintContigFormat(std::basic_fstream >*) const [408] 0.01 0.00 39390/2099102434 Vote* std::__copy_move_a2(Vote*, Vote*, Vote*) [714] 0.00 0.00 13130/2099102434 Contig::Contig(bool, int, int, ShortyString const&, int, ReadProcessor const*) [734] 0.00 0.00 13130/13130 Contig::AddRead(int, int, int, mar_types) [564] ----------------------------------------------- [464] 0.0 0.00 0.05 std::pair* std::__copy_move_a2*, std::pair*>(std::pair*, std::pair*, std::pair*) [464] 0.02 0.00 70208/2099102434 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [75] 0.02 0.00 70208/2099102434 void std::__adjust_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [121] ----------------------------------------------- [465] 0.0 0.00 0.05 void std::_Destroy<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [465] 0.02 0.00 70208/2099102434 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [75] 0.02 0.00 70208/2099102434 std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [151] ----------------------------------------------- [466] 0.0 0.04 0.00 std::_Identity::operator()(int const&) const [466] ----------------------------------------------- [467] 0.0 0.04 0.00 std::__niter_base*, false>::__b(std::pair*) [467] ----------------------------------------------- [468] 0.0 0.04 0.00 __gnu_cxx::new_allocator > >::deallocate(std::_Rb_tree_node >*, unsigned int) [468] ----------------------------------------------- [469] 0.0 0.04 0.00 std::map, std::allocator > >::map() [469] ----------------------------------------------- 0.00 0.04 70208/70208 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Contig const&) [428] [470] 0.0 0.00 0.04 70208 std::allocator::allocator() [470] 0.04 0.00 70208/280832 std::pair* std::__uninitialized_copy_a<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*, std::pair >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*, std::allocator >&) [427] ----------------------------------------------- 0.00 0.04 65769/65769 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] [471] 0.0 0.00 0.04 65769 void std::_Destroy*, triple >(triple*, triple*, std::allocator >&) [471] 0.04 0.00 88164/722176 Vote* std::__uninitialized_copy::uninitialized_copy(Vote*, Vote*, Vote*) [448] ----------------------------------------------- [472] 0.0 0.01 0.03 std::vector >::capacity() const [472] 0.03 0.00 16201587/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [240] ----------------------------------------------- 0.00 0.00 22395/2132137 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [542] 0.00 0.00 480071/2132137 std::_Vector_base >::_Vector_impl::~_Vector_impl() [581] 0.00 0.00 480071/2132137 void std::_Destroy(int*, int*, std::allocator&) [582] 0.00 0.01 960142/2132137 std::_Vector_base >::~_Vector_base() [547] 0.00 0.02 189458/2132137 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] [473] 0.0 0.00 0.04 2132137 std::_Vector_base >::~_Vector_base() [473] 0.04 0.00 568235/722176 Vote* std::__uninitialized_copy::uninitialized_copy(Vote*, Vote*, Vote*) [448] 0.00 0.00 88164/1528377 std::_Deque_base >::_Deque_base(std::allocator const&, unsigned int) [694] 0.00 0.00 88164/88164 std::_Vector_base, std::allocator > >::_M_get_Tp_allocator() [716] ----------------------------------------------- 0.00 0.02 1/2 std::_Vector_base >::_M_deallocate(SeededRead*, unsigned int) [506] 0.00 0.02 1/2 std::vector >::_M_check_len(unsigned int, char const*) const [505] [474] 0.0 0.00 0.03 2 Assembler::Assemble() [474] 0.00 0.03 2/28266 Assembler::MakeContigs(bool, Cluster const&, SeededRead const&) [21] 0.00 0.00 1/13130 Trie::Insert(std::string const&, int, mar_types) [175] 0.00 0.00 4/52520 SeededRead::~SeededRead() [251] 0.00 0.00 2/12451411 main [78] 0.00 0.00 10/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] 0.00 0.00 6/2099102434 std::vector >::operator=(std::vector > const&) [88] 0.00 0.00 1/2099102434 std::vector >::vector(std::vector > const&) [514] 0.00 0.00 1/2099102434 ReadSeededFastaFile(std::string const&, std::vector >*) [26] 0.00 0.00 3/52520 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [545] 0.00 0.00 1/13130 std::vector >::size() const [592] 0.00 0.00 1/5 void std::__push_heap<__gnu_cxx::__normal_iterator > >, int, UtilsMath::median_event_point>(__gnu_cxx::__normal_iterator > >, int, int, UtilsMath::median_event_point) [778] 0.00 0.00 1/176329 std::vector, std::allocator > >::end() const [708] 0.00 0.00 1/2 std::stack > >::push(SeededRead const&) [807] ----------------------------------------------- [475] 0.0 0.03 0.00 __gnu_cxx::new_allocator >::construct(triple*, triple const&) [475] 0.00 0.00 2447689/3096309 std::pair >, bool>::pair(std::_Rb_tree_iterator > const&, bool const&) [683] 0.00 0.00 2447689/2447689 std::_Vector_base, std::allocator > >::_M_allocate(unsigned int) [688] ----------------------------------------------- [476] 0.0 0.03 0.00 std::char_traits::compare(char const*, char const*, unsigned int) [476] ----------------------------------------------- [477] 0.0 0.03 0.00 void std::reverse<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [477] ----------------------------------------------- [478] 0.0 0.00 0.03 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_begin() [478] 0.01 0.02 2262139/196537847 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] ----------------------------------------------- [479] 0.0 0.00 0.03 void std::_Destroy*, triple >(triple*, triple*, std::allocator >&) [479] 0.03 0.00 87931/2099102434 void std::__introsort_loop<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj) [86] ----------------------------------------------- [480] 0.0 0.03 0.00 Cluster::GetMt(int) const [480] ----------------------------------------------- [481] 0.0 0.03 0.00 std::_Vector_base >::_M_get_Tp_allocator() const [481] ----------------------------------------------- [482] 0.0 0.00 0.02 std::allocator >::allocator() [482] 0.02 0.00 70208/2099102434 void std::__adjust_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [121] ----------------------------------------------- [483] 0.0 0.00 0.02 __gnu_cxx::new_allocator::new_allocator() [483] 0.02 0.00 65769/2099102434 mar_types* std::__copy_move::__copy_m(mar_types const*, mar_types const*, mar_types*) [717] ----------------------------------------------- 13153 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] 2 int* std::__copy_move_backward::__copy_move_b(int const*, int const*, int*) [805] 3 std::vector, std::allocator > >::~vector() [825] 8 std::vector, std::allocator > >::end() const [782] 0.00 0.00 1/2099102434 __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >::operator->() const [653] 0.00 0.00 2/2099102434 std::vector, std::allocator > >::begin() const [632] 0.00 0.00 2/2099102434 std::vector >::~vector() [629] 0.00 0.00 2/2099102434 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [631] 0.00 0.00 2/2099102434 mar_types* std::__copy_move_a(mar_types*, mar_types*, mar_types*) [633] 0.00 0.00 4/2099102434 bool __gnu_cxx::operator!= const*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > const&) [622] 0.00 0.00 4/2099102434 unsigned int const& std::max(unsigned int const&, unsigned int const&) [628] 0.00 0.00 8/2099102434 __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >::operator++() [614] 0.00 0.00 13129/2099102434 std::_Vector_base >::_M_allocate(unsigned int) [539] [484] 0.0 0.00 0.02 13167+13153 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] 0.00 0.02 1136472/1136472 std::vector, std::allocator > >::begin() [485] 0.00 0.00 1/1 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [667] 0.00 0.00 4/5 __gnu_cxx::new_allocator::destroy(SeededRead*) [777] 0.00 0.00 4/4 __gnu_cxx::new_allocator::construct(SeededRead*, SeededRead const&) [781] 0.00 0.00 2/2 std::vector >::max_size() const [798] 0.00 0.00 1/1 std::_Vector_base, std::allocator > >::_M_allocate(unsigned int) [822] 8 std::deque >::_M_push_back_aux(SeededRead const&) [770] 4 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [766] 2 std::_Deque_iterator::operator--() [804] 2 std::deque >::_M_pop_back_aux() [786] 2 __gnu_cxx::new_allocator::deallocate(int*, unsigned int) [796] 13153 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] ----------------------------------------------- 0.00 0.02 1136472/1136472 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] [485] 0.0 0.00 0.02 1136472 std::vector, std::allocator > >::begin() [485] 0.02 0.00 1136472/97678121 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [415] ----------------------------------------------- [486] 0.0 0.00 0.02 __gnu_cxx::__normal_iterator > > std::__copy_move_a2 > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [486] 0.01 0.00 49336/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [145] 0.00 0.00 12334/2099102434 std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [151] ----------------------------------------------- [487] 0.0 0.00 0.02 std::vector, std::allocator > >::begin() [487] 0.02 0.00 10409062/58525952 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_put_node(std::_Rb_tree_node >*) [429] ----------------------------------------------- [488] 0.0 0.02 0.00 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::__normal_iterator(std::pair* const&) [488] ----------------------------------------------- [489] 0.0 0.02 0.00 ShortyString::operator!=(std::string const&) const [489] ----------------------------------------------- [490] 0.0 0.02 0.00 void std::_Destroy_aux::__destroy*>(std::pair*, std::pair*) [490] ----------------------------------------------- [491] 0.0 0.02 0.00 std::__alloc_swap, true>::_S_do_it(std::allocator&, std::allocator&) [491] ----------------------------------------------- [492] 0.0 0.02 0.00 std::__niter_base<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, true>::__b(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [492] ----------------------------------------------- [493] 0.0 0.02 0.00 std::string* std::__uninitialized_copy::uninitialized_copy(std::string*, std::string*, std::string*) [493] ----------------------------------------------- [494] 0.0 0.02 0.00 std::deque >::deque() [494] ----------------------------------------------- [495] 0.0 0.02 0.00 std::vector, std::allocator > >::_M_erase_at_end(triple*) [495] ----------------------------------------------- [496] 0.0 0.02 0.00 std::vector >::vector() [496] ----------------------------------------------- [497] 0.0 0.01 0.01 void std::_Destroy*>(std::pair*, std::pair*) [497] 0.01 0.00 9828241/1755802966 std::vector, std::allocator > >::max_size() const [172] ----------------------------------------------- [498] 0.0 0.01 0.01 triple* std::copy_backward*, triple*>(triple*, triple*, triple*) [498] 0.00 0.00 648620/77934596 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair const&) [253] 0.00 0.00 648620/6612552 int* std::__uninitialized_copy_a<__gnu_cxx::__normal_iterator > >, int*, int>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int*, std::allocator&) [378] ----------------------------------------------- 0.00 0.02 2674989/2674989 std::vector, std::allocator > >::push_back(std::pair const&) [265] [499] 0.0 0.00 0.02 2674989 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::begin() const [499] 0.01 0.01 2674989/77934596 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair const&) [253] ----------------------------------------------- [500] 0.0 0.00 0.02 Contig::Contig(bool, int, int, ShortyString const&, int, ReadProcessor const*) [500] 0.01 0.00 26260/2099102434 Vote* std::__copy_move_a2(Vote*, Vote*, Vote*) [714] 0.00 0.00 13130/2099102434 Contig::PrintContigFormat(std::basic_fstream >*) const [408] 0.00 0.00 13130/2099102434 std::_Deque_base >::_M_create_nodes(SeededRead**, SeededRead**) [728] ----------------------------------------------- [501] 0.0 0.01 0.01 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [501] 0.01 0.00 21385/2099102434 std::vector >::operator=(std::vector > const&) [60] ----------------------------------------------- [502] 0.0 0.00 0.02 triple* std::__uninitialized_move_a*, triple*, std::allocator > >(triple*, triple*, triple*, std::allocator >&) [502] 0.01 0.00 2447689/77934596 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair const&) [253] ----------------------------------------------- [503] 0.0 0.00 0.02 std::vector >::vector(std::vector > const&) [503] 0.00 0.01 12334/13249 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::__unguarded_partition<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj) [537] 0.00 0.00 24668/24668 std::pair* std::__uninitialized_copy::uninitialized_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*>(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*) [576] 0.00 0.00 12334/24668 std::pair* std::__copy_move::__copy_m const*, std::pair*>(std::pair const*, std::pair const*, std::pair*) [540] 0.00 0.00 24668/64810 void std::_Destroy(int*, int*) [722] 0.00 0.00 24668/49336 __gnu_cxx::new_allocator > >::new_allocator() [725] ----------------------------------------------- [504] 0.0 0.00 0.02 Hash::Hash(int) [504] 0.00 0.02 2/2 std::vector >::_M_check_len(unsigned int, char const*) const [505] 0.00 0.00 1/7 Hash::Insert(std::string const&, int, int, int) [591] 0.00 0.00 1/13130 std::vector >::push_back(mar_types const&) [387] 0.00 0.00 1/2099102434 std::vector >::~vector() [208] 0.00 0.00 1/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] ----------------------------------------------- 0.00 0.02 2/2 Hash::Hash(int) [504] [505] 0.0 0.00 0.02 2 std::vector >::_M_check_len(unsigned int, char const*) const [505] 0.00 0.02 1/2 Assembler::Assemble() [474] 0.00 0.00 1/1 ShortyString::ShortyString() [650] ----------------------------------------------- [506] 0.0 0.00 0.02 std::_Vector_base >::_M_deallocate(SeededRead*, unsigned int) [506] 0.00 0.02 1/2 Assembler::Assemble() [474] ----------------------------------------------- [507] 0.0 0.00 0.01 void std::_Destroy_aux::__destroy<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [507] 0.01 0.00 44790/2099102434 ReadProcessor::ReadProcessor(std::string const&) [358] ----------------------------------------------- [508] 0.0 0.00 0.01 std::__niter_base<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, true>::__b(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [508] 0.01 0.00 44790/2099102434 ReadProcessor::ReadProcessor(std::string const&) [358] ----------------------------------------------- [509] 0.0 0.00 0.01 std::pair* std::__copy_move_a const*, std::pair*>(std::pair const*, std::pair const*, std::pair*) [509] 0.01 0.00 44790/2099102434 ReadProcessor::ReadProcessor(std::string const&) [358] ----------------------------------------------- [510] 0.0 0.00 0.01 void std::_Destroy(OverlapGraph::ContigInfo*) [510] 0.01 0.00 44790/2099102434 ReadProcessor::ReadProcessor(std::string const&) [358] ----------------------------------------------- [511] 0.0 0.01 0.00 std::vector, std::allocator > >::end() [511] 0.00 0.00 13130/2099102434 std::_Vector_base, std::allocator > >::_Vector_impl::_Vector_impl() [308] ----------------------------------------------- [512] 0.0 0.01 0.00 ShortyString::ShortyString(ShortyString const&) [512] 0.00 0.00 13129/2099102434 std::vector >::operator=(std::vector > const&) [88] ----------------------------------------------- [513] 0.0 0.00 0.01 std::vector, std::allocator > >::end() [513] 0.00 0.01 1083141/196537847 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] ----------------------------------------------- 13130 mar_types* std::__copy_move::__copy_m(mar_types const*, mar_types const*, mar_types*) [717] 0.00 0.00 1/2099102434 Assembler::Assemble() [474] 0.00 0.00 5786/2099102434 Assembler::MakeCluster(bool, std::vector, std::allocator > > const&, Cluster*, Cluster*, Contig*, Contig*) [27] 0.00 0.00 13130/2099102434 void std::_Destroy(SeededRead*, SeededRead*, std::allocator&) [572] 0.01 0.00 20472/2099102434 Assembler::ProcessNewSeeds() [38] [514] 0.0 0.00 0.01 52519 std::vector >::vector(std::vector > const&) [514] 0.01 0.00 26259/1397173708 std::vector >::push_back(int const&) [32] 0.00 0.00 123808/176329 std::vector, std::allocator > >::end() const [708] 88164 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [49] ----------------------------------------------- [515] 0.0 0.00 0.01 ReadProcessor::NumUsed(int) [515] 0.01 0.00 20853/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [145] 0.00 0.00 13129/2099102434 ReadSeededFastaFile(std::string const&, std::vector >*) [26] ----------------------------------------------- [516] 0.0 0.00 0.01 std::vector, std::allocator > >::operator[](unsigned int) const [516] 0.00 0.01 857934/196537847 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] ----------------------------------------------- [517] 0.0 0.00 0.01 OverlapGraph::ContigInfo::~ContigInfo() [517] 0.01 0.00 2674989/539451719 std::list, std::allocator > >::operator=(std::list, std::allocator > > const&) [210] ----------------------------------------------- 0.01 0.00 3546341/3546341 Assembler::MakeContigs(bool, Cluster const&, SeededRead const&) [21] [518] 0.0 0.01 0.00 3546341 std::pair::~pair() [518] ----------------------------------------------- 0.01 0.00 2416982/2416982 std::string* std::uninitialized_copy(std::string*, std::string*, std::string*) [536] [519] 0.0 0.01 0.00 2416982 operator>>(std::istream&, Vote&) [519] ----------------------------------------------- [520] 0.0 0.01 0.00 global constructors keyed to _ZN4Vote7MAX_VALE [520] ----------------------------------------------- [521] 0.0 0.01 0.00 global constructors keyed to _ZN8TrieNodeC2Ev [521] ----------------------------------------------- [522] 0.0 0.01 0.00 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [522] ----------------------------------------------- [523] 0.0 0.01 0.00 __gnu_cxx::__normal_iterator > >::base() const [523] ----------------------------------------------- [524] 0.0 0.01 0.00 std::_Identity >::operator()(std::pair const&) const [524] ----------------------------------------------- [525] 0.0 0.01 0.00 std::allocator >::~allocator() [525] ----------------------------------------------- [526] 0.0 0.01 0.00 std::allocator::allocator(std::allocator const&) [526] ----------------------------------------------- [527] 0.0 0.01 0.00 std::_Deque_base >::_M_get_Tp_allocator() [527] ----------------------------------------------- [528] 0.0 0.01 0.00 std::_Vector_base, std::allocator > >::_Vector_impl::_Vector_impl() [528] ----------------------------------------------- [529] 0.0 0.01 0.00 std::_Vector_base, std::allocator > >::_Vector_impl::~_Vector_impl() [529] ----------------------------------------------- [530] 0.0 0.01 0.00 std::__niter_base::__b(int*) [530] ----------------------------------------------- [531] 0.0 0.01 0.00 std::_Rb_tree_const_iterator::_Rb_tree_const_iterator(std::_Rb_tree_node const*) [531] ----------------------------------------------- [532] 0.0 0.01 0.00 std::vector >::insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [532] ----------------------------------------------- [533] 0.0 0.01 0.00 std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_S_key(std::_Rb_tree_node > const*) [533] ----------------------------------------------- [534] 0.0 0.01 0.00 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_erase(std::_Rb_tree_node >*) [534] ----------------------------------------------- [535] 0.0 0.01 0.00 std::_Rb_tree, std::less, std::allocator >::_S_right(std::_Rb_tree_node_base*) [535] ----------------------------------------------- [536] 0.0 0.00 0.01 std::string* std::uninitialized_copy(std::string*, std::string*, std::string*) [536] 0.01 0.00 2416982/2416982 operator>>(std::istream&, Vote&) [519] ----------------------------------------------- 0.00 0.00 915/13249 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] 0.00 0.01 12334/13249 std::vector >::vector(std::vector > const&) [503] [537] 0.0 0.00 0.01 13249 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::__unguarded_partition<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj) [537] 0.00 0.00 13249/2099102434 Contig::~Contig() [53] 0.00 0.00 13249/2099102434 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator+(int const&) const [410] ----------------------------------------------- 0.00 0.01 13130/13130 Assembler::MakeContigs(bool, Cluster const&, SeededRead const&) [21] [538] 0.0 0.00 0.01 13130 std::vector >::end() [538] 0.01 0.00 26260/2099102434 __gnu_cxx::__normal_iterator > > std::__copy_move_a2 > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [712] ----------------------------------------------- [539] 0.0 0.00 0.01 std::_Vector_base >::_M_allocate(unsigned int) [539] 0.00 0.00 13129/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] 0.00 0.00 13129/2099102434 std::_Deque_base >::_M_allocate_map(unsigned int) [731] 0.00 0.00 13129/13129 std::allocator::allocator() [749] ----------------------------------------------- 0.00 0.00 12334/24668 std::vector >::vector(std::vector > const&) [503] 0.00 0.00 12334/24668 std::vector >::vector(std::vector > const&) [548] [540] 0.0 0.00 0.01 24668 std::pair* std::__copy_move::__copy_m const*, std::pair*>(std::pair const*, std::pair const*, std::pair*) [540] 0.01 0.00 24668/2099102434 ReadProcessor::ReadProcessor(std::string const&) [358] ----------------------------------------------- [541] 0.0 0.00 0.01 std::allocator::~allocator() [541] 0.00 0.00 960143/116345246 std::deque >::~deque() [134] ----------------------------------------------- 0.00 0.01 22395/22395 triple const& std::__median, OverlapGraph::SortAdj>(triple const&, triple const&, triple const&, OverlapGraph::SortAdj) [380] [542] 0.0 0.00 0.01 22395 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [542] 0.01 0.00 22395/2099102434 ReadProcessor::ReadProcessor(std::string const&) [358] 0.00 0.00 22395/2132137 std::_Vector_base >::~_Vector_base() [473] 0.00 0.00 22395/982537 int* std::copy(int*, int*, int*) [698] 0.00 0.00 22395/2902821 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [685] ----------------------------------------------- [543] 0.0 0.00 0.01 std::allocator::allocator >(std::allocator > const&) [543] 0.01 0.00 22395/2099102434 ReadProcessor::ReadProcessor(std::string const&) [358] ----------------------------------------------- [544] 0.0 0.00 0.01 bool __gnu_cxx::operator!=*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [544] 0.01 0.00 21385/2099102434 __gnu_cxx::new_allocator::construct(Contig*, Contig const&) [268] 0.00 0.00 21385/196537847 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] ----------------------------------------------- 0.00 0.00 3/52520 Assembler::Assemble() [474] 0.00 0.00 13129/52520 Assembler::ProcessNewSeeds() [38] 0.00 0.00 13129/52520 __static_initialization_and_destruction_0(int, int) [593] 0.00 0.00 13130/52520 main [78] 0.00 0.01 13129/52520 ReadSeededFastaFile(std::string const&, std::vector >*) [26] [545] 0.0 0.00 0.01 52520 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [545] 0.01 0.00 52520/1397173708 std::vector >::push_back(int const&) [32] ----------------------------------------------- [546] 0.0 0.00 0.01 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::__normal_iterator(triple* const&) [546] 0.01 0.00 21385/2099102434 std::vector >::operator=(std::vector > const&) [283] ----------------------------------------------- [547] 0.0 0.00 0.01 std::_Vector_base >::~_Vector_base() [547] 0.00 0.01 960142/2132137 std::_Vector_base >::~_Vector_base() [473] 0.00 0.00 960142/1528377 std::_Deque_base >::_Deque_base(std::allocator const&, unsigned int) [694] 0.00 0.00 480071/1920284 std::_Deque_base >::_M_destroy_nodes(SeededRead**, SeededRead**) [693] ----------------------------------------------- [548] 0.0 0.00 0.01 std::vector >::vector(std::vector > const&) [548] 0.00 0.00 12334/24668 std::pair* std::__copy_move::__copy_m const*, std::pair*>(std::pair const*, std::pair const*, std::pair*) [540] 0.00 0.00 12334/20071 std::_Deque_base >::_M_get_map_allocator() const [577] 0.00 0.00 24668/64810 void std::_Destroy(int*, int*) [722] ----------------------------------------------- 13128 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] 0.00 0.00 2/2099102434 __gnu_cxx::__normal_iterator > >::__normal_iterator(int* const&) [636] 0.00 0.00 13130/2099102434 int* std::copy_backward(int*, int*, int*) [570] [549] 0.0 0.00 0.01 26260 std::deque >::push_back(SeededRead const&) [549] 0.01 0.00 13130/1397173708 std::vector >::push_back(int const&) [32] 13130 Contig::~Contig() [53] ----------------------------------------------- [550] 0.0 0.00 0.01 std::_Vector_base >::_M_allocate(unsigned int) [550] 0.00 0.01 39950/636508560 void std::__heap_select<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [61] ----------------------------------------------- [551] 0.0 0.00 0.01 OverlapGraph::ContigInfo::operator=(OverlapGraph::ContigInfo const&) [551] 0.00 0.00 13249/2099102434 void std::__introsort_loop<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj) [86] 0.00 0.00 26498/1397173708 std::vector >::push_back(int const&) [32] ----------------------------------------------- 0.01 0.00 480071/480071 std::_Vector_base >::_Vector_base(unsigned int, std::allocator const&) [557] [552] 0.0 0.01 0.00 480071 std::_Deque_base >::_M_deallocate_map(SeededRead**, unsigned int) [552] 0.00 0.00 960142/2902821 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [685] ----------------------------------------------- [553] 0.0 0.01 0.00 __gnu_cxx::new_allocator >::~new_allocator() [553] ----------------------------------------------- [554] 0.0 0.01 0.00 __gnu_cxx::__normal_iterator > >::__normal_iterator(readPointer* const&) [554] ----------------------------------------------- [555] 0.0 0.01 0.00 __gnu_cxx::new_allocator::max_size() const [555] ----------------------------------------------- [556] 0.0 0.01 0.00 void std::_Destroy_aux::__destroy*>(triple*, triple*) [556] ----------------------------------------------- [557] 0.0 0.00 0.01 std::_Vector_base >::_Vector_base(unsigned int, std::allocator const&) [557] 0.01 0.00 480071/480071 std::_Deque_base >::_M_deallocate_map(SeededRead**, unsigned int) [552] ----------------------------------------------- [558] 0.0 0.00 0.00 void std::swap(OverlapGraph::ContigInfo*&, OverlapGraph::ContigInfo*&) [558] 0.00 0.00 13249/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] 0.00 0.00 13249/1397173708 std::vector >::push_back(int const&) [32] ----------------------------------------------- [559] 0.0 0.00 0.00 std::_Rb_tree_const_iterator >::operator!=(std::_Rb_tree_const_iterator > const&) const [559] 0.00 0.00 13249/2099102434 std::vector >::operator=(std::vector > const&) [88] ----------------------------------------------- [560] 0.0 0.00 0.00 std::_Rb_tree_const_iterator >::operator++() [560] 0.00 0.00 13249/2099102434 std::vector >::operator=(std::vector > const&) [88] ----------------------------------------------- [561] 0.0 0.00 0.00 void std::_Destroy*, std::pair >(std::pair*, std::pair*, std::allocator >&) [561] 0.00 0.00 13249/2099102434 void std::__introsort_loop<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj) [86] ----------------------------------------------- [562] 0.0 0.00 0.00 __gnu_cxx::new_allocator::destroy(Contig*) [562] 0.00 0.00 3532923/317564878 std::list, std::allocator > >::_M_check_equal_allocators(std::list, std::allocator > >&) [188] ----------------------------------------------- 0.00 0.00 13130/13130 Assembler::MakeContigs(bool, Cluster const&, SeededRead const&) [21] [563] 0.0 0.00 0.00 13130 ShortyString::ShortyString(std::string const&, std::vector > const&) [563] 0.00 0.00 13130/2099102434 ShortyString::ShortyString(std::string const&) [743] 0.00 0.00 13130/13130 std::vector >::_M_erase_at_end(readPointer*) [746] ----------------------------------------------- 0.00 0.00 13130/13130 Contig::Contig(bool, int, int, ShortyString const&, ReadProcessor const*) [463] [564] 0.0 0.00 0.00 13130 Contig::AddRead(int, int, int, mar_types) [564] 0.00 0.00 13130/2099102434 Contig::PrintContigFormat(std::basic_fstream >*) const [408] ----------------------------------------------- [565] 0.0 0.00 0.00 std::_Vector_base >::_M_get_Tp_allocator() [565] 0.00 0.00 13130/2099102434 std::_Vector_base, std::allocator > >::~_Vector_base() [732] ----------------------------------------------- [566] 0.0 0.00 0.00 std::_Vector_base, std::allocator > >::_Vector_base() [566] 0.00 0.00 13130/2099102434 std::vector, std::allocator > >::_M_fill_insert(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, unsigned int, triple const&) [50] ----------------------------------------------- [567] 0.0 0.00 0.00 mar_types* std::__uninitialized_copy::uninitialized_copy(mar_types*, mar_types*, mar_types*) [567] 0.00 0.00 13130/2099102434 mar_types* std::__copy_move::__copy_m(mar_types const*, mar_types const*, mar_types*) [717] ----------------------------------------------- [568] 0.0 0.00 0.00 std::deque >::_S_buffer_size() [568] 0.00 0.00 13130/2099102434 Contig::~Contig() [53] ----------------------------------------------- [569] 0.0 0.00 0.00 std::vector, std::allocator > >::insert(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, unsigned int, triple const&) [569] 0.00 0.00 13130/2099102434 std::vector, std::allocator > >::_M_fill_insert(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, unsigned int, triple const&) [50] ----------------------------------------------- [570] 0.0 0.00 0.00 int* std::copy_backward(int*, int*, int*) [570] 0.00 0.00 13130/2099102434 std::deque >::push_back(SeededRead const&) [549] ----------------------------------------------- [571] 0.0 0.00 0.00 void std::_Destroy<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [571] 0.00 0.00 13130/2099102434 std::_Deque_base >::_M_create_nodes(SeededRead**, SeededRead**) [728] ----------------------------------------------- [572] 0.0 0.00 0.00 void std::_Destroy(SeededRead*, SeededRead*, std::allocator&) [572] 0.00 0.00 13130/2099102434 std::vector >::vector(std::vector > const&) [514] ----------------------------------------------- [573] 0.0 0.00 0.00 void std::_Destroy(Contig*, Contig*, std::allocator&) [573] 0.00 0.00 13130/2099102434 std::_Vector_base, std::allocator > >::~_Vector_base() [732] ----------------------------------------------- [574] 0.0 0.00 0.00 __gnu_cxx::__normal_iterator > >::__normal_iterator(Vote* const&) [574] 0.00 0.00 12533/2099102434 std::_Deque_base >::_M_allocate_map(unsigned int) [731] ----------------------------------------------- [575] 0.0 0.00 0.00 std::_Vector_base >::_Vector_impl::_Vector_impl() [575] 0.00 0.00 7737/2099102434 std::_Vector_base >::_Vector_impl::_Vector_impl(std::allocator const&) [404] 0.00 0.00 7737/20071 std::_Deque_base >::_M_get_map_allocator() const [577] ----------------------------------------------- 0.00 0.00 24668/24668 std::vector >::vector(std::vector > const&) [503] [576] 0.0 0.00 0.00 24668 std::pair* std::__uninitialized_copy::uninitialized_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*>(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*) [576] 0.00 0.00 12334/2099102434 ReadProcessor::ReadProcessor(std::string const&) [358] 0.00 0.00 24668/49336 __gnu_cxx::new_allocator > >::new_allocator() [725] ----------------------------------------------- 0.00 0.00 7737/20071 std::_Vector_base >::_Vector_impl::_Vector_impl() [575] 0.00 0.00 12334/20071 std::vector >::vector(std::vector > const&) [548] [577] 0.0 0.00 0.00 20071 std::_Deque_base >::_M_get_map_allocator() const [577] 0.00 0.00 12334/2099102434 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [726] ----------------------------------------------- [578] 0.0 0.00 0.00 std::__miter_base<__gnu_cxx::__normal_iterator > >, false>::__b(__gnu_cxx::__normal_iterator > >) [578] 0.00 0.00 12334/2099102434 ReadProcessor::ReadProcessor(std::string const&) [358] ----------------------------------------------- [579] 0.0 0.00 0.00 void std::_Destroy<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [579] 0.00 0.00 12334/2099102434 ReadProcessor::ReadProcessor(std::string const&) [358] ----------------------------------------------- [580] 0.0 0.00 0.00 ShortyString::size() const [580] 0.00 0.00 5786/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [145] 0.00 0.00 5786/2099102434 std::vector >::~vector() [208] ----------------------------------------------- [581] 0.0 0.00 0.00 std::_Vector_base >::_Vector_impl::~_Vector_impl() [581] 0.00 0.00 480071/2132137 std::_Vector_base >::~_Vector_base() [473] ----------------------------------------------- [582] 0.0 0.00 0.00 void std::_Destroy(int*, int*, std::allocator&) [582] 0.00 0.00 480071/2132137 std::_Vector_base >::~_Vector_base() [473] ----------------------------------------------- 42770 std::vector >::operator=(std::vector > const&) [60] 198453 std::vector >::operator=(std::vector > const&) [283] [583] 0.0 0.00 0.00 241223 OverlapGraph::ContigInfo* std::__uninitialized_copy::uninitialized_copy(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [583] 0.00 0.00 177068/1755802966 std::vector, std::allocator > >::max_size() const [172] 949495 ReadProcessor::ReadProcessor(std::string const&) [358] ----------------------------------------------- [584] 0.0 0.00 0.00 __gnu_cxx::new_allocator >::destroy(triple*) [584] 0.00 0.00 446402/6612552 int* std::__uninitialized_copy_a<__gnu_cxx::__normal_iterator > >, int*, int>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int*, std::allocator&) [378] ----------------------------------------------- [585] 0.0 0.00 0.00 __gnu_cxx::new_allocator::deallocate(OverlapGraph::ContigInfo*, unsigned int) [585] 0.00 0.00 70208/280832 std::pair* std::__uninitialized_copy_a<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*, std::pair >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*, std::allocator >&) [427] ----------------------------------------------- [586] 0.0 0.00 0.00 __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >::__normal_iterator(triple const* const&) [586] 0.00 0.00 65769/722176 Vote* std::__uninitialized_copy::uninitialized_copy(Vote*, Vote*, Vote*) [448] ----------------------------------------------- [587] 0.0 0.00 0.00 triple::triple(int, int, mar_types) [587] 0.00 0.00 1056643/158981148 operator<<(std::ostream&, ShortyString const&) [359] ----------------------------------------------- [588] 0.0 0.00 0.00 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator*() const [588] 0.00 0.00 648620/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [240] ----------------------------------------------- [589] 0.0 0.00 0.00 std::_Rb_tree_const_iterator >::_Rb_tree_const_iterator(std::_Rb_tree_node > const*) [589] 0.00 0.00 648620/332322227 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [240] ----------------------------------------------- 0.00 0.00 70208/70208 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Contig const&) [428] [590] 0.0 0.00 0.00 70208 std::pair* std::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [590] 0.00 0.00 70208/96407108 std::_Rb_tree, std::less, std::allocator >::get_allocator() const [447] ----------------------------------------------- 0.00 0.00 1/7 PrintConfigInfo() [601] 0.00 0.00 1/7 __static_initialization_and_destruction_0(int, int) [602] 0.00 0.00 1/7 __gnu_cxx::__normal_iterator std::transform<__gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator, int (*)(int)>(__gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator, int (*)(int)) [604] 0.00 0.00 1/7 std::_Vector_base >::~_Vector_base() [603] 0.00 0.00 1/7 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, SeededRead const&) [600] 0.00 0.00 1/7 SeededRead* std::uninitialized_copy(SeededRead*, SeededRead*, SeededRead*) [605] 0.00 0.00 1/7 Hash::Hash(int) [504] [591] 0.0 0.00 0.00 7 Hash::Insert(std::string const&, int, int, int) [591] 0.00 0.00 2502/2099102434 Hash::Insert(std::string const&, int, int, int, int) [220] 0.00 0.00 1/2099102434 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::resize(unsigned int, std::list, std::allocator > >) [788] ----------------------------------------------- 0.00 0.00 1/13130 Assembler::Assemble() [474] 0.00 0.00 13129/13130 Assembler::ProcessNewSeeds() [38] [592] 0.0 0.00 0.00 13130 std::vector >::size() const [592] 0.00 0.00 13130/1397173708 std::vector >::push_back(int const&) [32] ----------------------------------------------- [593] 0.0 0.00 0.00 __static_initialization_and_destruction_0(int, int) [593] 0.00 0.00 13129/52520 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [545] ----------------------------------------------- [594] 0.0 0.00 0.00 std::_Deque_base >::_Deque_impl::_Deque_impl(std::allocator const&) [594] 0.00 0.00 596/2099102434 std::deque >::_M_reallocate_map(unsigned int, bool) [758] 0.00 0.00 596/13130 __gnu_cxx::new_allocator::deallocate(SeededRead**, unsigned int) [744] ----------------------------------------------- [595] 0.0 0.00 0.00 std::__miter_base<__gnu_cxx::__normal_iterator > >, false>::__b(__gnu_cxx::__normal_iterator > >) [595] 0.00 0.00 596/2099102434 std::_Deque_base >::_M_allocate_map(unsigned int) [731] ----------------------------------------------- [596] 0.0 0.00 0.00 std::_Deque_iterator::_Deque_iterator() [596] 0.00 0.00 596/2099102434 std::deque >::_M_reallocate_map(unsigned int, bool) [758] ----------------------------------------------- [597] 0.0 0.00 0.00 bool std::operator!=, std::allocator >(std::basic_string, std::allocator > const&, std::basic_string, std::allocator > const&) [597] 0.00 0.00 499/2099102434 _fini [4] 0.00 0.00 499/66875224 UtilsString::OverlapFromCommonReadMapping(ShortyString const&, ShortyString const&, std::vector, std::allocator > > const&, std::vector, std::allocator > > const&, ReadProcessor const*, int*, int*, ShortyString*) [388] ----------------------------------------------- 0.00 0.00 1/1 std::vector >::~vector() [599] [598] 0.0 0.00 0.00 1 std::back_insert_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, std::back_insert_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::back_insert_iterator > >) [598] 0.00 0.00 499/2099102434 _fini [4] 0.00 0.00 1/1506635566 std::pair* std::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [115] ----------------------------------------------- [599] 0.0 0.00 0.00 std::vector >::~vector() [599] 0.00 0.00 1/1 std::back_insert_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, std::back_insert_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::back_insert_iterator > >) [598] ----------------------------------------------- [600] 0.0 0.00 0.00 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, SeededRead const&) [600] 0.00 0.00 1/7 Hash::Insert(std::string const&, int, int, int) [591] 0.00 0.00 1/8 std::vector >::~vector() [629] 0.00 0.00 1/1 RawRead* std::__copy_move_backward_a2(RawRead*, RawRead*, RawRead*) [668] 0.00 0.00 1/7 UtilsMath::median_event_point* std::__copy_move_a(UtilsMath::median_event_point*, UtilsMath::median_event_point*, UtilsMath::median_event_point*) [775] 0.00 0.00 1/1 std::_Vector_base >::_M_allocate(unsigned int) [818] 0.00 0.00 1/3 Hash::Hash(int) [792] ----------------------------------------------- [601] 0.0 0.00 0.00 PrintConfigInfo() [601] 0.00 0.00 1/7 Hash::Insert(std::string const&, int, int, int) [591] 0.00 0.00 1/8 std::vector >::~vector() [629] 0.00 0.00 1/3 Hash::Hash(int) [792] 0.00 0.00 1/7 UtilsMath::median_event_point* std::__copy_move_a(UtilsMath::median_event_point*, UtilsMath::median_event_point*, UtilsMath::median_event_point*) [775] ----------------------------------------------- [602] 0.0 0.00 0.00 __static_initialization_and_destruction_0(int, int) [602] 0.00 0.00 1/7 Hash::Insert(std::string const&, int, int, int) [591] 0.00 0.00 1/8 std::vector >::~vector() [629] 0.00 0.00 1/7 UtilsMath::median_event_point* std::__copy_move_a(UtilsMath::median_event_point*, UtilsMath::median_event_point*, UtilsMath::median_event_point*) [775] ----------------------------------------------- [603] 0.0 0.00 0.00 std::_Vector_base >::~_Vector_base() [603] 0.00 0.00 1/7 Hash::Insert(std::string const&, int, int, int) [591] 0.00 0.00 1/8 std::vector >::~vector() [629] 0.00 0.00 1/7 UtilsMath::median_event_point* std::__copy_move_a(UtilsMath::median_event_point*, UtilsMath::median_event_point*, UtilsMath::median_event_point*) [775] ----------------------------------------------- [604] 0.0 0.00 0.00 __gnu_cxx::__normal_iterator std::transform<__gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator, int (*)(int)>(__gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator, int (*)(int)) [604] 0.00 0.00 1/7 Hash::Insert(std::string const&, int, int, int) [591] 0.00 0.00 1/8 std::vector >::~vector() [629] 0.00 0.00 1/7 UtilsMath::median_event_point* std::__copy_move_a(UtilsMath::median_event_point*, UtilsMath::median_event_point*, UtilsMath::median_event_point*) [775] ----------------------------------------------- [605] 0.0 0.00 0.00 SeededRead* std::uninitialized_copy(SeededRead*, SeededRead*, SeededRead*) [605] 0.00 0.00 1/7 Hash::Insert(std::string const&, int, int, int) [591] ----------------------------------------------- [606] 0.0 0.00 0.00 ShortyString::substr(int, int) const [606] 0.00 0.00 44/44 ShortyString::PrintScores(std::ostream&) const [607] 0.00 0.00 66/2099102434 ShortyString::Print() const [764] 0.00 0.00 132/133 ShortyString::ReadVotesFromFile(std::istream&) [610] 0.00 0.00 22/1208491 ShortyString::push_back(char, Vote const&) [695] ----------------------------------------------- 0.00 0.00 44/44 ShortyString::substr(int, int) const [606] [607] 0.0 0.00 0.00 44 ShortyString::PrintScores(std::ostream&) const [607] 0.00 0.00 44/2099102434 ShortyString::Print() const [764] 0.00 0.00 22/2099102434 ShortyString::~ShortyString() [34] 0.00 0.00 22/2099102434 ShortyString::operator+(ShortyString const&) [761] 0.00 0.00 22/2099102434 ShortyString::ReverseComplement() const [763] ----------------------------------------------- [608] 0.0 0.00 0.00 ShortyString::GetMaxVote() const [608] 0.00 0.00 22/2099102434 ShortyString::ReverseComplement() const [763] 0.00 0.00 22/2099102434 ShortyString::Print() const [764] ----------------------------------------------- [609] 0.0 0.00 0.00 TrieNode::constructTrie() [609] 0.00 0.00 20/2099102434 std::deque >::_M_reallocate_map(unsigned int, bool) [758] 0.00 0.00 10/2099102434 TrieNode::addToTrie(myList*, int) [330] 0.00 0.00 10/2099102434 std::deque >::_M_push_back_aux(SeededRead const&) [770] ----------------------------------------------- 0.00 0.00 1/133 ShortyString::operator==(ShortyString const&) const [619] 0.00 0.00 132/133 ShortyString::substr(int, int) const [606] [610] 0.0 0.00 0.00 133 ShortyString::ReadVotesFromFile(std::istream&) [610] 0.00 0.00 22/2099102434 ShortyString::operator+(ShortyString const&) [761] ----------------------------------------------- [611] 0.0 0.00 0.00 TrieNode::addPairReadToTrie(int) [611] 0.00 0.00 10/2099102434 std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [151] 0.00 0.00 10/2099102434 std::_Deque_iterator std::__uninitialized_copy::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [767] ----------------------------------------------- 0.00 0.00 4/4 std::_Vector_base >::_M_allocate(unsigned int) [613] [612] 0.0 0.00 0.00 4 Vote* std::__uninitialized_copy::uninitialized_copy<__gnu_cxx::__normal_iterator > >, Vote*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, Vote*) [612] 0.00 0.00 8/2099102434 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] 0.00 0.00 4/4 std::_Deque_iterator::operator++() [620] 0.00 0.00 2/2099102434 std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [151] 0.00 0.00 2/13141 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_put_node(std::_Rb_tree_node >*) [740] ----------------------------------------------- [613] 0.0 0.00 0.00 std::_Vector_base >::_M_allocate(unsigned int) [613] 0.00 0.00 4/4 Vote* std::__uninitialized_copy::uninitialized_copy<__gnu_cxx::__normal_iterator > >, Vote*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, Vote*) [612] ----------------------------------------------- [614] 0.0 0.00 0.00 __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >::operator++() [614] 0.00 0.00 8/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] ----------------------------------------------- [615] 0.0 0.00 0.00 std::vector >::_M_check_len(unsigned int, char const*) const [615] 0.00 0.00 4/2099102434 std::_Vector_base, std::allocator > >::~_Vector_base() [732] 0.00 0.00 2/2099102434 Vote* std::__copy_move_a(Vote const*, Vote const*, Vote*) [789] 0.00 0.00 2/4 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::get_allocator() const [663] 0.00 0.00 2/722176 Vote* std::__uninitialized_copy::uninitialized_copy(Vote*, Vote*, Vote*) [448] ----------------------------------------------- 0.00 0.00 1/1 std::vector >::end() [617] [616] 0.0 0.00 0.00 1 Assembler::Assembler(std::vector > const&, ReadProcessor*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*) [616] 0.00 0.00 2/2 std::vector, std::allocator > >::begin() const [632] 0.00 0.00 2/2099102434 std::vector, std::allocator > >::end() const [782] 0.00 0.00 1/2099102434 std::vector, std::allocator > >::begin() const [711] 0.00 0.00 3/8 std::vector >::~vector() [629] 0.00 0.00 1/1 __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >::operator++() [813] 0.00 0.00 1/7 UtilsMath::median_event_point* std::__copy_move_a(UtilsMath::median_event_point*, UtilsMath::median_event_point*, UtilsMath::median_event_point*) [775] ----------------------------------------------- [617] 0.0 0.00 0.00 std::vector >::end() [617] 0.00 0.00 1/1 Assembler::Assembler(std::vector > const&, ReadProcessor*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*) [616] 0.00 0.00 1/3 Hash::Hash(int) [792] ----------------------------------------------- [618] 0.0 0.00 0.00 std::_Vector_base >::_Vector_base() [618] 0.00 0.00 499/1724816198 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [69] ----------------------------------------------- [619] 0.0 0.00 0.00 ShortyString::operator==(ShortyString const&) const [619] 0.00 0.00 2/2099102434 ShortyString::operator+(ShortyString const&) [761] 0.00 0.00 1/2099102434 ShortyString::~ShortyString() [791] 0.00 0.00 1/2099102434 ShortyString::ReverseComplement() const [763] 0.00 0.00 1/2099102434 ShortyString::push_back(char) [794] 0.00 0.00 1/133 ShortyString::ReadVotesFromFile(std::istream&) [610] ----------------------------------------------- 0.00 0.00 4/4 Vote* std::__uninitialized_copy::uninitialized_copy<__gnu_cxx::__normal_iterator > >, Vote*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, Vote*) [612] [620] 0.0 0.00 0.00 4 std::_Deque_iterator::operator++() [620] 0.00 0.00 4/2099102434 TrieNode::TrieNode() [773] 0.00 0.00 4/4 TrieNode::TrieNode() [779] ----------------------------------------------- 0.00 0.00 2/2 Assembler::ProcessNewSeeds() [38] [621] 0.0 0.00 0.00 2 __gnu_cxx::new_allocator::construct(int*, int const&) [621] 0.00 0.00 2/2099102434 std::deque >::pop_back() [787] 0.00 0.00 2/2099102434 std::_Vector_base, std::allocator > >::~_Vector_base() [732] ----------------------------------------------- [622] 0.0 0.00 0.00 bool __gnu_cxx::operator!= const*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > const&) [622] 0.00 0.00 4/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] ----------------------------------------------- [623] 0.0 0.00 0.00 std::allocator::~allocator() [623] 0.00 0.00 4/2099102434 std::deque >::_M_reallocate_map(unsigned int, bool) [758] ----------------------------------------------- [624] 0.0 0.00 0.00 std::_Vector_base >::_Vector_impl::_Vector_impl() [624] 0.00 0.00 4/2099102434 std::deque >::_M_reallocate_map(unsigned int, bool) [758] 0.00 0.00 4/4 std::__niter_base*, false>::__b(std::pair*) [785] ----------------------------------------------- [625] 0.0 0.00 0.00 std::_Vector_base >::_M_deallocate(Contig*, unsigned int) [625] 0.00 0.00 4/2099102434 Contig::~Contig() [53] ----------------------------------------------- [626] 0.0 0.00 0.00 std::_Vector_base, std::allocator > >::_M_deallocate(triple*, unsigned int) [626] 0.00 0.00 4/2099102434 std::_Deque_iterator std::__uninitialized_copy::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [767] ----------------------------------------------- [627] 0.0 0.00 0.00 std::pair* std::__copy_move_backward_a*, std::pair*>(std::pair*, std::pair*, std::pair*) [627] 0.00 0.00 4/2099102434 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [405] ----------------------------------------------- [628] 0.0 0.00 0.00 unsigned int const& std::max(unsigned int const&, unsigned int const&) [628] 0.00 0.00 4/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] ----------------------------------------------- 0.00 0.00 1/8 PrintConfigInfo() [601] 0.00 0.00 1/8 __static_initialization_and_destruction_0(int, int) [602] 0.00 0.00 1/8 __gnu_cxx::__normal_iterator std::transform<__gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator, int (*)(int)>(__gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator, int (*)(int)) [604] 0.00 0.00 1/8 std::_Vector_base >::~_Vector_base() [603] 0.00 0.00 1/8 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, SeededRead const&) [600] 0.00 0.00 3/8 Assembler::Assembler(std::vector > const&, ReadProcessor*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*) [616] [629] 0.0 0.00 0.00 8 std::vector >::~vector() [629] 0.00 0.00 2/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] ----------------------------------------------- 0.00 0.00 2/6 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::get_allocator() const [663] 0.00 0.00 4/6 std::allocator >::~allocator() [648] [630] 0.0 0.00 0.00 6 std::_Deque_iterator::operator++() [630] 0.00 0.00 2/2099102434 TrieNode::TrieNode() [773] ----------------------------------------------- 0.00 0.00 2/2 std::deque >::back() [644] [631] 0.0 0.00 0.00 2 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [631] 0.00 0.00 2/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] 0.00 0.00 2/4 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [780] ----------------------------------------------- 0.00 0.00 2/2 Assembler::Assembler(std::vector > const&, ReadProcessor*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*) [616] [632] 0.0 0.00 0.00 2 std::vector, std::allocator > >::begin() const [632] 0.00 0.00 2/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] ----------------------------------------------- 0.00 0.00 2/2 int* std::__uninitialized_copy::uninitialized_copy(int*, int*, int*) [642] [633] 0.0 0.00 0.00 2 mar_types* std::__copy_move_a(mar_types*, mar_types*, mar_types*) [633] 0.00 0.00 2/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] ----------------------------------------------- 0.00 0.00 2/2 std::vector, std::allocator > >::end() [646] [634] 0.0 0.00 0.00 2 mar_types* std::__copy_move_backward_a2(mar_types*, mar_types*, mar_types*) [634] 0.00 0.00 2/2099102434 std::deque >::_M_pop_back_aux() [786] ----------------------------------------------- [635] 0.0 0.00 0.00 ShortyString::ShortyString(std::string const&) [635] 0.00 0.00 2/2099102434 ShortyString::ShortyString(std::string const&, int) [7] ----------------------------------------------- [636] 0.0 0.00 0.00 __gnu_cxx::__normal_iterator > >::__normal_iterator(int* const&) [636] 0.00 0.00 2/2099102434 std::deque >::push_back(SeededRead const&) [549] ----------------------------------------------- [637] 0.0 0.00 0.00 __gnu_cxx::__normal_iterator > >::base() const [637] 0.00 0.00 2/2099102434 std::_Vector_base, std::allocator > >::~_Vector_base() [732] ----------------------------------------------- [638] 0.0 0.00 0.00 __gnu_cxx::__normal_iterator > >::operator*() const [638] 0.00 0.00 2/2099102434 std::_Vector_base, std::allocator > >::~_Vector_base() [732] ----------------------------------------------- [639] 0.0 0.00 0.00 std::_Deque_iterator::operator*() const [639] 0.00 0.00 2/2099102434 std::_Deque_iterator std::__uninitialized_copy::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [767] ----------------------------------------------- [640] 0.0 0.00 0.00 std::__niter_base::__b(Vote*) [640] 0.00 0.00 2/2099102434 mar_types* std::__copy_move_backward::__copy_move_b(mar_types const*, mar_types const*, mar_types*) [411] ----------------------------------------------- [641] 0.0 0.00 0.00 SeededRead** std::__copy_move_backward::__copy_move_b(SeededRead* const*, SeededRead* const*, SeededRead**) [641] 0.00 0.00 2/2099102434 TrieNode::searchWithErrorAllowed(std::string const&, int, int) [367] ----------------------------------------------- [642] 0.0 0.00 0.00 int* std::__uninitialized_copy::uninitialized_copy(int*, int*, int*) [642] 0.00 0.00 2/2 mar_types* std::__copy_move_a(mar_types*, mar_types*, mar_types*) [633] ----------------------------------------------- [643] 0.0 0.00 0.00 std::list, std::allocator > >::_M_insert(std::_List_iterator >, std::pair const&) [643] 0.00 0.00 1/2099102434 std::deque >::_M_reallocate_map(unsigned int, bool) [758] 0.00 0.00 1/2099102434 Hash::Insert(std::string const&, int, int, int, int) [220] 0.00 0.00 1/4 void std::_Destroy, std::allocator > >*, std::list, std::allocator > > >(std::list, std::allocator > >*, std::list, std::allocator > >*, std::allocator, std::allocator > > >&) [790] ----------------------------------------------- [644] 0.0 0.00 0.00 std::deque >::back() [644] 0.00 0.00 2/2 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [631] ----------------------------------------------- [645] 0.0 0.00 0.00 std::vector >::~vector() [645] 0.00 0.00 2/2099102434 ShortyString::ShortyString(std::string const&, int) [366] ----------------------------------------------- [646] 0.0 0.00 0.00 std::vector, std::allocator > >::end() [646] 0.00 0.00 2/2 mar_types* std::__copy_move_backward_a2(mar_types*, mar_types*, mar_types*) [634] ----------------------------------------------- [647] 0.0 0.00 0.00 int* std::__uninitialized_copy_a(int*, int*, int*, std::allocator&) [647] 0.00 0.00 2/2099102434 std::deque >::_M_reallocate_map(unsigned int, bool) [758] ----------------------------------------------- [648] 0.0 0.00 0.00 std::allocator >::~allocator() [648] 0.00 0.00 4/6 std::_Deque_iterator::operator++() [630] ----------------------------------------------- [649] 0.0 0.00 0.00 __static_initialization_and_destruction_0(int, int) [649] 0.00 0.00 1/1 std::_List_const_iterator >::operator++() [651] 0.00 0.00 1/2 std::_Vector_base, std::allocator > >, std::allocator, std::allocator > > > >::~_Vector_base() [669] 0.00 0.00 1/1 std::_Vector_base, std::allocator > >, std::allocator, std::allocator > > > >::_Vector_impl::~_Vector_impl() [821] ----------------------------------------------- 0.00 0.00 1/1 std::vector >::_M_check_len(unsigned int, char const*) const [505] [650] 0.0 0.00 0.00 1 ShortyString::ShortyString() [650] 0.00 0.00 1/2099102434 std::vector, std::allocator > >::_M_fill_insert(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, unsigned int, triple const&) [50] ----------------------------------------------- 0.00 0.00 1/1 __static_initialization_and_destruction_0(int, int) [649] [651] 0.0 0.00 0.00 1 std::_List_const_iterator >::operator++() [651] 0.00 0.00 1/2099102434 std::_List_base, std::allocator > >::_M_clear() [783] ----------------------------------------------- [652] 0.0 0.00 0.00 Hash::HashVal(std::string const&, int) const [652] 0.00 0.00 1/2099102434 Hash::LeftShiftHashVal(char, char, int) const [793] ----------------------------------------------- [653] 0.0 0.00 0.00 __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >::operator->() const [653] 0.00 0.00 1/2099102434 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] ----------------------------------------------- [654] 0.0 0.00 0.00 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::size() const [654] 0.00 0.00 1/2099102434 std::_List_base, std::allocator > >::_M_clear() [783] 0.00 0.00 1/7 std::vector >::operator[](unsigned int) [774] ----------------------------------------------- [655] 0.0 0.00 0.00 std::_List_base, std::allocator > >::~_List_base() [655] 0.00 0.00 1/2099102434 std::deque >::_M_reallocate_map(unsigned int, bool) [758] 0.00 0.00 1/4 void std::_Destroy, std::allocator > >*, std::list, std::allocator > > >(std::list, std::allocator > >*, std::list, std::allocator > >*, std::allocator, std::allocator > > >&) [790] ----------------------------------------------- [656] 0.0 0.00 0.00 std::_Vector_base >::_Vector_impl::_Vector_impl() [656] 0.00 0.00 1/2099102434 Hash::LeftShiftHashVal(char, char, int) const [793] 0.00 0.00 2/7 std::vector >::operator[](unsigned int) [774] ----------------------------------------------- [657] 0.0 0.00 0.00 std::_Vector_base, std::allocator > >, std::allocator, std::allocator > > > >::_M_get_Tp_allocator() [657] 0.00 0.00 1/2099102434 TrieNode::searchWithError(std::string const&, int) [691] ----------------------------------------------- [658] 0.0 0.00 0.00 std::_Vector_base, std::allocator > >, std::allocator, std::allocator > > > >::_Vector_base() [658] 0.00 0.00 1/2099102434 std::allocator > >::~allocator() [800] ----------------------------------------------- [659] 0.0 0.00 0.00 std::list, std::allocator > >::push_back(std::pair const&) [659] 0.00 0.00 1/2099102434 std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [151] 0.00 0.00 2/7 std::vector >::operator[](unsigned int) [774] ----------------------------------------------- [660] 0.0 0.00 0.00 std::list, std::allocator > >::list(std::list, std::allocator > > const&) [660] 0.00 0.00 1/2099102434 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::resize(unsigned int, std::list, std::allocator > >) [788] ----------------------------------------------- [661] 0.0 0.00 0.00 std::vector >::~vector() [661] 0.00 0.00 1/2099102434 ShortyString::ShortyString(std::string const&, int) [366] ----------------------------------------------- [662] 0.0 0.00 0.00 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::operator[](unsigned int) [662] 0.00 0.00 1/2099102434 bool std::operator!=(std::_Deque_iterator const&, std::_Deque_iterator const&) [759] ----------------------------------------------- 0.00 0.00 2/4 mar_types* std::copy_backward(mar_types*, mar_types*, mar_types*) [664] 0.00 0.00 2/4 std::vector >::_M_check_len(unsigned int, char const*) const [615] [663] 0.0 0.00 0.00 4 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::get_allocator() const [663] 0.00 0.00 2/6 std::_Deque_iterator::operator++() [630] ----------------------------------------------- [664] 0.0 0.00 0.00 mar_types* std::copy_backward(mar_types*, mar_types*, mar_types*) [664] 0.00 0.00 2/4 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::get_allocator() const [663] 0.00 0.00 2/722176 Vote* std::__uninitialized_copy::uninitialized_copy(Vote*, Vote*, Vote*) [448] ----------------------------------------------- [665] 0.0 0.00 0.00 __gnu_cxx::new_allocator::~new_allocator() [665] 0.00 0.00 2/722176 Vote* std::__uninitialized_copy::uninitialized_copy(Vote*, Vote*, Vote*) [448] ----------------------------------------------- [666] 0.0 0.00 0.00 std::allocator > >::allocator() [666] 0.00 0.00 2/722176 Vote* std::__uninitialized_copy::uninitialized_copy(Vote*, Vote*, Vote*) [448] ----------------------------------------------- 0.00 0.00 1/1 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] [667] 0.0 0.00 0.00 1 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [667] 0.00 0.00 1/97678121 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [415] ----------------------------------------------- 0.00 0.00 1/1 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, SeededRead const&) [600] [668] 0.0 0.00 0.00 1 RawRead* std::__copy_move_backward_a2(RawRead*, RawRead*, RawRead*) [668] 0.00 0.00 1/3393446 TrieNode::searchWithErrorAllowedNonRecursive(std::string const&, int) [312] ----------------------------------------------- 0.00 0.00 1/2 __static_initialization_and_destruction_0(int, int) [649] 0.00 0.00 1/2 global constructors keyed to _ZN4HashC2Ei [672] [669] 0.0 0.00 0.00 2 std::_Vector_base, std::allocator > >, std::allocator, std::allocator > > > >::~_Vector_base() [669] 0.00 0.00 2/67677006 std::list, std::allocator > >::begin() [255] ----------------------------------------------- 0.00 0.00 2/2 SeededRead* std::__uninitialized_copy::uninitialized_copy(SeededRead*, SeededRead*, SeededRead*) [671] [670] 0.0 0.00 0.00 2 UtilsString::PrintContig(std::string const&, std::string const&) [670] 0.00 0.00 2/271331188 __static_initialization_and_destruction_0(int, int) [252] ----------------------------------------------- [671] 0.0 0.00 0.00 SeededRead* std::__uninitialized_copy::uninitialized_copy(SeededRead*, SeededRead*, SeededRead*) [671] 0.00 0.00 2/2 UtilsString::PrintContig(std::string const&, std::string const&) [670] ----------------------------------------------- [672] 0.0 0.00 0.00 global constructors keyed to _ZN4HashC2Ei [672] 0.00 0.00 1/2 std::_Vector_base, std::allocator > >, std::allocator, std::allocator > > > >::~_Vector_base() [669] ----------------------------------------------- [673] 0.0 0.00 0.00 std::list, std::allocator > >::list() [673] 0.00 0.00 1/67677006 std::list, std::allocator > >::begin() [255] ----------------------------------------------- [674] 0.0 0.00 0.00 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::~vector() [674] 0.00 0.00 1/67677006 std::list, std::allocator > >::begin() [255] 0.00 0.00 2/4 void std::_Destroy, std::allocator > >*, std::list, std::allocator > > >(std::list, std::allocator > >*, std::list, std::allocator > >*, std::allocator, std::allocator > > >&) [790] 0.00 0.00 1/2 std::_List_base, std::allocator > >::_List_base() [802] ----------------------------------------------- [675] 0.0 0.00 0.00 __gnu_cxx::__enable_if::__value, void>::__type std::__fill_a(short*, short*, int const&) [675] 0.00 0.00 1/271331188 __static_initialization_and_destruction_0(int, int) [252] ----------------------------------------------- 0.00 0.00 13931508/13931508 Contig::operator=(Contig const&) [174] [678] 0.0 0.00 0.00 13931508 __gnu_cxx::__normal_iterator > >::__normal_iterator(Contig* const&) [678] ----------------------------------------------- 0.00 0.00 177068/9828241 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] 0.00 0.00 9651173/9828241 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] [679] 0.0 0.00 0.00 9828241 std::allocator >::~allocator() [679] ----------------------------------------------- 1004933 __gnu_cxx::new_allocator >::deallocate(std::pair*, unsigned int) [697] 1920286 std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [151] 0.58 0.07 1920286/2099102434 void std::_Destroy_aux::__destroy(mar_types*, mar_types*) [306] [680] 0.0 0.00 0.00 4845505 SeededRead** std::copy_backward(SeededRead**, SeededRead**, SeededRead**) [680] 1920286 TrieNode::searchWithError(std::string const&, int) [691] ----------------------------------------------- 0.00 0.00 44790/4238020 std::__niter_base<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, true>::__b(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >) [1291] 0.00 0.00 352658/4238020 std::vector, std::allocator > >::end() const [708] 0.00 0.00 960143/4238020 std::vector >::end() const [353] 0.00 0.00 2880429/4238020 Vote* std::vector >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator > > >(unsigned int, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [243] [681] 0.0 0.00 0.00 4238020 std::pair::operator=(std::pair const&) [681] ----------------------------------------------- 0.00 0.00 3840572/3840572 TrieNode::addToTrie(myList*, int) [330] [682] 0.0 0.00 0.00 3840572 std::_Deque_iterator::_Deque_iterator(std::_Deque_iterator const&) [682] ----------------------------------------------- 0.00 0.00 648620/3096309 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [337] 0.00 0.00 2447689/3096309 __gnu_cxx::new_allocator >::construct(triple*, triple const&) [475] [683] 0.0 0.00 0.00 3096309 std::pair >, bool>::pair(std::_Rb_tree_iterator > const&, bool const&) [683] ----------------------------------------------- 0.00 0.00 1004933/2925217 std::_Deque_base >::_M_initialize_map(unsigned int) [242] 0.00 0.00 1920284/2925217 TrieNode::addToTrie(myList*, int) [330] [684] 0.0 0.00 0.00 2925217 std::pair* std::__copy_move_backward_a2*, std::pair*>(std::pair*, std::pair*, std::pair*) [684] ----------------------------------------------- 0.00 0.00 22395/2902821 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [542] 0.00 0.00 960142/2902821 std::_Deque_base >::_M_deallocate_map(SeededRead**, unsigned int) [552] 0.00 0.00 1920284/2902821 std::deque >::_M_destroy_data_aux(std::_Deque_iterator, std::_Deque_iterator) [397] [685] 0.0 0.00 0.00 2902821 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [685] 0.00 0.00 960142/982537 int* std::copy(int*, int*, int*) [698] ----------------------------------------------- 0.00 0.00 22395/2902821 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, std::string const&) [706] 0.00 0.00 960142/2902821 TrieNode::searchWithErrorAllowedNonRecursive(std::string const&, int) [312] 0.00 0.00 1920284/2902821 TrieNode::traceTrie() [317] [686] 0.0 0.00 0.00 2902821 __gnu_cxx::new_allocator::max_size() const [686] ----------------------------------------------- 0.00 0.00 412850/2674989 std::set, OverlapGraph::IntPairEq, std::allocator > >::insert(std::pair const&) [269] 0.00 0.00 2262139/2674989 std::_Vector_base, std::allocator > >::_Vector_base() [451] [687] 0.0 0.00 0.00 2674989 std::vector, std::allocator > >::size() const [687] ----------------------------------------------- 0.00 0.00 2447689/2447689 __gnu_cxx::new_allocator >::construct(triple*, triple const&) [475] [688] 0.0 0.00 0.00 2447689 std::_Vector_base, std::allocator > >::_M_allocate(unsigned int) [688] ----------------------------------------------- 0.00 0.00 12334/2357247 Contig* std::uninitialized_copy(Contig*, Contig*, Contig*) [753] 0.00 0.00 2344913/2357247 std::vector >::operator=(std::vector > const&) [283] [689] 0.0 0.00 0.00 2357247 std::pair* std::__copy_move::__copy_m*, std::pair*>(std::pair*, std::pair*, std::pair*) [689] ----------------------------------------------- 0.00 0.00 44790/1965076 Contig* std::__uninitialized_copy_a(Contig*, Contig*, Contig*, std::allocator&) [383] 0.00 0.00 1920286/1965076 std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [151] [690] 0.0 0.00 0.00 1965076 SeededRead** std::copy(SeededRead**, SeededRead**, SeededRead**) [690] ----------------------------------------------- 600 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [405] 1920286 SeededRead** std::copy_backward(SeededRead**, SeededRead**, SeededRead**) [680] 0.00 0.00 1/2099102434 std::_Vector_base, std::allocator > >, std::allocator, std::allocator > > > >::_M_get_Tp_allocator() [657] [691] 0.0 0.00 0.00 1920887 TrieNode::searchWithError(std::string const&, int) [691] 1920887 TrieNode::addToTrie(myList*, int) [330] ----------------------------------------------- 0.00 0.00 1920286/1920286 std::_Deque_base >::_M_initialize_map(unsigned int) [242] [692] 0.0 0.00 0.00 1920286 std::allocator::allocator() [692] ----------------------------------------------- 0.00 0.00 480071/1920284 std::_Vector_base >::_Vector_base() [1262] 0.00 0.00 480071/1920284 std::_Vector_base >::~_Vector_base() [547] 0.00 0.00 960142/1920284 std::deque >::_M_destroy_data_aux(std::_Deque_iterator, std::_Deque_iterator) [397] [693] 0.0 0.00 0.00 1920284 std::_Deque_base >::_M_destroy_nodes(SeededRead**, SeededRead**) [693] ----------------------------------------------- 0.00 0.00 88164/1528377 std::_Vector_base >::~_Vector_base() [473] 0.00 0.00 480071/1528377 std::allocator > >::~allocator() [1167] 0.00 0.00 960142/1528377 std::_Vector_base >::~_Vector_base() [547] [694] 0.0 0.00 0.00 1528377 std::_Deque_base >::_Deque_base(std::allocator const&, unsigned int) [694] 0.00 0.00 960142/960142 __gnu_cxx::new_allocator::~new_allocator() [700] ----------------------------------------------- 0.00 0.00 22/1208491 ShortyString::substr(int, int) const [606] 0.00 0.00 1208469/1208491 ShortyString::ShortyString(std::string const&, int) [7] [695] 0.0 0.00 0.00 1208491 ShortyString::push_back(char, Vote const&) [695] ----------------------------------------------- 0.00 0.00 1208491/1208491 RawRead* std::__uninitialized_copy::uninitialized_copy(RawRead*, RawRead*, RawRead*) [249] [696] 0.0 0.00 0.00 1208491 ShortyString::operator==(std::string const&) const [696] ----------------------------------------------- 1004933 std::_Deque_base >::_M_initialize_map(unsigned int) [242] [697] 0.0 0.00 0.00 1004933 __gnu_cxx::new_allocator >::deallocate(std::pair*, unsigned int) [697] 1004933 SeededRead** std::copy_backward(SeededRead**, SeededRead**, SeededRead**) [680] ----------------------------------------------- 0.00 0.00 22395/982537 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [542] 0.00 0.00 960142/982537 __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [685] [698] 0.0 0.00 0.00 982537 int* std::copy(int*, int*, int*) [698] ----------------------------------------------- 0.00 0.00 960143/960143 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Rb_tree_impl, false>::~_Rb_tree_impl() [1401] [699] 0.0 0.00 0.00 960143 std::vector >::end() [699] ----------------------------------------------- 0.00 0.00 960142/960142 std::_Deque_base >::_Deque_base(std::allocator const&, unsigned int) [694] [700] 0.0 0.00 0.00 960142 __gnu_cxx::new_allocator::~new_allocator() [700] ----------------------------------------------- 0.00 0.00 656399/656399 Vote* std::__uninitialized_copy::uninitialized_copy(Vote*, Vote*, Vote*) [448] [701] 0.0 0.00 0.00 656399 void std::_Destroy_aux::__destroy(SeededRead*, SeededRead*) [701] ----------------------------------------------- 0.00 0.00 22395/502466 ReadProcessor::ReadProcessor(std::string const&) [358] 0.00 0.00 480071/502466 std::_Vector_base >::~_Vector_base() [398] [702] 0.0 0.00 0.00 502466 std::_Deque_base >::_M_get_Tp_allocator() const [702] ----------------------------------------------- 0.00 0.00 480071/480071 std::deque >::~deque() [134] [703] 0.0 0.00 0.00 480071 std::_Deque_base >::_Deque_base() [703] ----------------------------------------------- 0.00 0.00 480071/480071 std::deque >::~deque() [134] [704] 0.0 0.00 0.00 480071 Vote* std::__uninitialized_copy_a(Vote*, Vote*, Vote*, std::allocator&) [704] ----------------------------------------------- 131539 std::vector, std::allocator > >::begin() const [711] 0.05 0.01 176329/2099102434 __gnu_cxx::new_allocator >::construct(std::pair*, std::pair const&) [425] [705] 0.0 0.00 0.00 307868 std::pair::pair(std::pair const&) [705] 307868 std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [92] ----------------------------------------------- 67185 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, std::string const&) [706] 223950 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, RawRead const&) [235] [706] 0.0 0.00 0.00 223950+67185 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, std::string const&) [706] 0.00 0.00 44790/44790 ReadProcessor::~ReadProcessor() [727] 0.00 0.00 22395/2902821 __gnu_cxx::new_allocator::max_size() const [686] 201555 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, RawRead const&) [235] 89580 ReadProcessor::LocateRead(std::string const&) const [709] 44790 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [405] 67185 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, std::string const&) [706] ----------------------------------------------- 186838 std::vector >::operator=(std::vector > const&) [60] [707] 0.0 0.00 0.00 186838 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [707] 15474 ReadProcessor::ReadProcessor(std::string const&) [59] ----------------------------------------------- 0.00 0.00 1/176329 Assembler::Assemble() [474] 0.00 0.00 52520/176329 std::vector >::operator=(std::vector > const&) [88] 0.00 0.00 123808/176329 std::vector >::vector(std::vector > const&) [514] [708] 0.0 0.00 0.00 176329 std::vector, std::allocator > >::end() const [708] 0.00 0.00 352658/4238020 std::pair::operator=(std::pair const&) [681] ----------------------------------------------- 67185 ReadProcessor::ReadProcessor(std::string const&) [358] 89580 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, std::string const&) [706] [709] 0.0 0.00 0.00 156765 ReadProcessor::LocateRead(std::string const&) const [709] 22395 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, RawRead const&) [235] ----------------------------------------------- 140416 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Contig const&) [428] [710] 0.0 0.00 0.00 140416 std::_Rb_tree, std::less, std::allocator >::_Rb_tree_impl, false>::_M_initialize() [710] 140416 void std::__adjust_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [121] ----------------------------------------------- 52520 std::vector >::operator=(std::vector > const&) [88] 0.00 0.00 1/2099102434 Assembler::Assembler(std::vector > const&, ReadProcessor*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*) [616] 0.02 0.00 79018/2099102434 main [78] [711] 0.0 0.00 0.00 131539 std::vector, std::allocator > >::begin() const [711] 131539 std::pair::pair(std::pair const&) [705] ----------------------------------------------- 13130 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [145] 13130 Vote* std::__copy_move_a2(Vote*, Vote*, Vote*) [714] 65650 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] 0.01 0.00 26260/2099102434 std::vector >::end() [538] [712] 0.0 0.00 0.00 118170 __gnu_cxx::__normal_iterator > > std::__copy_move_a2 > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [712] 13130 std::_Deque_base >::_M_create_nodes(SeededRead**, SeededRead**) [728] ----------------------------------------------- 0.00 0.00 39390/91910 std::vector, std::allocator > >::_M_fill_insert(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, unsigned int, triple const&) [50] 0.00 0.00 52520/91910 Contig::PrintContigFormat(std::basic_fstream >*) const [408] [713] 0.0 0.00 0.00 91910 std::vector >::_M_check_len(unsigned int, char const*) const [713] ----------------------------------------------- 26260 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [145] 0.01 0.00 26260/2099102434 Contig::Contig(bool, int, int, ShortyString const&, int, ReadProcessor const*) [500] 0.01 0.00 39390/2099102434 Contig::Contig(bool, int, int, ShortyString const&, ReadProcessor const*) [463] [714] 0.0 0.00 0.00 91910 Vote* std::__copy_move_a2(Vote*, Vote*, Vote*) [714] 13130 __gnu_cxx::__normal_iterator > > std::__copy_move_a2 > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [712] ----------------------------------------------- 0.00 0.00 88164/88164 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] [715] 0.0 0.00 0.00 88164 __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >::base() const [715] ----------------------------------------------- 0.00 0.00 88164/88164 std::_Vector_base >::~_Vector_base() [473] [716] 0.0 0.00 0.00 88164 std::_Vector_base, std::allocator > >::_M_get_Tp_allocator() [716] ----------------------------------------------- 2 mar_types* std::__copy_move_backward::__copy_move_b(mar_types const*, mar_types const*, mar_types*) [411] 0.00 0.00 13130/2099102434 mar_types* std::__uninitialized_copy::uninitialized_copy(mar_types*, mar_types*, mar_types*) [567] 0.02 0.00 65769/2099102434 __gnu_cxx::new_allocator::new_allocator() [483] [717] 0.0 0.00 0.00 78901 mar_types* std::__copy_move::__copy_m(mar_types const*, mar_types const*, mar_types*) [717] 13130 std::vector >::vector(std::vector > const&) [514] ----------------------------------------------- 0.00 0.00 70208/70208 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [65] [718] 0.0 0.00 0.00 70208 std::vector, std::allocator > >::begin() const [718] ----------------------------------------------- 0.00 0.00 70208/70208 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Contig const&) [428] [719] 0.0 0.00 0.00 70208 void std::_Destroy_aux::__destroy(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [719] ----------------------------------------------- 70208 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Contig const&) [428] [720] 0.0 0.00 0.00 70208 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::__copy_move_a2 const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [720] 140416 std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [75] 70208 void std::__adjust_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [121] ----------------------------------------------- 0.00 0.00 65769/65769 Vote* std::__uninitialized_copy::uninitialized_copy(Vote*, Vote*, Vote*) [448] [721] 0.0 0.00 0.00 65769 __gnu_cxx::new_allocator::max_size() const [721] ----------------------------------------------- 0.00 0.00 15474/64810 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [145] 0.00 0.00 24668/64810 std::vector >::vector(std::vector > const&) [503] 0.00 0.00 24668/64810 std::vector >::vector(std::vector > const&) [548] [722] 0.0 0.00 0.00 64810 void std::_Destroy(int*, int*) [722] ----------------------------------------------- 0.00 0.00 61670/61670 ReadProcessor::ReadProcessor(std::string const&) [358] [723] 0.0 0.00 0.00 61670 ReadProcessor::GetMar(int, mar_types) const [723] ----------------------------------------------- 26260 std::_Deque_base >::_M_create_nodes(SeededRead**, SeededRead**) [728] 26260 std::_Deque_iterator::_M_set_node(SeededRead**) [729] [724] 0.0 0.00 0.00 52520 void std::_Destroy >(std::_Deque_iterator, std::_Deque_iterator) [724] 4 TrieNode::TrieNode() [773] ----------------------------------------------- 0.00 0.00 24668/49336 std::vector >::vector(std::vector > const&) [503] 0.00 0.00 24668/49336 std::pair* std::__uninitialized_copy::uninitialized_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*>(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*) [576] [725] 0.0 0.00 0.00 49336 __gnu_cxx::new_allocator > >::new_allocator() [725] ----------------------------------------------- 7737 std::_Deque_iterator::_M_set_node(SeededRead**) [729] 7737 std::_Deque_base >::_M_deallocate_node(SeededRead*) [756] 20071 std::allocator::~allocator() [739] 0.00 0.00 12334/2099102434 std::_Deque_base >::_M_get_map_allocator() const [577] [726] 0.0 0.00 0.00 47879 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [726] 30132 TrieNode::destructNode() [730] ----------------------------------------------- 0.00 0.00 44790/44790 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, std::string const&) [706] [727] 0.0 0.00 0.00 44790 ReadProcessor::~ReadProcessor() [727] ----------------------------------------------- 13130 __gnu_cxx::__normal_iterator > > std::__copy_move_a2 > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [712] 0.00 0.00 13130/2099102434 void std::_Destroy<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [571] 0.00 0.00 13130/2099102434 Contig::Contig(bool, int, int, ShortyString const&, int, ReadProcessor const*) [500] [728] 0.0 0.00 0.00 39390 std::_Deque_base >::_M_create_nodes(SeededRead**, SeededRead**) [728] 26260 void std::_Destroy >(std::_Deque_iterator, std::_Deque_iterator) [724] 596 std::deque >::_M_reallocate_map(unsigned int, bool) [758] 596 std::_Deque_base >::_M_allocate_map(unsigned int) [731] ----------------------------------------------- 7737 std::_Vector_base >::_Vector_impl::_Vector_impl(std::allocator const&) [404] 26260 Vote* std::uninitialized_copy(Vote*, Vote*, Vote*) [364] [729] 0.0 0.00 0.00 33997 std::_Deque_iterator::_M_set_node(SeededRead**) [729] 26260 void std::_Destroy >(std::_Deque_iterator, std::_Deque_iterator) [724] 7737 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [726] ----------------------------------------------- 10 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [405] 30132 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [726] [730] 0.0 0.00 0.00 30142 TrieNode::destructNode() [730] 22395 std::vector >::operator=(std::vector > const&) [88] ----------------------------------------------- 596 std::_Deque_base >::_M_create_nodes(SeededRead**, SeededRead**) [728] 0.00 0.00 596/2099102434 std::__miter_base<__gnu_cxx::__normal_iterator > >, false>::__b(__gnu_cxx::__normal_iterator > >) [595] 0.00 0.00 12533/2099102434 __gnu_cxx::__normal_iterator > >::__normal_iterator(Vote* const&) [574] 0.00 0.00 13129/2099102434 std::_Vector_base >::_M_allocate(unsigned int) [539] [731] 0.0 0.00 0.00 26854 std::_Deque_base >::_M_allocate_map(unsigned int) [731] 13129 std::vector >::~vector() [208] 596 std::deque >::_M_reallocate_map(unsigned int, bool) [758] ----------------------------------------------- 2 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] 0.00 0.00 2/2099102434 __gnu_cxx::new_allocator::construct(int*, int const&) [621] 0.00 0.00 2/2099102434 __gnu_cxx::__normal_iterator > >::base() const [637] 0.00 0.00 2/2099102434 __gnu_cxx::__normal_iterator > >::operator*() const [638] 0.00 0.00 4/2099102434 std::vector >::_M_check_len(unsigned int, char const*) const [615] 0.00 0.00 13130/2099102434 std::_Vector_base >::_M_get_Tp_allocator() [565] 0.00 0.00 13130/2099102434 void std::_Destroy(Contig*, Contig*, std::allocator&) [573] [732] 0.0 0.00 0.00 26272 std::_Vector_base, std::allocator > >::~_Vector_base() [732] 13134 Vote* std::__copy_move_a(Vote*, Vote*, Vote*) [742] 2 Vote* std::__copy_move_a(Vote const*, Vote const*, Vote*) [789] 2 std::deque >::pop_back() [787] ----------------------------------------------- 0.00 0.00 26260/26260 Contig::PrintFastaFormat(std::basic_fstream >*) const [737] [733] 0.0 0.00 0.00 26260 __static_initialization_and_destruction_0(int, int) [733] ----------------------------------------------- 13130 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [368] 0.00 0.00 13130/2099102434 Contig::Contig(bool, int, int, ShortyString const&, ReadProcessor const*) [463] [734] 0.0 0.00 0.00 26260 Contig::Contig(bool, int, int, ShortyString const&, int, ReadProcessor const*) [734] 26260 Contig::PrintContigFormat(std::basic_fstream >*) const [408] ----------------------------------------------- 0.00 0.00 26260/26260 Assembler::MakeContigs(bool, Cluster const&, SeededRead const&) [21] [735] 0.0 0.00 0.00 26260 __gnu_cxx::new_allocator::construct(mar_types*, mar_types const&) [735] ----------------------------------------------- 0.00 0.00 26260/26260 Contig::PrintGeoFormat(std::basic_fstream >*) const [409] [736] 0.0 0.00 0.00 26260 __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [736] ----------------------------------------------- 0.00 0.00 26260/26260 Contig::PrintContigFormat(std::basic_fstream >*) const [408] [737] 0.0 0.00 0.00 26260 Contig::PrintFastaFormat(std::basic_fstream >*) const [737] 0.00 0.00 26260/26260 __static_initialization_and_destruction_0(int, int) [733] ----------------------------------------------- 0.00 0.00 13130/26260 std::vector >::begin() [747] 0.00 0.00 13130/26260 Contig::PrintContigFormat(std::basic_fstream >*) const [408] [738] 0.0 0.00 0.00 26260 readPointer* std::__uninitialized_copy::uninitialized_copy(readPointer*, readPointer*, readPointer*) [738] ----------------------------------------------- 20071 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Rb_tree_impl, false>::_Rb_tree_impl() [750] [739] 0.0 0.00 0.00 20071 std::allocator::~allocator() [739] 20071 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [726] ----------------------------------------------- 0.00 0.00 2/13141 std::_Vector_base >::_M_deallocate(mar_types*, unsigned int) [741] 0.00 0.00 2/13141 Vote* std::__uninitialized_copy::uninitialized_copy<__gnu_cxx::__normal_iterator > >, Vote*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, Vote*) [612] 0.00 0.00 13137/13141 __gnu_cxx::__normal_iterator > >::__normal_iterator(mar_types* const&) [981] [740] 0.0 0.00 0.00 13141 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_put_node(std::_Rb_tree_node >*) [740] ----------------------------------------------- 0.00 0.00 13137/13137 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] [741] 0.0 0.00 0.00 13137 std::_Vector_base >::_M_deallocate(mar_types*, unsigned int) [741] 0.00 0.00 2/13141 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_put_node(std::_Rb_tree_node >*) [740] ----------------------------------------------- 13134 std::_Vector_base, std::allocator > >::~_Vector_base() [732] [742] 0.0 0.00 0.00 13134 Vote* std::__copy_move_a(Vote*, Vote*, Vote*) [742] 13134 mar_types* std::__copy_move_backward::__copy_move_b(mar_types const*, mar_types const*, mar_types*) [411] ----------------------------------------------- 1 ShortyString::ShortyString(std::string const&, int) [7] 0.00 0.00 13130/2099102434 ShortyString::ShortyString(std::string const&, std::vector > const&) [563] [743] 0.0 0.00 0.00 13131 ShortyString::ShortyString(std::string const&) [743] 26260 ShortyString::~ShortyString() [34] 13130 ShortyString::ShortyString(std::string const&, int) [7] ----------------------------------------------- 0.00 0.00 1/13130 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::vector() [1384] 0.00 0.00 596/13130 std::_Deque_base >::_Deque_impl::_Deque_impl(std::allocator const&) [594] 0.00 0.00 12533/13130 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Rb_tree_impl, false>::_Rb_tree_impl() [750] [744] 0.0 0.00 0.00 13130 __gnu_cxx::new_allocator::deallocate(SeededRead**, unsigned int) [744] ----------------------------------------------- 0.00 0.00 13130/13130 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [368] [745] 0.0 0.00 0.00 13130 readPointer* std::__copy_move_backward::__copy_move_b(readPointer*, readPointer*, readPointer*) [745] ----------------------------------------------- 0.00 0.00 13130/13130 ShortyString::ShortyString(std::string const&, std::vector > const&) [563] [746] 0.0 0.00 0.00 13130 std::vector >::_M_erase_at_end(readPointer*) [746] ----------------------------------------------- 0.00 0.00 13130/13130 std::vector, std::allocator > >::_M_fill_insert(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, unsigned int, triple const&) [50] [747] 0.0 0.00 0.00 13130 std::vector >::begin() [747] 0.00 0.00 13130/26260 readPointer* std::__uninitialized_copy::uninitialized_copy(readPointer*, readPointer*, readPointer*) [738] ----------------------------------------------- 0.00 0.00 13129/13129 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] [748] 0.0 0.00 0.00 13129 __gnu_cxx::__normal_iterator > >::__normal_iterator(Vote const* const&) [748] ----------------------------------------------- 0.00 0.00 13129/13129 std::_Vector_base >::_M_allocate(unsigned int) [539] [749] 0.0 0.00 0.00 13129 std::allocator::allocator() [749] ----------------------------------------------- 13129 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [145] [750] 0.0 0.00 0.00 13129 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Rb_tree_impl, false>::_Rb_tree_impl() [750] 0.00 0.00 12533/13130 __gnu_cxx::new_allocator::deallocate(SeededRead**, unsigned int) [744] 20071 std::allocator::~allocator() [739] ----------------------------------------------- 0.00 0.00 13129/13129 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] [751] 0.0 0.00 0.00 13129 void std::_Destroy(Vote*, Vote*) [751] ----------------------------------------------- 0.00 0.00 12334/12334 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [199] [752] 0.0 0.00 0.00 12334 void std::__insertion_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [752] ----------------------------------------------- 0.00 0.00 12334/12334 std::allocator::~allocator() [1175] [753] 0.0 0.00 0.00 12334 Contig* std::uninitialized_copy(Contig*, Contig*, Contig*) [753] 0.00 0.00 12334/2357247 std::pair* std::__copy_move::__copy_m*, std::pair*>(std::pair*, std::pair*, std::pair*) [689] ----------------------------------------------- 0.00 0.00 12334/12334 void std::__unguarded_insertion_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [1514] [754] 0.0 0.00 0.00 12334 void std::_Destroy<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [754] ----------------------------------------------- 0.00 0.00 7737/7737 std::vector, std::allocator > >::push_back(std::pair const&) [265] [755] 0.0 0.00 0.00 7737 __static_initialization_and_destruction_0(int, int) [755] ----------------------------------------------- 7737 std::_Vector_base >::_Vector_impl::_Vector_impl(std::allocator const&) [404] [756] 0.0 0.00 0.00 7737 std::_Deque_base >::_M_deallocate_node(SeededRead*) [756] 7737 std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [726] ----------------------------------------------- 0.00 0.00 7737/7737 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [145] [757] 0.0 0.00 0.00 7737 Vote* std::uninitialized_copy<__gnu_cxx::__normal_iterator > >, Vote*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, Vote*) [757] ----------------------------------------------- 2 __gnu_cxx::new_allocator::deallocate(int*, unsigned int) [796] 4 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [766] 28 std::_Deque_iterator std::__uninitialized_copy::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [767] 46 std::deque >::_M_push_back_aux(SeededRead const&) [770] 596 std::_Deque_base >::_M_allocate_map(unsigned int) [731] 596 std::_Deque_base >::_M_create_nodes(SeededRead**, SeededRead**) [728] 0.00 0.00 1/2099102434 std::_List_base, std::allocator > >::~_List_base() [655] 0.00 0.00 1/2099102434 std::list, std::allocator > >::_M_insert(std::_List_iterator >, std::pair const&) [643] 0.00 0.00 2/2099102434 int* std::__uninitialized_copy_a(int*, int*, int*, std::allocator&) [647] 0.00 0.00 4/2099102434 std::_Vector_base >::_Vector_impl::_Vector_impl() [624] 0.00 0.00 4/2099102434 std::allocator::~allocator() [623] 0.00 0.00 20/2099102434 TrieNode::constructTrie() [609] 0.00 0.00 596/2099102434 std::_Deque_iterator::_Deque_iterator() [596] 0.00 0.00 596/2099102434 std::_Deque_base >::_Deque_impl::_Deque_impl(std::allocator const&) [594] [758] 0.0 0.00 0.00 2496 std::deque >::_M_reallocate_map(unsigned int, bool) [758] 2418 bool std::operator!=(std::_Deque_iterator const&, std::_Deque_iterator const&) [759] 600 Contig::~Contig() [53] 56 SeededRead** std::__copy_move_a(SeededRead**, SeededRead**, SeededRead**) [765] 28 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [766] 6 SeededRead** std::__copy_move_backward_a(SeededRead**, SeededRead**, SeededRead**) [776] 4 std::_Deque_iterator std::__uninitialized_copy::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [767] 2 int* std::__copy_move_a(int*, int*, int*) [809] ----------------------------------------------- 2418 std::deque >::_M_reallocate_map(unsigned int, bool) [758] 0.00 0.00 1/2099102434 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::operator[](unsigned int) [662] [759] 0.0 0.00 0.00 2419 bool std::operator!=(std::_Deque_iterator const&, std::_Deque_iterator const&) [759] 1818 Contig::~Contig() [53] ----------------------------------------------- 596 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_destroy_node(std::_Rb_tree_node >*) [406] [760] 0.0 0.00 0.00 596 std::_Deque_iterator::difference_type std::operator-(std::_Deque_iterator const&, std::_Deque_iterator const&) [760] 1192 std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [405] ----------------------------------------------- 22 ShortyString::ReverseComplement() const [763] 25 ShortyString::RepresentativeVotes() const [768] 45 ShortyString::Print() const [764] 176 ShortyString::GetConfidentClone() const [332] 0.00 0.00 2/2099102434 ShortyString::operator==(ShortyString const&) const [619] 0.00 0.00 22/2099102434 ShortyString::PrintScores(std::ostream&) const [607] 0.00 0.00 22/2099102434 ShortyString::ReadVotesFromFile(std::istream&) [610] [761] 0.0 0.00 0.00 314 ShortyString::operator+(ShortyString const&) [761] 201 ShortyString::operator+(std::string const&) [762] 22 ShortyString::ReverseComplement() const [763] ----------------------------------------------- 177 ShortyString::operator+(std::string const&) [762] 111 ShortyString::ReverseComplement() const [763] 201 ShortyString::operator+(ShortyString const&) [761] [762] 0.0 0.00 0.00 312+177 ShortyString::operator+(std::string const&) [762] 111 ShortyString::operator+=(ShortyString const&) [334] 177 ShortyString::operator+(std::string const&) [762] ----------------------------------------------- 22 ShortyString::ReverseComplement() const [763] 22 ShortyString::operator+(ShortyString const&) [761] 132 ShortyString::GetConfidentClone() const [332] 0.00 0.00 1/2099102434 ShortyString::operator==(ShortyString const&) const [619] 0.00 0.00 22/2099102434 ShortyString::GetMaxVote() const [608] 0.00 0.00 22/2099102434 ShortyString::PrintScores(std::ostream&) const [607] [763] 0.0 0.00 0.00 199+22 ShortyString::ReverseComplement() const [763] 111 ShortyString::operator+(std::string const&) [762] 88 ShortyString::ShortyString(std::string const&, int) [366] 22 std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [151] 22 ShortyString::operator+(ShortyString const&) [761] 22 ShortyString::ReverseComplement() const [763] ----------------------------------------------- 1 ShortyString::push_back(char) [794] 0.00 0.00 22/2099102434 ShortyString::GetMaxVote() const [608] 0.00 0.00 44/2099102434 ShortyString::PrintScores(std::ostream&) const [607] 0.00 0.00 66/2099102434 ShortyString::substr(int, int) const [606] [764] 0.0 0.00 0.00 133 ShortyString::Print() const [764] 66 ShortyString::~ShortyString() [34] 45 ShortyString::operator+(ShortyString const&) [761] 22 std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [151] ----------------------------------------------- 56 std::deque >::_M_reallocate_map(unsigned int, bool) [758] [765] 0.0 0.00 0.00 56 SeededRead** std::__copy_move_a(SeededRead**, SeededRead**, SeededRead**) [765] 28 TrieNode::searchWithErrorAllowed(std::string const&, int, int) [367] ----------------------------------------------- 4 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] 28 std::deque >::_M_reallocate_map(unsigned int, bool) [758] [766] 0.0 0.00 0.00 32 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [766] 4 std::deque >::_M_reallocate_map(unsigned int, bool) [758] ----------------------------------------------- 1 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::resize(unsigned int, std::list, std::allocator > >) [788] 4 std::_Deque_iterator::operator--() [804] 4 std::deque >::_M_reallocate_map(unsigned int, bool) [758] 5 std::deque >::_M_pop_back_aux() [786] 0.00 0.00 2/2099102434 std::_Deque_iterator::operator*() const [639] 0.00 0.00 4/2099102434 std::_Vector_base, std::allocator > >::_M_deallocate(triple*, unsigned int) [626] 0.00 0.00 10/2099102434 TrieNode::addPairReadToTrie(int) [611] [767] 0.0 0.00 0.00 30 std::_Deque_iterator std::__uninitialized_copy::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [767] 28 std::deque >::_M_reallocate_map(unsigned int, bool) [758] 17 mar_types* std::__copy_move_a2(mar_types*, mar_types*, mar_types*) [771] ----------------------------------------------- 1 ShortyString::push_back(char) [794] 4 ShortyString::~ShortyString() [791] 22 ShortyString::GetConfidentClone() const [332] [768] 0.0 0.00 0.00 27 ShortyString::RepresentativeVotes() const [768] 25 ShortyString::operator+(ShortyString const&) [761] ----------------------------------------------- 22 ShortyString::ShortyString(std::string const&, int) [366] [769] 0.0 0.00 0.00 22 ShortyString::reverse() [769] 1208491 Contig::~Contig() [53] ----------------------------------------------- 8 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] 0.00 0.00 10/2099102434 TrieNode::constructTrie() [609] [770] 0.0 0.00 0.00 18 std::deque >::_M_push_back_aux(SeededRead const&) [770] 46 std::deque >::_M_reallocate_map(unsigned int, bool) [758] ----------------------------------------------- 17 std::_Deque_iterator std::__uninitialized_copy::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [767] [771] 0.0 0.00 0.00 17 mar_types* std::__copy_move_a2(mar_types*, mar_types*, mar_types*) [771] 14 TrieNode::searchWithErrorAllowed(std::string const&, int, int) [367] ----------------------------------------------- 1 UtilsString::Complement(std::string const&) [772] 0.00 0.00 1/14 _fini [4] 0.00 0.00 6/14 UtilsMath::median_event_point* std::__copy_move::__copy_m(UtilsMath::median_event_point const*, UtilsMath::median_event_point const*, UtilsMath::median_event_point*) [1190] 0.00 0.00 7/14 UtilsMath::median_event_point* std::__copy_move_a(UtilsMath::median_event_point*, UtilsMath::median_event_point*, UtilsMath::median_event_point*) [775] [772] 0.0 0.00 0.00 14+1 UtilsString::Complement(std::string const&) [772] 1 UtilsString::Complement(std::string const&) [772] ----------------------------------------------- 4 void std::_Destroy >(std::_Deque_iterator, std::_Deque_iterator) [724] 0.00 0.00 2/2099102434 std::_Deque_iterator::operator++() [630] 0.00 0.00 4/2099102434 std::_Deque_iterator::operator++() [620] [773] 0.0 0.00 0.00 10 TrieNode::TrieNode() [773] 4 TrieNode::searchWithErrorAllowed(std::string const&, int, int) [367] ----------------------------------------------- 0.00 0.00 1/7 Assembler::~Assembler() [901] 0.00 0.00 1/7 std::_List_const_iterator >::operator->() const [1106] 0.00 0.00 1/7 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::size() const [654] 0.00 0.00 2/7 std::_Vector_base >::_Vector_impl::_Vector_impl() [656] 0.00 0.00 2/7 std::list, std::allocator > >::push_back(std::pair const&) [659] [774] 0.0 0.00 0.00 7 std::vector >::operator[](unsigned int) [774] ----------------------------------------------- 0.00 0.00 1/7 Assembler::Assembler(std::vector > const&, ReadProcessor*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*) [616] 0.00 0.00 1/7 PrintConfigInfo() [601] 0.00 0.00 1/7 __static_initialization_and_destruction_0(int, int) [602] 0.00 0.00 1/7 __gnu_cxx::__normal_iterator std::transform<__gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator, int (*)(int)>(__gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator, int (*)(int)) [604] 0.00 0.00 1/7 std::_Vector_base >::~_Vector_base() [603] 0.00 0.00 1/7 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, SeededRead const&) [600] 0.00 0.00 1/7 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [924] [775] 0.0 0.00 0.00 7 UtilsMath::median_event_point* std::__copy_move_a(UtilsMath::median_event_point*, UtilsMath::median_event_point*, UtilsMath::median_event_point*) [775] 0.00 0.00 7/14 UtilsString::Complement(std::string const&) [772] ----------------------------------------------- 6 std::deque >::_M_reallocate_map(unsigned int, bool) [758] [776] 0.0 0.00 0.00 6 SeededRead** std::__copy_move_backward_a(SeededRead**, SeededRead**, SeededRead**) [776] 6 TrieNode::searchWithErrorAllowed(std::string const&, int, int) [367] ----------------------------------------------- 0.00 0.00 1/5 Hash::Insert(std::string const&, int, int, int, int) [220] 0.00 0.00 4/5 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] [777] 0.0 0.00 0.00 5 __gnu_cxx::new_allocator::destroy(SeededRead*) [777] ----------------------------------------------- 0.00 0.00 1/5 Assembler::Assemble() [474] 0.00 0.00 1/5 __gnu_cxx::__normal_iterator > >::operator*() const [1053] 0.00 0.00 1/5 RawRead::RawRead(int, int, int, int, int) [894] 0.00 0.00 2/5 SeededRead* std::copy_backward(SeededRead*, SeededRead*, SeededRead*) [1429] [778] 0.0 0.00 0.00 5 void std::__push_heap<__gnu_cxx::__normal_iterator > >, int, UtilsMath::median_event_point>(__gnu_cxx::__normal_iterator > >, int, int, UtilsMath::median_event_point) [778] ----------------------------------------------- 0.00 0.00 4/4 std::_Deque_iterator::operator++() [620] [779] 0.0 0.00 0.00 4 TrieNode::TrieNode() [779] ----------------------------------------------- 0.00 0.00 2/4 std::vector >::size() const [1127] 0.00 0.00 2/4 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [631] [780] 0.0 0.00 0.00 4 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [780] ----------------------------------------------- 0.00 0.00 4/4 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] [781] 0.0 0.00 0.00 4 __gnu_cxx::new_allocator::construct(SeededRead*, SeededRead const&) [781] ----------------------------------------------- 2 std::vector >::operator=(std::vector > const&) [88] 0.00 0.00 2/2099102434 Assembler::Assembler(std::vector > const&, ReadProcessor*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*) [616] [782] 0.0 0.00 0.00 4 std::vector, std::allocator > >::end() const [782] 8 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] ----------------------------------------------- 2 std::allocator > >::~allocator() [800] 0.00 0.00 1/2099102434 std::_List_const_iterator >::operator++() [651] 0.00 0.00 1/2099102434 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::size() const [654] [783] 0.0 0.00 0.00 4 std::_List_base, std::allocator > >::_M_clear() [783] 0.00 0.00 2/4 std::_List_base, std::allocator > >::_List_base(std::allocator > const&) [784] 2 TrieNode::addToTrie(myList*, int) [330] ----------------------------------------------- 0.00 0.00 2/4 std::_List_base, std::allocator > >::_M_clear() [783] 0.00 0.00 2/4 std::allocator >::allocator > >(std::allocator > > const&) [1171] [784] 0.0 0.00 0.00 4 std::_List_base, std::allocator > >::_List_base(std::allocator > const&) [784] ----------------------------------------------- 0.00 0.00 4/4 std::_Vector_base >::_Vector_impl::_Vector_impl() [624] [785] 0.0 0.00 0.00 4 std::__niter_base*, false>::__b(std::pair*) [785] ----------------------------------------------- 2 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] 0.00 0.00 2/2099102434 mar_types* std::__copy_move_backward_a2(mar_types*, mar_types*, mar_types*) [634] [786] 0.0 0.00 0.00 4 std::deque >::_M_pop_back_aux() [786] 5 std::_Deque_iterator std::__uninitialized_copy::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [767] 4 Contig::~Contig() [53] 4 std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [151] ----------------------------------------------- 2 std::_Vector_base, std::allocator > >::~_Vector_base() [732] 0.00 0.00 2/2099102434 __gnu_cxx::new_allocator::construct(int*, int const&) [621] [787] 0.0 0.00 0.00 4 std::deque >::pop_back() [787] 0.00 0.00 2/2 std::__niter_base<__gnu_cxx::__normal_iterator > >, true>::__b(__gnu_cxx::__normal_iterator > >) [803] 2 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [795] ----------------------------------------------- 2 Hash::Insert(std::string const&, int, int, int, int) [220] 0.00 0.00 1/2099102434 Hash::Insert(std::string const&, int, int, int) [591] 0.00 0.00 1/2099102434 std::list, std::allocator > >::list(std::list, std::allocator > > const&) [660] [788] 0.0 0.00 0.00 4 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::resize(unsigned int, std::list, std::allocator > >) [788] 1 std::allocator > >::~allocator() [800] 1 std::_Deque_iterator std::__uninitialized_copy::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [767] ----------------------------------------------- 2 std::_Vector_base, std::allocator > >::~_Vector_base() [732] 0.00 0.00 2/2099102434 std::vector >::_M_check_len(unsigned int, char const*) const [615] [789] 0.0 0.00 0.00 4 Vote* std::__copy_move_a(Vote const*, Vote const*, Vote*) [789] 2 mar_types* std::__copy_move_backward::__copy_move_b(mar_types const*, mar_types const*, mar_types*) [411] ----------------------------------------------- 0.00 0.00 1/4 std::_List_base, std::allocator > >::~_List_base() [655] 0.00 0.00 1/4 std::list, std::allocator > >::_M_insert(std::_List_iterator >, std::pair const&) [643] 0.00 0.00 2/4 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::~vector() [674] [790] 0.0 0.00 0.00 4 void std::_Destroy, std::allocator > >*, std::list, std::allocator > > >(std::list, std::allocator > >*, std::list, std::allocator > >*, std::allocator, std::allocator > > >&) [790] ----------------------------------------------- 1 ShortyString::ShortyString(std::string const&, int) [7] 1 ShortyString::push_back(char) [794] 0.00 0.00 1/2099102434 ShortyString::operator==(ShortyString const&) const [619] [791] 0.0 0.00 0.00 3 ShortyString::~ShortyString() [791] 4 ShortyString::RepresentativeVotes() const [768] 1 ShortyString::~ShortyString() [34] ----------------------------------------------- 0.00 0.00 1/3 PrintConfigInfo() [601] 0.00 0.00 1/3 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, SeededRead const&) [600] 0.00 0.00 1/3 std::vector >::end() [617] [792] 0.0 0.00 0.00 3 Hash::Hash(int) [792] ----------------------------------------------- 1 _fini [4] 0.00 0.00 1/2099102434 std::_Vector_base >::_Vector_impl::_Vector_impl() [656] 0.00 0.00 1/2099102434 Hash::HashVal(std::string const&, int) const [652] [793] 0.0 0.00 0.00 3 Hash::LeftShiftHashVal(char, char, int) const [793] 0.00 0.00 1/1 Hash::~Hash() [811] 1 std::vector >::~vector() [208] 1 Hash::Insert(std::string const&, int, int, int, int) [220] ----------------------------------------------- 1 ShortyString::ShortyString(std::string const&, int) [7] 0.00 0.00 1/2099102434 ShortyString::operator==(ShortyString const&) const [619] [794] 0.0 0.00 0.00 2 ShortyString::push_back(char) [794] 1 ShortyString::RepresentativeVotes() const [768] 1 ShortyString::Print() const [764] 1 ShortyString::~ShortyString() [791] ----------------------------------------------- 2 std::deque >::pop_back() [787] [795] 0.0 0.00 0.00 2 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [795] 2 int* std::__copy_move_backward::__copy_move_b(int const*, int const*, int*) [805] 2 mar_types* std::__copy_move_backward::__copy_move_b(mar_types const*, mar_types const*, mar_types*) [411] ----------------------------------------------- 2 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] [796] 0.0 0.00 0.00 2 __gnu_cxx::new_allocator::deallocate(int*, unsigned int) [796] 2 std::deque >::_M_reallocate_map(unsigned int, bool) [758] ----------------------------------------------- 0.00 0.00 2/2 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] [797] 0.0 0.00 0.00 2 __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >::__normal_iterator(std::pair const* const&) [797] ----------------------------------------------- 0.00 0.00 2/2 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] [798] 0.0 0.00 0.00 2 std::vector >::max_size() const [798] ----------------------------------------------- 0.00 0.00 2/2 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] [799] 0.0 0.00 0.00 2 std::vector >::_M_check_len(unsigned int, char const*) const [799] ----------------------------------------------- 1 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::resize(unsigned int, std::list, std::allocator > >) [788] 0.00 0.00 1/2099102434 std::_Vector_base, std::allocator > >, std::allocator, std::allocator > > > >::_Vector_base() [658] [800] 0.0 0.00 0.00 2 std::allocator > >::~allocator() [800] 2 std::_List_base, std::allocator > >::_M_clear() [783] ----------------------------------------------- 0.00 0.00 2/2 int* std::__uninitialized_move_a >(int*, int*, int*, std::allocator&) [1497] [801] 0.0 0.00 0.00 2 std::allocator::allocator() [801] ----------------------------------------------- 0.00 0.00 1/2 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::~vector() [674] 0.00 0.00 1/2 std::_List_base, std::allocator > >::_List_impl::~_List_impl() [1179] [802] 0.0 0.00 0.00 2 std::_List_base, std::allocator > >::_List_base() [802] ----------------------------------------------- 0.00 0.00 2/2 std::deque >::pop_back() [787] [803] 0.0 0.00 0.00 2 std::__niter_base<__gnu_cxx::__normal_iterator > >, true>::__b(__gnu_cxx::__normal_iterator > >) [803] ----------------------------------------------- 2 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] [804] 0.0 0.00 0.00 2 std::_Deque_iterator::operator--() [804] 4 std::_Deque_iterator std::__uninitialized_copy::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [767] ----------------------------------------------- 2 __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [795] [805] 0.0 0.00 0.00 2 int* std::__copy_move_backward::__copy_move_b(int const*, int const*, int*) [805] 2 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] ----------------------------------------------- 0.00 0.00 2/2 std::list, std::allocator > >::begin() const [1113] [806] 0.0 0.00 0.00 2 void std::list, std::allocator > >::_M_initialize_dispatch > >(std::_List_const_iterator >, std::_List_const_iterator >, std::__false_type) [806] ----------------------------------------------- 0.00 0.00 1/2 Assembler::Assemble() [474] 0.00 0.00 1/2 Assembler::ProcessNewSeeds() [38] [807] 0.0 0.00 0.00 2 std::stack > >::push(SeededRead const&) [807] ----------------------------------------------- 0.00 0.00 2/2 __gnu_cxx::new_allocator::destroy(int*) [975] [808] 0.0 0.00 0.00 2 std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Rb_tree_impl, false>::_M_initialize() [808] ----------------------------------------------- 2 std::deque >::_M_reallocate_map(unsigned int, bool) [758] [809] 0.0 0.00 0.00 2 int* std::__copy_move_a(int*, int*, int*) [809] 2 TrieNode::searchWithErrorAllowed(std::string const&, int, int) [367] ----------------------------------------------- 0.00 0.00 2/2 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [385] [810] 0.0 0.00 0.00 2 mar_types* std::__uninitialized_move_a >(mar_types*, mar_types*, mar_types*, std::allocator&) [810] ----------------------------------------------- 0.00 0.00 1/1 Hash::LeftShiftHashVal(char, char, int) const [793] [811] 0.0 0.00 0.00 1 Hash::~Hash() [811] ----------------------------------------------- 1 Contig::~Contig() [53] [812] 0.0 0.00 0.00 1 Cluster::Cluster() [812] 7737 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [145] 7737 OverlapGraph::Traverse(int, int, int, int) [245] ----------------------------------------------- 0.00 0.00 1/1 Assembler::Assembler(std::vector > const&, ReadProcessor*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*) [616] [813] 0.0 0.00 0.00 1 __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >::operator++() [813] ----------------------------------------------- 0.00 0.00 1/1 operator>>(std::istream&, ShortyString&) [827] [814] 0.0 0.00 0.00 1 ShortyString::operator[](int) const [814] ----------------------------------------------- 1 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::_M_check_len(unsigned int, char const*) const [815] 0.00 0.00 1/1 _fini [4] [815] 0.0 0.00 0.00 1+1 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::_M_check_len(unsigned int, char const*) const [815] 1 std::vector, std::allocator > >, std::allocator, std::allocator > > > >::_M_check_len(unsigned int, char const*) const [815] ----------------------------------------------- 0.00 0.00 1/1 _fini [4] [816] 0.0 0.00 0.00 1 std::vector, std::allocator > >::max_size() const [816] 0.00 0.00 1/1 std::allocator >::allocator() [817] ----------------------------------------------- 0.00 0.00 1/1 std::vector, std::allocator > >::max_size() const [816] [817] 0.0 0.00 0.00 1 std::allocator >::allocator() [817] ----------------------------------------------- 0.00 0.00 1/1 std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, SeededRead const&) [600] [818] 0.0 0.00 0.00 1 std::_Vector_base >::_M_allocate(unsigned int) [818] ----------------------------------------------- 0.00 0.00 1/1 std::_Vector_base >::_M_deallocate(UtilsMath::median_event_point*, unsigned int) [820] [819] 0.0 0.00 0.00 1 std::_Vector_base >::_Vector_impl::_Vector_impl() [819] ----------------------------------------------- 0.00 0.00 1/1 _fini [4] [820] 0.0 0.00 0.00 1 std::_Vector_base >::_M_deallocate(UtilsMath::median_event_point*, unsigned int) [820] 0.00 0.00 1/1 std::_Vector_base >::_Vector_impl::_Vector_impl() [819] ----------------------------------------------- 0.00 0.00 1/1 __static_initialization_and_destruction_0(int, int) [649] [821] 0.0 0.00 0.00 1 std::_Vector_base, std::allocator > >, std::allocator, std::allocator > > > >::_Vector_impl::~_Vector_impl() [821] ----------------------------------------------- 0.00 0.00 1/1 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] [822] 0.0 0.00 0.00 1 std::_Vector_base, std::allocator > >::_M_allocate(unsigned int) [822] 0.00 0.00 1/1 std::_Deque_iterator::_S_buffer_size() [824] ----------------------------------------------- 0.00 0.00 1/1 SeededRead* std::__copy_move_backward::__copy_move_b(SeededRead*, SeededRead*, SeededRead*) [1313] [823] 0.0 0.00 0.00 1 std::__niter_base::__b(short*) [823] ----------------------------------------------- 0.00 0.00 1/1 std::_Vector_base, std::allocator > >::_M_allocate(unsigned int) [822] [824] 0.0 0.00 0.00 1 std::_Deque_iterator::_S_buffer_size() [824] 0.00 0.00 1/1 int* std::__copy_move_a2(int*, int*, int*) [826] ----------------------------------------------- 1 std::vector, std::allocator > >::~vector() [825] 1 std::vector >::operator=(std::vector > const&) [88] [825] 0.0 0.00 0.00 1+1 std::vector, std::allocator > >::~vector() [825] 3 std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [484] 1 std::vector, std::allocator > >::~vector() [825] ----------------------------------------------- 0.00 0.00 1/1 std::_Deque_iterator::_S_buffer_size() [824] [826] 0.0 0.00 0.00 1 int* std::__copy_move_a2(int*, int*, int*) [826] ----------------------------------------------- 0.00 0.00 1/1 _fini [4] [827] 0.0 0.00 0.00 1 operator>>(std::istream&, ShortyString&) [827] 0.00 0.00 1/1 ShortyString::operator[](int) const [814] ----------------------------------------------- This table describes the call tree of the program, and was sorted by the total amount of time spent in each function and its children. Each entry in this table consists of several lines. The line with the index number at the left hand margin lists the current function. The lines above it list the functions that called this function, and the lines below it list the functions this one called. This line lists: index A unique number given to each element of the table. Index numbers are sorted numerically. The index number is printed next to every function name so it is easier to look up where the function in the table. % time This is the percentage of the `total' time that was spent in this function and its children. Note that due to different viewpoints, functions excluded by options, etc, these numbers will NOT add up to 100%. self This is the total amount of time spent in this function. children This is the total amount of time propagated into this function by its children. called This is the number of times the function was called. If the function called itself recursively, the number only includes non-recursive calls, and is followed by a `+' and the number of recursive calls. name The name of the current function. The index number is printed after it. If the function is a member of a cycle, the cycle number is printed between the function's name and the index number. For the function's parents, the fields have the following meanings: self This is the amount of time that was propagated directly from the function into this parent. children This is the amount of time that was propagated from the function's children into this parent. called This is the number of times this parent called the function `/' the total number of times the function was called. Recursive calls to the function are not included in the number after the `/'. name This is the name of the parent. The parent's index number is printed after it. If the parent is a member of a cycle, the cycle number is printed between the name and the index number. If the parents of the function cannot be determined, the word `' is printed in the `name' field, and all the other fields are blank. For the function's children, the fields have the following meanings: self This is the amount of time that was propagated directly from the child into the function. children This is the amount of time that was propagated from the child's children to the function. called This is the number of times the function called this child `/' the total number of times the child was called. Recursive calls by the child are not listed in the number after the `/'. name This is the name of the child. The child's index number is printed after it. If the child is a member of a cycle, the cycle number is printed between the name and the index number. If there are any cycles (circles) in the call graph, there is an entry for the cycle-as-a-whole. This entry shows who called the cycle (as parents) and the members of the cycle (as children.) The `+' recursive calls entry shows the number of function calls that were internal to the cycle, and the calls entry for each member shows, for that member, how many times it was called from other members of the cycle. Index by function name [391] global constructors keyed to _ZN12ShortyStringC2Ev (shorty-string.cc) [349] std::vector, std::allocator > >::capacity() const [87] std::vector >::swap(std::vector >&) [520] global constructors keyed to _ZN4Vote7MAX_VALE (vote.cc) [129] std::vector, std::allocator > >::size() const [455] std::vector >::push_back(Vote const&) [341] global constructors keyed to _ZN7RawReadC2Eiiiii (raw-read.cc) [172] std::vector, std::allocator > >::max_size() const [514] std::vector >::vector(std::vector > const&) [521] global constructors keyed to _ZN8TrieNodeC2Ev (compact-trie.cc) [461] std::vector >::size() const [88] std::vector >::operator=(std::vector > const&) [422] GetFirstLine(std::basic_fstream >&, char*) [386] std::vector >::begin() const [428] std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Contig const&) [44] missMatchNumber(std::string, std::string, int, int) [472] std::vector >::capacity() const [446] std::vector >::begin() [26] ReadSeededFastaFile(std::string const&, std::vector >*) [798] std::vector >::max_size() const [323] std::vector >::push_back(Contig const&) [227] __static_initialization_and_destruction_0(int, int) (compact-trie.cc) [3] std::vector >::_M_check_len(unsigned int, char const*) const [629] std::vector >::~vector() [733] __static_initialization_and_destruction_0(int, int) (contig.cc) [195] std::vector >::size() const [774] std::vector >::operator[](unsigned int) [755] __static_initialization_and_destruction_0(int, int) (overlap-graph.cc) [373] std::vector >::max_size() const [12] std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [100] __static_initialization_and_destruction_0(int, int) (read-processor.cc) [423] std::vector >::size() const [50] std::vector, std::allocator > >::_M_fill_insert(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, unsigned int, triple const&) [211] __static_initialization_and_destruction_0(int, int) (raw-read.cc) [815] std::vector, std::allocator > >, std::allocator, std::allocator > > > >::_M_check_len(unsigned int, char const*) const [495] std::vector, std::allocator > >::_M_erase_at_end(triple*) [263] __static_initialization_and_destruction_0(int, int) (shorty-string.cc) [92] std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [196] triple* std::vector, std::allocator > >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > >(unsigned int, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >) [159] __static_initialization_and_destruction_0(int, int) (utils-file.cc) [708] std::vector, std::allocator > >::end() const [511] std::vector, std::allocator > >::end() [252] __static_initialization_and_destruction_0(int, int) (utils-string.cc) [30] std::vector, std::allocator > >::size() const [84] std::vector, std::allocator > >::push_back(triple const&) [62] getIndex(char) [711] std::vector, std::allocator > >::begin() const [825] std::vector, std::allocator > >::~vector() [203] SeededRead::SeededRead(SeededRead const&) [96] std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [389] std::vector, std::allocator > >::operator=(std::vector, std::allocator > > const&) [251] SeededRead::~SeededRead() [816] std::vector, std::allocator > >::max_size() const [199] std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple const&) [772] UtilsString::Complement(std::string const&) [117] std::vector, std::allocator > >::_M_check_len(unsigned int, char const*) const [168] std::vector, std::allocator > >::begin() [670] UtilsString::PrintContig(std::string const&, std::string const&) [213] std::vector, std::allocator > >::end() const [209] std::vector, std::allocator > >::vector() [388] UtilsString::OverlapFromCommonReadMapping(ShortyString const&, ShortyString const&, std::vector, std::allocator > > const&, std::vector, std::allocator > > const&, ReadProcessor const*, int*, int*, ShortyString*) [687] std::vector, std::allocator > >::size() const [142] std::vector, std::allocator > >::~vector() [118] readPointer::stringData() [718] std::vector, std::allocator > >::begin() const [362] std::vector, std::allocator > >::operator[](unsigned int) [160] readPointer::readPointer() [376] std::vector, std::allocator > >::max_size() const [235] std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, RawRead const&) [23] OverlapGraph::BuildGraph() [799] std::vector >::_M_check_len(unsigned int, char const*) const [153] std::vector >::push_back(RawRead const&) [124] OverlapGraph::ContigInfo::ContigInfo(ShortyString const&, int, int, int, mar_types) [592] std::vector >::size() const [496] std::vector >::vector() [40] OverlapGraph::MergeReads(std::vector, std::allocator > > const&) [241] std::vector >::capacity() const [144] std::vector >::operator[](unsigned int) [112] OverlapGraph::AllocateData() [413] std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::get_allocator() const [145] std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, mar_types const&) [245] OverlapGraph::Traverse(int, int, int, int) [282] std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::end() const [152] mar_types* std::vector >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator > > >(unsigned int, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [610] ShortyString::ReadVotesFromFile(std::istream&) [499] std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::begin() const [387] std::vector >::push_back(mar_types const&) [226] ShortyString::Str(std::string const&) [663] std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::get_allocator() const [392] std::vector >::vector() [417] ShortyString::Votes(std::vector > const&) [260] std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_get_Node_allocator() const [281] std::vector >::~vector() [769] ShortyString::reverse() [447] std::_Rb_tree, std::less, std::allocator >::get_allocator() const [60] std::vector >::operator=(std::vector > const&) [794] ShortyString::push_back(char) [178] std::_Rb_tree, std::less, std::allocator >::end() const [6] std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, OverlapGraph::ContigInfo const&) [695] ShortyString::push_back(char, Vote const&) [165] std::_Rb_tree, std::less, std::allocator >::begin() const [258] std::vector >::end() [512] ShortyString::ShortyString(ShortyString const&) [524] std::_Identity >::operator()(std::pair const&) const [85] std::vector >::swap(std::vector >&) [48] ShortyString::ShortyString(std::string const&, std::vector > const&) [466] std::_Identity::operator()(int const&) const [56] std::vector >::begin() [366] ShortyString::ShortyString(std::string const&, int) [749] std::allocator::allocator() [36] std::vector >::push_back(OverlapGraph::ContigInfo const&) [650] ShortyString::ShortyString() [442] std::allocator >::allocator() [222] std::vector >::~vector() [743] ShortyString::ShortyString(std::string const&) [525] std::allocator >::~allocator() [67] std::vector >::operator[](unsigned int) [563] ShortyString::ShortyString(std::string const&, std::vector > const&) [526] std::allocator::allocator(std::allocator const&) [22] std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, UtilsMath::median_event_point const&) [7] ShortyString::ShortyString(std::string const&, int) [692] std::allocator::allocator() [185] std::vector >::begin() [202] ShortyString::ShortyString() [470] std::allocator::allocator() [169] std::vector >::push_back(UtilsMath::median_event_point const&) [791] ShortyString::~ShortyString() [739] std::allocator::~allocator() [335] std::vector >::vector() [34] ShortyString::~ShortyString() [800] std::allocator > >::~allocator() [201] std::vector >::operator[](unsigned int) [407] ShortyString::operator=(std::string const&) [90] std::allocator > >::allocator() [706] std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, std::string const&) [334] ShortyString::operator+=(ShortyString const&) [233] std::allocator >::~allocator() [215] std::vector >::push_back(std::string const&) [333] ShortyString::operator+=(std::string const&) [309] std::allocator >::allocator() [459] std::vector >::operator[](unsigned int) [761] ShortyString::operator+(ShortyString const&) [336] std::allocator >::~allocator() [788] std::vector, std::allocator > >, std::allocator, std::allocator > > > >::resize(unsigned int, std::list, std::allocator > >) [762] ShortyString::operator+(std::string const&) [133] std::allocator >::allocator > >(std::allocator > > const&) [484] std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [59] ReadProcessor::ReadProcessor(std::string const&) [817] std::allocator >::allocator() [25] std::vector, std::allocator > >::_M_erase_at_end(std::pair*) [358] ReadProcessor::ReadProcessor(std::string const&) [363] std::allocator >::allocator() [485] std::vector, std::allocator > >::begin() [727] ReadProcessor::~ReadProcessor() [679] std::allocator >::~allocator() [223] std::vector, std::allocator > >::push_back(std::pair const&) [216] NavidIntIntStruct::NavidIntIntStruct() [801] std::allocator::allocator() [375] std::vector, std::allocator > >::vector() [591] Hash::Insert(std::string const&, int, int, int) [783] std::_List_base, std::allocator > >::_M_clear() [266] std::vector, std::allocator > >::~vector() [220] Hash::Insert(std::string const&, int, int, int, int) [784] std::_List_base, std::allocator > >::_List_base(std::allocator > const&) [57] std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [792] Hash::Hash(int) [802] std::_List_base, std::allocator > >::_List_base() [65] std::vector, std::allocator > >::_M_insert_aux(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair const&) [811] Hash::~Hash() [356] std::_Deque_base >::_Deque_impl::_Deque_impl() [167] std::vector, std::allocator > >::_M_erase_at_end(std::pair*) [175] Trie::Insert(std::string const&, int, mar_types) [731] std::_Deque_base >::_M_allocate_map(unsigned int) [89] std::pair* std::vector, std::allocator > >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > > >(unsigned int, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >) [267] Vote::operator+=(Vote const&) [728] std::_Deque_base >::_M_create_nodes(SeededRead**, SeededRead**) [204] std::vector, std::allocator > >::end() [179] Contig::Add(Contig const&) [262] std::_Deque_base >::_M_allocate_node() [265] std::vector, std::allocator > >::push_back(std::pair const&) [564] Contig::AddRead(int, int, int, mar_types) [693] std::_Deque_base >::_M_destroy_nodes(SeededRead**, SeededRead**) [41] std::vector, std::allocator > >::~vector() [214] Contig::Contig(Contig const&) [552] std::_Deque_base >::_M_deallocate_map(SeededRead**, unsigned int) [42] std::vector, std::allocator > >::operator=(std::vector, std::allocator > > const&) [734] Contig::Contig(bool, int, int, ShortyString const&, int, ReadProcessor const*) [242] std::_Deque_base >::_M_initialize_map(unsigned int) [385] std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, int const&) [53] Contig::~Contig() [756] std::_Deque_base >::_M_deallocate_node(SeededRead*) [143] int* std::vector >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator > > >(unsigned int, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [174] Contig::operator=(Contig const&) [527] std::_Deque_base >::_M_get_Tp_allocator() [538] std::vector >::end() [16] myList::checkString(std::string const&, int, int) [694] std::_Deque_base >::_Deque_base(std::allocator const&, unsigned int) [32] std::vector >::push_back(int const&) [37] myList::size() [703] std::_Deque_base >::_Deque_base() [208] std::vector >::~vector() [224] myList::destruct() [80] std::_Deque_base >::~_Deque_base() [283] std::vector >::operator=(std::vector > const&) [460] myList::addToList(myList*) [52] Vote* std::__copy_move::__copy_m(Vote*, Vote*, Vote*) [344] std::vector >::operator[](unsigned int) [205] myList::myList(readPointer) [164] Vote* std::__copy_move::__copy_m(Vote const*, Vote const*, Vote*) [253] std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, std::pair const&) [228] myList::~myList() [540] std::pair* std::__copy_move::__copy_m const*, std::pair*>(std::pair const*, std::pair const*, std::pair*) [429] std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_put_node(std::_Rb_tree_node >*) [812] Cluster::Cluster() [689] std::pair* std::__copy_move::__copy_m*, std::pair*>(std::pair*, std::pair*, std::pair*) [218] std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree_impl::_M_initialize() [730] TrieNode::destructNode() [717] mar_types* std::__copy_move::__copy_m(mar_types const*, mar_types const*, mar_types*) [139] std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree_impl::_Rb_tree_impl() [691] TrieNode::searchWithError(std::string const&, int) [476] std::char_traits::compare(char const*, char const*, unsigned int) [19] std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_Rb_tree_impl::~_Rb_tree_impl() [367] TrieNode::searchWithErrorAllowed(std::string const&, int, int) [701] void std::_Destroy_aux::__destroy(SeededRead*, SeededRead*) [384] std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_create_node(std::pair const&) [138] TrieNode::searchWithErrorWholeSeed(std::string const&, int, int) [171] void std::_Destroy_aux::__destroy(Contig*, Contig*) [141] std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_destroy_node(std::_Rb_tree_node >*) [312] TrieNode::searchWithErrorAllowedNonRecursive(std::string const&, int) [719] void std::_Destroy_aux::__destroy(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [2] std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_insert_unique(std::pair const&) [298] TrieNode::Insert(int, mar_types) [315] void std::_Destroy_aux::__destroy(std::string*, std::string*) [190] std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_end() [320] TrieNode::Search(std::string const&) [403] void std::_Destroy_aux::__destroy >(std::_Deque_iterator, std::_Deque_iterator) [533] std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_S_key(std::_Rb_tree_node > const*) [102] TrieNode::addToTrie(readPointer, int) [419] void std::_Destroy_aux::__destroy<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [462] std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::_M_erase(std::_Rb_tree_node >*) [330] TrieNode::addToTrie(myList*, int) [556] void std::_Destroy_aux::__destroy*>(triple*, triple*) [8] std::_Rb_tree, std::pair, std::_Identity >, OverlapGraph::IntPairEq, std::allocator > >::~_Rb_tree() [317] TrieNode::traceTrie() [490] void std::_Destroy_aux::__destroy*>(std::pair*, std::pair*) [740] std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_put_node(std::_Rb_tree_node >*) [773] TrieNode::TrieNode() [818] std::_Vector_base >::_M_allocate(unsigned int) [808] std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Rb_tree_impl, false>::_M_initialize() [779] TrieNode::TrieNode() [17] std::_Vector_base >::_M_allocate(unsigned int) [750] std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_Rb_tree_impl, false>::_Rb_tree_impl() [352] TrieNode::~TrieNode() [149] std::_Vector_base >::_Vector_impl::_Vector_impl() [406] std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_destroy_node(std::_Rb_tree_node >*) [21] Assembler::MakeContigs(bool, Cluster const&, SeededRead const&) [180] std::_Vector_base >::_M_deallocate(readPointer*, unsigned int) [534] std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::_M_erase(std::_Rb_tree_node >*) [474] Assembler::Assemble() [404] std::_Vector_base >::_Vector_impl::_Vector_impl(std::allocator const&) [237] std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::~_Rb_tree() [616] Assembler::Assembler(std::vector > const&, ReadProcessor*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*, std::basic_fstream >*) [354] std::_Vector_base >::_M_deallocate(Vote*, unsigned int) [93] std::_Rb_tree, std::less, std::allocator >::_M_insert_(std::_Rb_tree_node_base const*, std::_Rb_tree_node_base const*, int const&) [58] UtilsFile::Log(std::ostream*, std::string const&) [382] std::_Vector_base >::_M_allocate(unsigned int) [311] std::_Rb_tree, std::less, std::allocator >::_M_put_node(std::_Rb_tree_node*) [54] UtilsFile::OpenFile(std::string const&, std::string const&) [473] std::_Vector_base >::~_Vector_base() [710] std::_Rb_tree, std::less, std::allocator >::_Rb_tree_impl, false>::_M_initialize() [20] UtilsFile::CloseFile(std::basic_fstream >*) [308] std::_Vector_base, std::allocator > >::_Vector_impl::_Vector_impl() [287] std::_Rb_tree, std::less, std::allocator >::_Rb_tree_impl, false>::~_Rb_tree_impl() [9] UtilsMath::MedianOfIntervals(std::vector, std::allocator > > const&, int*, int*) [716] std::_Vector_base, std::allocator > >::_M_get_Tp_allocator() [370] std::_Rb_tree, std::less, std::allocator >::_M_create_node(int const&) [777] __gnu_cxx::new_allocator::destroy(SeededRead*) [732] std::_Vector_base, std::allocator > >::~_Vector_base() [184] std::_Rb_tree, std::less, std::allocator >::_M_destroy_node(std::_Rb_tree_node*) [780] __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [688] std::_Vector_base, std::allocator > >::_M_allocate(unsigned int) [75] std::_Rb_tree, std::less, std::allocator >::_M_insert_unique(int const&) [781] __gnu_cxx::new_allocator::construct(SeededRead*, SeededRead const&) [186] std::_Vector_base, std::allocator > >::_Vector_impl::_Vector_impl() [212] std::_Rb_tree, std::less, std::allocator >::begin() [368] __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [451] std::_Vector_base, std::allocator > >::_Vector_base() [420] std::_Rb_tree, std::less, std::allocator >::_M_end() [795] __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [348] std::_Vector_base, std::allocator > >::~_Vector_base() [137] std::_Rb_tree, std::less, std::allocator >::_S_key(std::_Rb_tree_node const*) [293] __gnu_cxx::new_allocator::new_allocator(__gnu_cxx::new_allocator const&) [324] std::_Vector_base >::_Vector_impl::_Vector_impl() [230] std::_Rb_tree, std::less, std::allocator >::_M_erase(std::_Rb_tree_node*) [177] __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [454] std::_Vector_base >::_Vector_impl::~_Vector_impl() [535] std::_Rb_tree, std::less, std::allocator >::_S_right(std::_Rb_tree_node_base*) [268] __gnu_cxx::new_allocator::construct(Contig*, Contig const&) [741] std::_Vector_base >::_M_deallocate(mar_types*, unsigned int) [82] std::_Rb_tree, std::less, std::allocator >::_S_value(std::_Rb_tree_node const*) [700] __gnu_cxx::new_allocator::~new_allocator() [294] std::_Vector_base >::_M_get_Tp_allocator() [13] std::_Rb_tree, std::less, std::allocator >::~_Rb_tree() [24] __gnu_cxx::new_allocator >::construct(triple*, triple const&) [437] std::_Vector_base >::_Vector_base(unsigned int, std::allocator const&) [147] void std::__push_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [110] __gnu_cxx::new_allocator >::deallocate(triple*, unsigned int) [329] std::_Vector_base >::_Vector_base() [778] void std::__push_heap<__gnu_cxx::__normal_iterator > >, int, UtilsMath::median_event_point>(__gnu_cxx::__normal_iterator > >, int, int, UtilsMath::median_event_point) [33] __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [68] std::_Vector_base >::~_Vector_base() [135] void std::partial_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [475] __gnu_cxx::new_allocator >::construct(triple*, triple const&) [183] std::_Vector_base >::_Vector_impl::_Vector_impl() [121] void std::__adjust_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, int, triple, OverlapGraph::SortAdj) [553] __gnu_cxx::new_allocator >::~new_allocator() [194] std::_Vector_base >::~_Vector_base() [742] Vote* std::__copy_move_a(Vote*, Vote*, Vote*) [631] __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [819] std::_Vector_base >::_Vector_impl::_Vector_impl() [633] mar_types* std::__copy_move_a(mar_types*, mar_types*, mar_types*) [735] __gnu_cxx::new_allocator::construct(mar_types*, mar_types const&) [820] std::_Vector_base >::_M_deallocate(UtilsMath::median_event_point*, unsigned int) [789] Vote* std::__copy_move_a(Vote const*, Vote const*, Vote*) [219] __gnu_cxx::new_allocator::destroy(OverlapGraph::ContigInfo*) [379] std::_Vector_base >::_M_get_Tp_allocator() [104] int* std::__copy_move_a(int const*, int const*, int*) [307] __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [424] std::_Vector_base >::_Vector_base() [775] UtilsMath::median_event_point* std::__copy_move_a(UtilsMath::median_event_point*, UtilsMath::median_event_point*, UtilsMath::median_event_point*) [264] __gnu_cxx::new_allocator::construct(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo const&) [46] std::_Vector_base >::~_Vector_base() [765] SeededRead** std::__copy_move_a(SeededRead**, SeededRead**, SeededRead**) [108] __gnu_cxx::new_allocator::construct(UtilsMath::median_event_point*, UtilsMath::median_event_point const&) [821] std::_Vector_base, std::allocator > >, std::allocator, std::allocator > > > >::_Vector_impl::~_Vector_impl() [809] int* std::__copy_move_a(int*, int*, int*) [744] __gnu_cxx::new_allocator::deallocate(SeededRead**, unsigned int) [669] std::_Vector_base, std::allocator > >, std::allocator, std::allocator > > > >::~_Vector_base() [61] void std::__heap_select<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [415] __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [822] std::_Vector_base, std::allocator > >::_M_allocate(unsigned int) [240] __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy_backward<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [522] __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [187] std::_Vector_base, std::allocator > >::_Vector_impl::_Vector_impl() [498] triple* std::copy_backward*, triple*>(triple*, triple*, triple*) [191] __gnu_cxx::new_allocator::construct(std::string*, std::string const&) [396] std::_Vector_base, std::allocator > >::_Vector_impl::~_Vector_impl() [122] OverlapGraph::ContigInfo* std::copy_backward(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [468] __gnu_cxx::new_allocator > >::deallocate(std::_Rb_tree_node >*, unsigned int) [319] std::_Vector_base, std::allocator > >::_M_deallocate(std::pair*, unsigned int) [680] SeededRead** std::copy_backward(SeededRead**, SeededRead**, SeededRead**) [250] __gnu_cxx::new_allocator > >::new_allocator() [292] std::_Vector_base, std::allocator > >::_M_get_Tp_allocator() [99] std::pair* std::copy_backward*, std::pair*>(std::pair*, std::pair*, std::pair*) [120] __gnu_cxx::new_allocator > >::allocate(unsigned int, void const*) [431] std::_Vector_base, std::allocator > >::_Vector_base() [712] __gnu_cxx::__normal_iterator > > std::__copy_move_a2 > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [725] __gnu_cxx::new_allocator > >::new_allocator() [64] std::_Vector_base, std::allocator > >::~_Vector_base() [95] std::back_insert_iterator > > std::__copy_move_a2 > >, std::back_insert_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::back_insert_iterator > >) [238] __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [150] std::_Vector_base, std::allocator > >::_M_allocate(unsigned int) [394] mar_types* std::__copy_move_a2 > >, mar_types*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*) [697] __gnu_cxx::new_allocator >::deallocate(std::pair*, unsigned int) [528] std::_Vector_base, std::allocator > >::_Vector_impl::_Vector_impl() [720] __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::__copy_move_a2 const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [685] __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [529] std::_Vector_base, std::allocator > >::_Vector_impl::~_Vector_impl() [98] int* std::__copy_move_a2 > >, int*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int*) [425] __gnu_cxx::new_allocator >::construct(std::pair*, std::pair const&) [321] std::_Vector_base, std::allocator > >::_M_deallocate(std::pair*, unsigned int) [714] Vote* std::__copy_move_a2(Vote*, Vote*, Vote*) [369] __gnu_cxx::new_allocator >::~new_allocator() [325] std::_Vector_base, std::allocator > >::~_Vector_base() [771] mar_types* std::__copy_move_a2(mar_types*, mar_types*, mar_types*) [435] __gnu_cxx::new_allocator >::new_allocator() [128] std::_Vector_base >::_Vector_base(unsigned int, std::allocator const&) [119] SeededRead** std::__copy_move_a2(SeededRead**, SeededRead**, SeededRead**) [140] __gnu_cxx::new_allocator >::allocate(unsigned int, void const*) [491] std::__alloc_swap, true>::_S_do_it(std::allocator&, std::allocator&) [826] int* std::__copy_move_a2(int*, int*, int*) [796] __gnu_cxx::new_allocator::deallocate(int*, unsigned int) [803] std::__niter_base<__gnu_cxx::__normal_iterator > >, true>::__b(__gnu_cxx::__normal_iterator > >) [752] void std::__insertion_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [766] __gnu_cxx::new_allocator::allocate(unsigned int, void const*) [492] std::__niter_base<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, true>::__b(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [86] void std::__introsort_loop<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, int, OverlapGraph::SortAdj) [621] __gnu_cxx::new_allocator::construct(int*, int const&) [300] std::__niter_base<__gnu_cxx::__normal_iterator > >, true>::__b(__gnu_cxx::__normal_iterator > >) [35] void std::__introsort_loop<__gnu_cxx::__normal_iterator > >, int>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int) [182] __gnu_cxx::new_allocator::new_allocator() [105] std::__niter_base<__gnu_cxx::__normal_iterator > >, true>::__b(__gnu_cxx::__normal_iterator > >) [757] Vote* std::uninitialized_copy<__gnu_cxx::__normal_iterator > >, Vote*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, Vote*) [554] __gnu_cxx::__normal_iterator > >::__normal_iterator(readPointer* const&) [106] std::__niter_base<__gnu_cxx::__normal_iterator > >, true>::__b(__gnu_cxx::__normal_iterator > >) [364] Vote* std::uninitialized_copy(Vote*, Vote*, Vote*) [678] __gnu_cxx::__normal_iterator > >::__normal_iterator(Contig* const&) [197] std::__niter_base::__b(mar_types*) [753] Contig* std::uninitialized_copy(Contig*, Contig*, Contig*) [166] __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::__normal_iterator(triple* const&) [785] std::__niter_base*, false>::__b(std::pair*) [115] std::pair* std::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [316] __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator--() [467] std::__niter_base*, false>::__b(std::pair*) [590] std::pair* std::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [127] __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator++() [221] std::__niter_base::__b(char*) [288] int* std::uninitialized_copy(int*, int*, int*) [748] __gnu_cxx::__normal_iterator > >::__normal_iterator(Vote const* const&) [530] std::__niter_base::__b(int*) [151] std::_Deque_iterator std::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [797] __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >::__normal_iterator(std::pair const* const&) [823] std::__niter_base::__b(short*) [97] std::iterator_traits<__gnu_cxx::__normal_iterator > > >::iterator_category std::__iterator_category<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > > const&) [813] __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >::operator++() [217] std::_List_iterator >::operator++() [537] __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::__unguarded_partition<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj) [39] __gnu_cxx::__normal_iterator > >::__normal_iterator(OverlapGraph::ContigInfo* const&) [355] std::_Deque_iterator::_M_set_node(SeededRead**) [10] mar_types* std::__copy_move_backward_a(mar_types*, mar_types*, mar_types*) [432] __gnu_cxx::__normal_iterator > >::__normal_iterator(UtilsMath::median_event_point* const&) [682] std::_Deque_iterator::_Deque_iterator(std::_Deque_iterator const&) [776] SeededRead** std::__copy_move_backward_a(SeededRead**, SeededRead**, SeededRead**) [488] __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::__normal_iterator(std::pair* const&) [630] std::_Deque_iterator::operator++() [304] std::pair* std::__copy_move_backward_a*, std::pair*>(std::pair*, std::pair*, std::pair*) [107] bool __gnu_cxx::operator==*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [729] std::_Deque_iterator::_M_set_node(SeededRead**) [328] int* std::__copy_move_backward_a(int*, int*, int*) [289] bool __gnu_cxx::operator== > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [824] std::_Deque_iterator::_S_buffer_size() [71] void std::__final_insertion_sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [244] bool __gnu_cxx::operator< *, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [77] std::_Deque_iterator::_Deque_iterator(std::_Deque_iterator const&) [55] void std::__final_insertion_sort<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [297] __gnu_cxx::__normal_iterator > >::difference_type __gnu_cxx::operator- > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [804] std::_Deque_iterator::operator--() [427] std::pair* std::__uninitialized_copy_a<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*, std::pair >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*, std::allocator >&) [736] __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [620] std::_Deque_iterator::operator++() [378] int* std::__uninitialized_copy_a<__gnu_cxx::__normal_iterator > >, int*, int>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int*, std::allocator&) [501] __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [327] std::_Rb_tree_iterator::_Rb_tree_iterator(std::_Rb_tree_node*) [704] Vote* std::__uninitialized_copy_a(Vote*, Vote*, Vote*, std::allocator&) [66] __gnu_cxx::__normal_iterator > >::difference_type __gnu_cxx::operator- > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [651] std::_List_const_iterator >::operator++() [383] Contig* std::__uninitialized_copy_a(Contig*, Contig*, Contig*, std::allocator&) [399] __gnu_cxx::__normal_iterator > >::difference_type __gnu_cxx::operator- > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [745] readPointer* std::__copy_move_backward::__copy_move_b(readPointer*, readPointer*, readPointer*) [45] triple* std::__uninitialized_copy_a*, triple*, triple >(triple*, triple*, triple*, std::allocator >&) [667] __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [79] Contig* std::__copy_move_backward::__copy_move_b(Contig*, Contig*, Contig*) [436] OverlapGraph::ContigInfo* std::__uninitialized_copy_a(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, std::allocator&) [545] __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [101] triple* std::__copy_move_backward::__copy_move_b*, triple*>(triple*, triple*, triple*) [301] std::pair* std::__uninitialized_copy_a*, std::pair*, std::pair >(std::pair*, std::pair*, std::pair*, std::allocator >&) [148] __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::difference_type __gnu_cxx::operator-*, std::vector, std::allocator > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > const&) [229] RawRead* std::__copy_move_backward::__copy_move_b(RawRead*, RawRead*, RawRead*) [322] std::pair* std::__uninitialized_copy_a*, std::pair*, std::pair >(std::pair*, std::pair*, std::pair*, std::allocator >&) [14] bool __gnu_cxx::operator!= > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [331] OverlapGraph::ContigInfo* std::__copy_move_backward::__copy_move_b(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [51] std::_Deque_iterator std::__uninitialized_copy_a, std::_Deque_iterator, SeededRead>(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator, std::allocator&) [295] bool __gnu_cxx::operator!= > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [285] std::string* std::__copy_move_backward::__copy_move_b(std::string*, std::string*, std::string*) [365] Contig* std::__uninitialized_move_a >(Contig*, Contig*, Contig*, std::allocator&) [116] bool __gnu_cxx::operator!= > >(__gnu_cxx::__normal_iterator > > const&, __gnu_cxx::__normal_iterator > > const&) [726] std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [810] mar_types* std::__uninitialized_move_a >(mar_types*, mar_types*, mar_types*, std::allocator&) [418] OverlapGraph::ContigInfo::size() const [28] std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [113] OverlapGraph::ContigInfo* std::__uninitialized_move_a >(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, std::allocator&) [125] OverlapGraph::SortAdj::operator()(triple const&, triple const&) const [707] std::pair* std::__copy_move_backward::__copy_move_b*, std::pair*>(std::pair*, std::pair*, std::pair*) [192] std::pair* std::__uninitialized_move_a*, std::pair*, std::allocator > >(std::pair*, std::pair*, std::pair*, std::allocator >&) [206] OverlapGraph::IntPairEq::operator()(std::pair const&, std::pair const&) const [411] mar_types* std::__copy_move_backward::__copy_move_b(mar_types const*, mar_types const*, mar_types*) [390] Contig* std::__copy_move_backward_a2(Contig*, Contig*, Contig*) [607] ShortyString::PrintScores(std::ostream&) const [805] int* std::__copy_move_backward::__copy_move_b(int const*, int const*, int*) [158] triple* std::__copy_move_backward_a2*, triple*>(triple*, triple*, triple*) [332] ShortyString::GetConfidentClone() const [612] Vote* std::__uninitialized_copy::uninitialized_copy<__gnu_cxx::__normal_iterator > >, Vote*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, Vote*) [668] RawRead* std::__copy_move_backward_a2(RawRead*, RawRead*, RawRead*) [763] ShortyString::ReverseComplement() const [576] std::pair* std::__uninitialized_copy::uninitialized_copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*>(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, std::pair*) [634] mar_types* std::__copy_move_backward_a2(mar_types*, mar_types*, mar_types*) [768] ShortyString::RepresentativeVotes() const [738] readPointer* std::__uninitialized_copy::uninitialized_copy(readPointer*, readPointer*, readPointer*) [123] OverlapGraph::ContigInfo* std::__copy_move_backward_a2(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [764] ShortyString::Print() const [448] Vote* std::__uninitialized_copy::uninitialized_copy(Vote*, Vote*, Vote*) [72] SeededRead** std::__copy_move_backward_a2(SeededRead**, SeededRead**, SeededRead**) [696] ShortyString::operator==(std::string const&) const [114] Contig* std::__uninitialized_copy::uninitialized_copy(Contig*, Contig*, Contig*) [684] std::pair* std::__copy_move_backward_a2*, std::pair*>(std::pair*, std::pair*, std::pair*) [814] ShortyString::operator[](int) const [161] triple* std::__uninitialized_copy::uninitialized_copy*, triple*>(triple*, triple*, triple*) [156] std::pair* std::__copy_move_backward_a2*, std::pair*>(std::pair*, std::pair*, std::pair*) [489] ShortyString::operator!=(std::string const&) const [249] RawRead* std::__uninitialized_copy::uninitialized_copy(RawRead*, RawRead*, RawRead*) [131] void std::__unguarded_linear_insert<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple, OverlapGraph::SortAdj) [709] ReadProcessor::LocateRead(std::string const&) const [583] OverlapGraph::ContigInfo* std::__uninitialized_copy::uninitialized_copy(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*) [598] std::back_insert_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, std::back_insert_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::back_insert_iterator > >) [310] ReadProcessor::TotalPairs() const [493] std::string* std::__uninitialized_copy::uninitialized_copy(std::string*, std::string*, std::string*) [342] __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [723] ReadProcessor::GetMar(int, mar_types) const [405] std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [136] __gnu_cxx::__normal_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [232] ReadProcessor::GetMarLen(int, mar_types) const [69] std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [155] mar_types* std::copy<__gnu_cxx::__normal_iterator > >, mar_types*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*) [793] Hash::LeftShiftHashVal(char, char, int) const [542] std::pair* std::__uninitialized_copy::uninitialized_copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [109] __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > std::copy<__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [412] Contig::IsGoodSeed(std::basic_fstream >*, Contig const&) const [767] std::_Deque_iterator std::__uninitialized_copy::uninitialized_copy, std::_Deque_iterator >(std::_Deque_iterator, std::_Deque_iterator, std::_Deque_iterator) [346] __gnu_cxx::__normal_iterator > > std::copy<__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [409] Contig::PrintGeoFormat(std::basic_fstream >*) const [130] mar_types* std::__uninitialized_copy::uninitialized_copy<__gnu_cxx::__normal_iterator > >, mar_types*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, mar_types*) [225] int* std::copy<__gnu_cxx::__normal_iterator > >, int*>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, int*) [737] Contig::PrintFastaFormat(std::basic_fstream >*) const [531] std::_Rb_tree_const_iterator::_Rb_tree_const_iterator(std::_Rb_tree_node const*) [257] Vote* std::copy(Vote*, Vote*, Vote*) [408] Contig::PrintContigFormat(std::basic_fstream >*) const [469] std::map, std::allocator > >::map() [76] triple* std::copy*, triple*>(triple*, triple*, triple*) [181] Contig::GetMt(int) const [269] std::set, OverlapGraph::IntPairEq, std::allocator > >::insert(std::pair const&) [256] mar_types* std::copy(mar_types*, mar_types*, mar_types*) [480] Cluster::GetMt(int) const [18] std::set, OverlapGraph::IntPairEq, std::allocator > >::set() [690] SeededRead** std::copy(SeededRead**, SeededRead**, SeededRead**) [271] Cluster::GetGen(int) const [198] std::set, std::allocator >::insert(int const&) [372] std::pair* std::copy*, std::pair*>(std::pair*, std::pair*, std::pair*) [272] Cluster::GetIndex(int) const [449] std::set, std::allocator >::set() [698] int* std::copy(int*, int*, int*) [340] UtilsMath::median_event_point::operator<(UtilsMath::median_event_point const&) const [806] void std::list, std::allocator > >::_M_initialize_dispatch > >(std::_List_const_iterator >, std::_List_const_iterator >, std::__false_type) [193] void std::fill(char*, char*, int const&) [686] __gnu_cxx::new_allocator::max_size() const [188] std::list, std::allocator > >::_M_check_equal_allocators(std::list, std::allocator > >&) [270] void std::sort<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [11] __gnu_cxx::new_allocator::max_size() const [255] std::list, std::allocator > >::begin() [47] void std::sort<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [721] __gnu_cxx::new_allocator::max_size() const [231] std::list, std::allocator > >::_M_erase(std::_List_iterator >) [83] void std::swap >(triple&, triple&) [555] __gnu_cxx::new_allocator::max_size() const [210] std::list, std::allocator > >::operator=(std::list, std::allocator > > const&) [456] void std::swap(Vote*&, Vote*&) [433] __gnu_cxx::new_allocator >::max_size() const [705] std::pair::pair(std::pair const&) [477] void std::reverse<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [248] __gnu_cxx::__normal_iterator > >::base() const [518] std::pair::~pair() [305] void std::reverse<__gnu_cxx::__normal_iterator >(__gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator) [410] __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator+(int const&) const [681] std::pair::operator=(std::pair const&) [94] void std::_Destroy(SeededRead*) [290] __gnu_cxx::__normal_iterator > >::base() const [683] std::pair >, bool>::pair(std::_Rb_tree_iterator > const&, bool const&) [430] void std::_Destroy<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, triple >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::allocator >&) [284] __gnu_cxx::__normal_iterator > >::operator*() const [441] std::pair >, bool>::pair(std::_Rb_tree_const_iterator > const&, bool const&) [350] void std::_Destroy<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::pair >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, std::allocator >&) [715] __gnu_cxx::__normal_iterator const*, std::vector, std::allocator > > >::base() const [273] std::pair, bool>::pair(std::_Rb_tree_const_iterator const&, bool const&) [754] void std::_Destroy<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [523] __gnu_cxx::__normal_iterator > >::base() const [261] std::pair::pair() [414] void std::_Destroy<__gnu_cxx::__normal_iterator > >, int>(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::allocator&) [445] __gnu_cxx::__normal_iterator > >::base() const [70] std::deque >::_M_destroy_data(std::_Deque_iterator, std::_Deque_iterator, std::allocator const&) [751] void std::_Destroy(Vote*, Vote*) [347] __gnu_cxx::__normal_iterator > >::base() const [786] std::deque >::_M_pop_back_aux() [471] void std::_Destroy*, triple >(triple*, triple*, std::allocator >&) [416] __gnu_cxx::__normal_iterator > >::operator*() const [770] std::deque >::_M_push_back_aux(SeededRead const&) [162] void std::_Destroy(mar_types*, mar_types*, std::allocator&) [318] __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::base() const [758] std::deque >::_M_reallocate_map(unsigned int, bool) [234] void std::_Destroy(OverlapGraph::ContigInfo*, OverlapGraph::ContigInfo*, std::allocator&) [163] __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator*() const [397] std::deque >::_M_destroy_data_aux(std::_Deque_iterator, std::_Deque_iterator) [154] void std::_Destroy(UtilsMath::median_event_point*, UtilsMath::median_event_point*, std::allocator&) [126] __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::operator*() const [91] std::deque >::_M_reserve_map_at_back(unsigned int) [790] void std::_Destroy, std::allocator > >*, std::list, std::allocator > > >(std::list, std::allocator > >*, std::list, std::allocator > >*, std::allocator, std::allocator > > >&) [702] std::_Deque_base >::_M_get_Tp_allocator() const [296] std::deque >::end() [450] void std::_Destroy*>(std::pair*, std::pair*) [577] std::_Deque_base >::_M_get_map_allocator() const [299] std::deque >::begin() [29] void std::_Destroy*, std::pair >(std::pair*, std::pair*, std::allocator >&) [338] std::_Vector_base >::_M_get_Tp_allocator() const [787] std::deque >::pop_back() [497] void std::_Destroy*>(std::pair*, std::pair*) [481] std::_Vector_base >::_M_get_Tp_allocator() const [549] std::deque >::push_back(SeededRead const&) [722] void std::_Destroy(int*, int*) [381] std::_List_iterator >::operator*() const [31] std::deque >::deque(std::deque > const&) [724] void std::_Destroy >(std::_Deque_iterator, std::_Deque_iterator) [280] std::_Rb_tree_iterator::operator==(std::_Rb_tree_iterator const&) const [494] std::deque >::deque() [146] __gnu_cxx::__enable_if::__value, void>::__type std::__fill_a(char*, char*, int const&) [377] std::less::operator()(int const&, int const&) const [134] std::deque >::~deque() [400] __gnu_cxx::__enable_if::__value, void>::__type std::__fill_a(int*, int*, int const&) [200] std::list, std::allocator > >::empty() const [453] std::stack > >::pop() [73] void std::__reverse<__gnu_cxx::__normal_iterator > > >(__gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >, std::random_access_iterator_tag) [111] std::deque >::end() const [351] std::stack > >::top() [74] void std::__reverse<__gnu_cxx::__normal_iterator >(__gnu_cxx::__normal_iterator, __gnu_cxx::__normal_iterator, std::random_access_iterator_tag) [434] std::deque >::begin() const [807] std::stack > >::push(SeededRead const&) [236] void std::iter_swap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > > >(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >) [343] std::stack > >::empty() const [395] std::stack > >::stack(std::deque > const&) [103] void std::sort_heap<__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj>(__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, __gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >, OverlapGraph::SortAdj) [505] std::vector >::_M_check_len(unsigned int, char const*) const [5] std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [81] bool std::operator==(std::_Deque_iterator const&, std::_Deque_iterator const&) [443] std::vector >::size() const [746] std::vector >::_M_erase_at_end(readPointer*) [760] std::_Deque_iterator::difference_type std::operator-(std::_Deque_iterator const&, std::_Deque_iterator const&) [401] std::vector >::operator[](unsigned int) const [747] std::vector >::begin() [759] bool std::operator!=(std::_Deque_iterator const&, std::_Deque_iterator const&) [713] std::vector >::_M_check_len(unsigned int, char const*) const [532] std::vector >::insert(__gnu_cxx::__normal_iterator > >, unsigned int, readPointer const&) [247] std::basic_string, std::allocator > std::operator+, std::allocator >(std::basic_string, std::allocator > const&, char const*) [353] std::vector >::end() const [173] std::vector >::vector() [359] operator<<(std::ostream&, ShortyString const&) [303] std::vector >::capacity() const [207] std::vector >::~vector() [827] operator>>(std::istream&, ShortyString&) [43] std::vector >::_M_check_len(unsigned int, char const*) const [49] std::vector >::_M_insert_aux(__gnu_cxx::__normal_iterator > >, Vote const&) [519] operator>>(std::istream&, Vote&) [239] std::vector >::max_size() const [15] std::vector >::_M_fill_insert(__gnu_cxx::__normal_iterator > >, unsigned int, Vote const&) [4] _fini [782] std::vector, std::allocator > >::end() const [254] std::vector >::_M_erase_at_end(Vote*) [78] main [274] std::vector, std::allocator > >::size() const [243] Vote* std::vector >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator > > >(unsigned int, __gnu_cxx::__normal_iterator > >, __gnu_cxx::__normal_iterator > >) [1] [632] std::vector, std::allocator > >::begin() const [699] std::vector >::end()