LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_c_makefile_star2_O1/ramirezsebas[P]TP-LISTINGS/./src/capitulo_4/4.14/condvar.c
// Function: do_work
void do_work(){
	int i;
	for(i = 0; i < TAM; ++i)
		lista_random[i] = rand() % 100;
	clear_thread_flag();
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %r14
pushq %rbx
xorl %ebx, %ebx
leaq 0x2dac(%rip), %r14      # 0x4110
callq 0x1100
cltq
imulq $0x51eb851f, %rax, %rcx # imm = 0x51EB851F
movq %rcx, %rdx
shrq $0x3f, %rdx
sarq $0x25, %rcx
addl %edx, %ecx
imull $0x64, %ecx, %ecx
subl %ecx, %eax
movl %eax, (%rbx,%r14)
addq $0x4, %rbx
cmpq $0x50, %rbx
jne 0x1364
popq %rbx
popq %r14
popq %rbp
jmp 0x1400
// File: /workspace/github_c_makefile_star2_O1/ramirezsebas[P]TP-LISTINGS/./src/capitulo_4/4.14/condvar.c
// Function: set_thread_flag
void set_thread_flag ()
{
	/* Lock the mutex before accessing the flag value. */
	int val = pthread_mutex_trylock (&thread_flag_mutex);
	/* Set the flag value, and then signal in case thread_function is
	blocked, waiting for the flag to become set. However,
	thread_function can’t actually check the flag until the mutex is
	unlocked. */
	thread_flag = 1;
	pthread_cond_signal (&thread_flag_cv);
	/* Unlock the mutex. */
	pthread_mutex_unlock (&thread_flag_mutex);
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %rbx
pushq %rax
leaq 0x2cdc(%rip), %rbx      # 0x40b0
movq %rbx, %rdi
callq 0x1070
movl $0x1, 0x2cf2(%rip)      # 0x40d8
leaq 0x2cf3(%rip), %rdi      # 0x40e0
callq 0x1080
movq %rbx, %rdi
addq $0x8, %rsp
popq %rbx
popq %rbp
jmp 0x10b0
// File: /workspace/github_c_makefile_star2_O1/ramirezsebas[P]TP-LISTINGS/./src/capitulo_4/4.14/condvar.c
// Function: clear_thread_flag
void clear_thread_flag ()
{
	/* Lock the mutex before accessing the flag value. */
	pthread_mutex_trylock (&thread_flag_mutex);
	/* Set the flag value, and then signal in case thread_function is
	blocked, waiting for the flag to become set. However,
	thread_function can’t actually check the flag until the mutex is
	unlocked. */
	thread_flag = 0;
	pthread_cond_signal (&thread_flag_cv);
	/* Unlock the mutex. */
	pthread_mutex_unlock (&thread_flag_mutex);
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %rbx
pushq %rax
leaq 0x2ca3(%rip), %rbx      # 0x40b0
movq %rbx, %rdi
callq 0x1070
movl $0x0, 0x2cb9(%rip)      # 0x40d8
leaq 0x2cba(%rip), %rdi      # 0x40e0
callq 0x1080
movq %rbx, %rdi
addq $0x8, %rsp
popq %rbx
popq %rbp
jmp 0x10b0
// File: /workspace/github_c_makefile_star2_O1/agraf[P]kvmbench/ht.c
// Function: pin_thread
int pin_thread(pthread_t t, int core_id) {
    cpu_set_t cpuset;

    CPU_ZERO(&cpuset);
    CPU_SET(core_id, &cpuset);

    return pthread_setaffinity_np(t, sizeof(cpu_set_t), &cpuset);
}

// Assembly:
subq $0x88, %rsp
xorps %xmm0, %xmm0
movaps %xmm0, 0x70(%rsp)
movaps %xmm0, 0x60(%rsp)
movaps %xmm0, 0x50(%rsp)
movaps %xmm0, 0x40(%rsp)
movaps %xmm0, 0x30(%rsp)
movaps %xmm0, 0x20(%rsp)
movaps %xmm0, 0x10(%rsp)
movaps %xmm0, (%rsp)
cmpl $0x3ff, %esi            # imm = 0x3FF
ja 0x1296
movl $0x1, %eax
movl %esi, %ecx
shlq %cl, %rax
shrl $0x6, %esi
orq %rax, (%rsp,%rsi,8)
movq %rsp, %rdx
movl $0x80, %esi
callq 0x1040
addq $0x88, %rsp
retq
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/./db_construction_parameters.h
// Function: DbConstructionParameters::DbConstructionParameters()
DbConstructionParameters(){
    _db_filename = "";
    _input_filename = "";
    _hash_size = 8;
    _repeat_flag = 0;
    _maximal_span = 70;
    _min_accessible_length = 5;
  }

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
movq %rdi, %rbx
leaq 0x10(%rdi), %r14
movq %r14, (%rdi)
xorl %eax, %eax
movq %rax, 0x8(%rdi)
movb %al, 0x10(%rdi)
leaq 0x20(%rdi), %r15
leaq 0x30(%rdi), %r13
movq %r13, 0x20(%rdi)
movq %rax, 0x28(%rdi)
movb %al, 0x30(%rdi)
leaq 0x175d7(%rip), %rcx     # 0x1b833
xorl %esi, %esi
xorl %edx, %edx
xorl %r8d, %r8d
callq 0x3360
movq 0x28(%rbx), %rdx
leaq 0x175c0(%rip), %rcx     # 0x1b833
movq %r15, %rdi
xorl %esi, %esi
xorl %r8d, %r8d
callq 0x3360
movaps 0x16d89(%rip), %xmm0    # 0x1b010
movups %xmm0, 0x40(%rbx)
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
movq %rax, %r12
movq (%r15), %rdi
cmpq %r13, %rdi
je 0x42ac
movq (%r13), %rsi
incq %rsi
callq 0x3230
movq %rbx, %rdi
movq %r14, %rsi
callq 0x3450
movq %r12, %rdi
callq 0x33e0
nop
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/./rna_interaction_search_parameters.h
// Function: RnaInteractionSearchParameters::RnaInteractionSearchParameters()
RnaInteractionSearchParameters(){
    _db_filename = "";
    _input_filename = "";
    _hash_size = 0;
    _repeat_flag = 0;
    _maximal_span = 0;
    _min_accessible_length = 0;
    _output_style = 0;
    _max_seed_length = 20;
    _hybrid_energy_threshold = -6.0;
    _interaction_energy_threshold = -4;
    _final_threshold = -8.0;
    _drop_out_length_wo_gap = 5;
    _drop_out_length_w_gap = 16;
    _min_helix_length = 3;
  }

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rdi, %rbx
leaq 0x10(%rdi), %r14
movq %r14, (%rdi)
xorl %eax, %eax
movq %rax, 0x8(%rdi)
movb %al, 0x10(%rdi)
leaq 0x20(%rdi), %r15
leaq 0x30(%rdi), %r12
movq %r12, 0x20(%rdi)
movq %rax, 0x28(%rdi)
movb %al, 0x30(%rdi)
leaq 0x50(%rdi), %rbp
movq %rbp, 0x40(%rdi)
movq %rax, 0x48(%rdi)
movb %al, 0x50(%rdi)
leaq 0x174f6(%rip), %rcx     # 0x1b833
xorl %esi, %esi
xorl %edx, %edx
xorl %r8d, %r8d
callq 0x3360
movq 0x28(%rbx), %rdx
leaq 0x174df(%rip), %rcx     # 0x1b833
movq %r15, %rdi
xorl %esi, %esi
xorl %r8d, %r8d
callq 0x3360
xorps %xmm0, %xmm0
movups %xmm0, 0x60(%rbx)
movabsq $0x1400000000, %rax     # imm = 0x1400000000
movq %rax, 0x70(%rbx)
movabsq $-0x3fe8000000000000, %rax # imm = 0xC018000000000000
movq %rax, 0x80(%rbx)
movabsq $-0x3ff0000000000000, %rax # imm = 0xC010000000000000
movq %rax, 0x78(%rbx)
movabsq $-0x3fe0000000000000, %rax # imm = 0xC020000000000000
movq %rax, 0x88(%rbx)
movabsq $0x1000000005, %rax     # imm = 0x1000000005
movq %rax, 0x90(%rbx)
movl $0x3, 0x98(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %r13
movq 0x40(%rbx), %rdi
cmpq %rbp, %rdi
je 0x43e8
movq (%rbp), %rsi
incq %rsi
callq 0x3230
movq %r15, %rdi
movq %r12, %rsi
movq %rbx, %rdx
movq %r14, %rcx
callq 0x3464
movq %r13, %rdi
callq 0x33e0
nop
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/./rna_interaction_search.h
// Function: RnaInteractionSearch::RnaInteractionSearch(int)
RnaInteractionSearch(int hash_size) {
    int nucleotide_size = 4;
    _start_hash.reserve(hash_size);
    _end_hash.reserve(hash_size);
    for(int i = 0; i < hash_size; i++){
      vector <int> temp_vector; temp_vector.resize((int)pow(nucleotide_size,i+1), 0);
      _start_hash.push_back(temp_vector);
      vector <int> temp2_vector; temp_vector.resize((int)pow(nucleotide_size,i+1), 0);
      _end_hash.push_back(temp_vector);
    }
  }

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x38, %rsp
movl %esi, %ebp
leaq 0x78(%rdi), %rbx
leaq 0x90(%rdi), %r15
movslq %esi, %r12
movl $0xf0, %edx
movq %rdi, 0x30(%rsp)
xorl %esi, %esi
callq 0x3140
movq %rbx, 0x8(%rsp)
movq %rbx, %rdi
movq %r12, %rsi
callq 0x4782
movq %r15, %rdi
movq %r12, %rsi
callq 0x4782
testl %ebp, %ebp
jle 0x44ff
movl $0x2, %ebx
leaq 0x10(%rsp), %r12
leaq 0x4(%rsp), %r13
xorps %xmm0, %xmm0
movaps %xmm0, 0x10(%rsp)
movq $0x0, 0x20(%rsp)
movl %ebx, %r14d
xorps %xmm0, %xmm0
cvtsi2sd %r14, %xmm0
callq 0x31f0
cvttsd2si %xmm0, %eax
movslq %eax, %rsi
movl $0x0, 0x4(%rsp)
movq %r12, %rdi
movq %r13, %rdx
callq 0x4868
movq 0x8(%rsp), %rdi
movq %r12, %rsi
callq 0x489c
xorps %xmm0, %xmm0
cvtsi2sd %r14, %xmm0
callq 0x31f0
cvttsd2si %xmm0, %eax
movslq %eax, %rsi
movl $0x0, 0x4(%rsp)
movq %r12, %rdi
movq %r13, %rdx
callq 0x4868
movq %r15, %rdi
movq %r12, %rsi
callq 0x489c
movq 0x10(%rsp), %rdi
testq %rdi, %rdi
je 0x44f4
movq 0x20(%rsp), %rsi
subq %rdi, %rsi
callq 0x3230
addl $0x2, %ebx
decl %ebp
jne 0x4463
addq $0x38, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %r12
jmp 0x4533
jmp 0x4519
jmp 0x4519
jmp 0x4519
movq %rax, %r12
movq 0x10(%rsp), %rdi
testq %rdi, %rdi
je 0x4533
movq 0x20(%rsp), %rsi
subq %rdi, %rsi
callq 0x3230
movq 0x30(%rsp), %rbx
movq 0xd8(%rbx), %rdi
testq %rdi, %rdi
je 0x4553
movq 0xe8(%rbx), %rsi
subq %rdi, %rsi
callq 0x3230
movq 0xc0(%rbx), %rdi
testq %rdi, %rdi
je 0x456e
movq 0xd0(%rbx), %rsi
subq %rdi, %rsi
callq 0x3230
movq 0xa8(%rbx), %rdi
testq %rdi, %rdi
je 0x4589
movq 0xb8(%rbx), %rsi
subq %rdi, %rsi
callq 0x3230
movq %r15, %rdi
callq 0x48c8
movq 0x8(%rsp), %rdi
callq 0x48c8
movq 0x60(%rbx), %rdi
testq %rdi, %rdi
je 0x45b0
movq 0x70(%rbx), %rsi
subq %rdi, %rsi
callq 0x3230
movq 0x48(%rbx), %rdi
testq %rdi, %rdi
je 0x45c5
movq 0x58(%rbx), %rsi
subq %rdi, %rsi
callq 0x3230
leaq 0x30(%rbx), %rdi
leaq 0x18(%rbx), %r14
callq 0x4916
movq %r14, %rdi
callq 0x4972
movq %rbx, %rdi
callq 0x4972
movq %r12, %rdi
callq 0x33e0
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/db_construction_parameters.cpp
// Function: DbConstructionParameters::SetParameters(int, char**)
void DbConstructionParameters::SetParameters(int argc, char* argv[]) {
  int c;
  extern char *optarg;
  while ((c = getopt(argc, argv, "i:o:r:s:w:d:t:")) != -1) {
    switch (c) {
    case 'i':
      _input_filename = optarg;
      break;

    case 'o':
      _db_filename = optarg;
      break;

    case 'r':
      _repeat_flag = atoi(optarg);
      break;

    case 's':
      _hash_size = atoi(optarg);
      break;

    case 'w':
      _maximal_span = atoi(optarg);
      break;
      
    case 'd':
      _min_accessible_length = atoi(optarg);
      break;

    default:
      cerr << "The argument is invalid command." << endl;
      exit(1);
    }
  }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rdx, %rbx
movl %esi, %ebp
movq %rdi, %r14
leaq 0x20(%rdi), %rax
movq %rax, (%rsp)
leaq 0x16976(%rip), %r15     # 0x1b804
movq 0xe111b(%rip), %r13     # 0xe5fb0
leaq 0x16944(%rip), %r12     # 0x1b7e0
movl %ebp, %edi
movq %rbx, %rsi
movq %r15, %rdx
callq 0x3070
cmpl $0x6e, %eax
jle 0x4eee
addl $-0x6f, %eax
cmpl $0x8, %eax
ja 0x4f95
movslq (%r12,%rax,4), %rax
addq %r12, %rax
jmpq *%rax
movq (%r13), %r15
movq 0x8(%r14), %r13
movq %r15, %rdi
callq 0x3100
movq %r14, %rdi
xorl %esi, %esi
movq %r13, %rdx
movq 0xe10ce(%rip), %r13     # 0xe5fb0
movq %r15, %rcx
leaq 0x16918(%rip), %r15     # 0x1b804
jmp 0x4f2c
cmpl $0x64, %eax
je 0x4f6f
cmpl $0x69, %eax
jne 0x4f81
movq 0xe10ad(%rip), %rax     # 0xe5fb0
movq (%rax), %r13
movq 0x28(%r14), %r15
movq %r13, %rdi
callq 0x3100
movq (%rsp), %rdi
xorl %esi, %esi
movq %r15, %rdx
leaq 0x168e2(%rip), %r15     # 0x1b804
movq %r13, %rcx
movq 0xe1084(%rip), %r13     # 0xe5fb0
movq %rax, %r8
callq 0x3360
jmp 0x4e9c
movq (%r13), %rdi
callq 0x3370
movl %eax, 0x48(%r14)
jmp 0x4e9c
movq (%r13), %rdi
callq 0x3370
movl %eax, 0x40(%r14)
jmp 0x4e9c
movq (%r13), %rdi
callq 0x3370
movl %eax, 0x44(%r14)
jmp 0x4e9c
movq (%r13), %rdi
callq 0x3370
movl %eax, 0x4c(%r14)
jmp 0x4e9c
cmpl $-0x1, %eax
jne 0x4f95
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0xe1054(%rip), %rdi     # 0xe5ff0
leaq 0x78e13(%rip), %rsi     # 0x7ddb6
callq 0x3210
movq %rax, %rdi
callq 0x3120
movl $0x1, %edi
callq 0x32a0
nop
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/db_construction.cpp
// Function: DbConstruction::ReadFastaFile(DbConstructionParameters, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>>>&)
void DbConstruction::ReadFastaFile(const DbConstructionParameters parameters,  vector<string> &sequences){
  vector<string> names; names.reserve(10);
  FastafileReader fastafile_reader;
  fastafile_reader.ReadFastafile(parameters.GetInputFilename(), sequences, names);
  SaveBasicInformation(parameters, names);
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
subq $0xa0, %rsp
movq %rdx, %r14
movq %rsi, %rbx
xorps %xmm0, %xmm0
leaq 0x30(%rsp), %rdi
movaps %xmm0, (%rdi)
movq $0x0, 0x10(%rdi)
movl $0xa, %esi
callq 0x7078
leaq 0x20(%rsp), %r15
movq %r15, -0x10(%r15)
movq 0x20(%rbx), %rsi
movq 0x28(%rbx), %rdx
addq %rsi, %rdx
leaq 0x10(%rsp), %rdi
callq 0x46f2
leaq 0xf(%rsp), %rdi
leaq 0x10(%rsp), %rsi
leaq 0x30(%rsp), %rcx
movq %r14, %rdx
callq 0x4fbc
movq 0x10(%rsp), %rdi
cmpq %r15, %rdi
je 0x6343
movq 0x20(%rsp), %rsi
incq %rsi
callq 0x3230
leaq 0x60(%rsp), %r14
movq %r14, -0x10(%r14)
movq (%rbx), %rsi
movq 0x8(%rbx), %rdx
addq %rsi, %rdx
leaq 0x50(%rsp), %rdi
callq 0x46f2
leaq 0x70(%rsp), %rdi
leaq 0x80(%rsp), %r15
movq %r15, -0x10(%r15)
movq 0x20(%rbx), %rsi
movq 0x28(%rbx), %rdx
addq %rsi, %rdx
callq 0x46f2
movups 0x40(%rbx), %xmm0
leaq 0x50(%rsp), %rsi
movups %xmm0, 0x40(%rsi)
leaq 0x30(%rsp), %rdx
callq 0x6c1e
movq 0x70(%rsp), %rdi
cmpq %r15, %rdi
je 0x63b2
movq 0x80(%rsp), %rsi
incq %rsi
callq 0x3230
movq 0x50(%rsp), %rdi
cmpq %r14, %rdi
je 0x63c9
movq 0x60(%rsp), %rsi
incq %rsi
callq 0x3230
leaq 0x30(%rsp), %rdi
callq 0x4916
addq $0xa0, %rsp
popq %rbx
popq %r14
popq %r15
retq
movq %rax, %rbx
leaq 0x50(%rsp), %rdi
callq 0x42c0
jmp 0x6424
movq %rax, %rbx
movq 0x50(%rsp), %rdi
cmpq %r14, %rdi
je 0x6424
movq 0x60(%rsp), %rsi
jmp 0x6415
movq %rax, %rbx
movq 0x10(%rsp), %rdi
cmpq %r15, %rdi
je 0x6424
movq 0x20(%rsp), %rsi
incq %rsi
callq 0x3230
jmp 0x6424
jmp 0x6421
movq %rax, %rbx
leaq 0x30(%rsp), %rdi
callq 0x4916
movq %rbx, %rdi
callq 0x33e0
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/db_construction.cpp
// Function: DbConstruction::ConstructSuffixArray(DbConstructionParameters, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>>>&, std::vector<unsigned char, std::allocator<unsigned char>>&, std::vector<int, std::allocator<int>>&)
void DbConstruction::ConstructSuffixArray(const DbConstructionParameters parameters, vector<string> &sequences,  vector<unsigned char> &encoded_sequences, vector<int> &suffix_array){
  Encoder encoder(parameters.GetRepeatFlag());
  encoder.Encode(sequences, encoded_sequences, 1);
  suffix_array.resize(encoded_sequences.size());
  sais(&encoded_sequences[0], &suffix_array[0], encoded_sequences.size());
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x108, %rsp            # imm = 0x108
movq %r8, %rbx
movq %rcx, %r14
movq %rdx, %r15
movl 0x44(%rsi), %esi
leaq 0x7(%rsp), %r12
movq %r12, %rdi
callq 0x760a
movq %r12, %rdi
movq %r15, %rsi
movq %r14, %rdx
movl $0x1, %ecx
callq 0x7e84
movq 0x8(%r14), %rsi
subq (%r14), %rsi
movq %rbx, %rdi
callq 0x770e
movq (%r14), %rdi
movq (%rbx), %rsi
movl 0x8(%r14), %edx
subl %edi, %edx
callq 0x183b4
addq $0x108, %rsp            # imm = 0x108
popq %rbx
popq %r12
popq %r14
popq %r15
retq
nop
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/db_construction.cpp
// Function: DbConstruction::SaveSequenceData(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>>>&, std::vector<unsigned char, std::allocator<unsigned char>>&)
void DbConstruction::SaveSequenceData(string file_name, vector<string> &sequences, vector<unsigned char> &encoded_sequences){
  ofstream of((file_name+".seq").c_str(), ios::out | ios::binary);
  int number_of_seq = sequences.size();
  of.write(reinterpret_cast<const char*>(&number_of_seq), sizeof(int));
  for(int i = 0; i < number_of_seq; i++){
    int seq_size = sequences[i].size();
    of.write(reinterpret_cast<const char*>(&seq_size), sizeof(int));
  }
  int count = encoded_sequences.size();
  vector<unsigned char>::iterator it;
  of.write(reinterpret_cast<const char*>(&count), sizeof(int));
  for(it = encoded_sequences.begin(); it != encoded_sequences.end(); it++){
    of.write(reinterpret_cast<const char*>(&*it), sizeof(unsigned char));
  }
  of.close();
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x228, %rsp            # imm = 0x228
movq %rcx, %rbx
movq %rdx, %r14
leaq 0x18(%rsp), %r12
movq %r12, -0x10(%r12)
movq (%rsi), %rax
movq 0x8(%rsi), %rdx
addq %rax, %rdx
leaq 0x8(%rsp), %r15
movq %r15, %rdi
movq %rax, %rsi
callq 0x46f2
leaq 0x14da4(%rip), %rsi     # 0x1b860
movq %r15, %rdi
callq 0x3420
movq 0x8(%rsp), %rsi
leaq 0x28(%rsp), %rdi
movl $0x14, %edx
callq 0x3250
movq 0x8(%rsp), %rdi
cmpq %r12, %rdi
je 0x6aef
movq 0x18(%rsp), %rsi
incq %rsi
callq 0x3230
movq 0x8(%r14), %rax
subq (%r14), %rax
shrq $0x5, %rax
leaq 0x8(%rsp), %rsi
movl %eax, (%rsi)
leaq 0x28(%rsp), %rdi
movl $0x4, %edx
callq 0x32f0
cmpl $0x0, 0x8(%rsp)
jle 0x6b55
movl $0x8, %r13d
xorl %ebp, %ebp
leaq 0x28(%rsp), %r15
leaq 0x4(%rsp), %r12
movq (%r14), %rax
movl (%rax,%r13), %eax
movl %eax, 0x4(%rsp)
movl $0x4, %edx
movq %r15, %rdi
movq %r12, %rsi
callq 0x32f0
incq %rbp
movslq 0x8(%rsp), %rax
addq $0x20, %r13
cmpq %rax, %rbp
jl 0x6b29
movl 0x8(%rbx), %eax
subl (%rbx), %eax
leaq 0x4(%rsp), %rsi
movl %eax, (%rsi)
leaq 0x28(%rsp), %rdi
movl $0x4, %edx
callq 0x32f0
movq (%rbx), %r14
cmpq 0x8(%rbx), %r14
je 0x6b97
leaq 0x28(%rsp), %r15
movl $0x1, %edx
movq %r15, %rdi
movq %r14, %rsi
callq 0x32f0
incq %r14
cmpq 0x8(%rbx), %r14
jne 0x6b7e
leaq 0x28(%rsp), %rdi
callq 0x3320
movq 0xdf418(%rip), %rax     # 0xe5fc0
movq (%rax), %rcx
movq 0x18(%rax), %rax
leaq 0x30(%rsp), %rdi
movq %rcx, -0x8(%rdi)
movq -0x18(%rcx), %rcx
movq %rax, 0x28(%rsp,%rcx)
callq 0x31d0
leaq 0x120(%rsp), %rdi
callq 0x30d0
addq $0x228, %rsp            # imm = 0x228
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
jmp 0x6c09
jmp 0x6be9
movq %rax, %rbx
movq 0x8(%rsp), %rdi
cmpq %r12, %rdi
je 0x6c16
movq 0x18(%rsp), %rsi
incq %rsi
callq 0x3230
jmp 0x6c16
jmp 0x6c09
jmp 0x6c09
movq %rax, %rbx
leaq 0x28(%rsp), %rdi
callq 0x3340
movq %rbx, %rdi
callq 0x33e0
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/db_construction.cpp
// Function: DbConstruction::Search(std::vector<unsigned char, std::allocator<unsigned char>>&, std::vector<int, std::allocator<int>>&, int*, int*, unsigned char, int)
void DbConstruction::Search(vector<unsigned char> &encoded_sequences, vector<int> &suffix_array, int* start, int* end, unsigned char c, int offset){
  int s = *start;
  int e = *end;
  int m;

  if (suffix_array[s] + offset >= encoded_sequences.size()) {
    ++(*start);
  }
  
  if(s>e){
    *start = 1;
    *end = 0;
    return;
  }else if (s == e) {
    if (encoded_sequences[suffix_array[s]+offset] == c) {
      return;
    } else {
      *start = 1;
      *end = 0;
      return;
    }
  }
  
  if (encoded_sequences[suffix_array[s]+offset] != c) {
    while (s < e - 1) {
      m = (s + e) / 2;
      if (encoded_sequences[suffix_array[m]+offset] < c) {
        s = m;
      } else {
        e = m;
      }
    }
    if (encoded_sequences[suffix_array[e]+offset] != c) {
      *start = 1;
      *end = 0;
      return;
    }
    *start = e;
    s = e;
    e = *end;
  }

  if (encoded_sequences[suffix_array[e]+offset] != c) {
    while (s < e - 1) {
      m = (s + e) / 2;
      if (encoded_sequences[suffix_array[m]+offset] > c) {
        e = m;
      } else {
        s = m;
      }
    }
    if (encoded_sequences[suffix_array[s]+offset] != c) {
      *start = 1;
      *end = 0;
      return;
    }
    *end = s;
  }
  return;
}

// Assembly:
pushq %r14
pushq %rbx
movslq 0x18(%rsp), %r10
movl (%rcx), %r11d
movl (%r8), %edi
movslq %r11d, %rbx
movq (%rdx), %rax
movslq (%rax,%rbx,4), %r14
addq %r10, %r14
movq (%rsi), %rdx
movq 0x8(%rsi), %rsi
subq %rdx, %rsi
cmpq %r14, %rsi
ja 0x6f82
leal 0x1(%r11), %esi
movl %esi, (%rcx)
cmpl %edi, %r11d
jle 0x6f97
movl $0x1, (%rcx)
xorl %r10d, %r10d
movl %r10d, (%r8)
popq %rbx
popq %r14
retq
movslq (%rax,%rbx,4), %rbx
movslq %r10d, %rsi
addq %rsi, %rbx
movb (%rdx,%rbx), %r10b
cmpl %edi, %r11d
jne 0x6fb1
cmpb %r9b, %r10b
jne 0x6f87
jmp 0x6f93
cmpb %r9b, %r10b
jne 0x6fbb
movl %r11d, %r10d
jmp 0x7016
leal -0x1(%rdi), %r10d
cmpl %r10d, %r11d
jge 0x6ff9
leal (%rdi,%r11), %ebx
movl %ebx, %r10d
shrl $0x1f, %r10d
addl %ebx, %r10d
sarl %r10d
movslq %r10d, %rbx
movslq (%rax,%rbx,4), %rbx
addq %rsi, %rbx
cmpb %r9b, (%rdx,%rbx)
jae 0x6feb
movl %r10d, %r11d
movl %edi, %r10d
leal -0x1(%r10), %ebx
movl %r10d, %edi
cmpl %ebx, %r11d
jl 0x6fc4
jmp 0x6ffc
movl %edi, %r10d
movslq %r10d, %rdi
movslq (%rax,%rdi,4), %rdi
addq %rsi, %rdi
cmpb %r9b, (%rdx,%rdi)
jne 0x6f87
movl %r10d, (%rcx)
movl (%r8), %edi
movslq %edi, %r11
movslq (%rax,%r11,4), %r11
addq %rsi, %r11
cmpb %r9b, (%rdx,%r11)
je 0x6f93
leal -0x1(%rdi), %r11d
cmpl %r11d, %r10d
jge 0x705e
leal (%rdi,%r10), %ebx
movl %ebx, %r11d
shrl $0x1f, %r11d
addl %ebx, %r11d
sarl %r11d
movslq %r11d, %rbx
movslq (%rax,%rbx,4), %rbx
addq %rsi, %rbx
cmpb %r9b, (%rdx,%rbx)
ja 0x7059
movl %r11d, %r10d
jmp 0x702a
movl %r11d, %edi
jmp 0x702a
movslq %r10d, %rdi
movslq (%rax,%rdi,4), %rax
addq %rsi, %rax
cmpb %r9b, (%rdx,%rax)
jne 0x6f87
jmp 0x6f90
nop
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/./encoder.h
// Function: Encoder::Encoder(int)
Encoder(int flag) {
    _sentinel_character = 0;
    _unknown_character = 1; 
    if(flag == 0){
      for (int i = 0; i < UCHAR_MAX; ++i) {
	_code_table[i] = _unknown_character;
      }
      
      _code_table[static_cast<int>('A')] = 2;
      _code_table[static_cast<int>('C')] = 3;
      _code_table[static_cast<int>('G')] = 4;
      _code_table[static_cast<int>('T')] = 5;
      _code_table[static_cast<int>('U')] = 5;
      
    }else if(flag == 1){
      for (int i = 0; i < UCHAR_MAX; ++i) {
	_code_table[i] = _unknown_character;
      }
      
      _code_table[static_cast<int>('A')] = 2;
      _code_table[static_cast<int>('C')] = 3;
      _code_table[static_cast<int>('G')] = 4;
      _code_table[static_cast<int>('T')] = 5;
      _code_table[static_cast<int>('U')] = 5;
      _code_table[static_cast<int>('a')] = 6;
      _code_table[static_cast<int>('c')] = 7;
      _code_table[static_cast<int>('g')] = 8;
      _code_table[static_cast<int>('t')] = 9;
      _code_table[static_cast<int>('u')] = 9;
      
    }else if(flag == 2){
      for (int i = 0; i < UCHAR_MAX; ++i) {
	_code_table[i] = _unknown_character;
      }
      _code_table[static_cast<int>('A')] = 2;
      _code_table[static_cast<int>('C')] = 3;
      _code_table[static_cast<int>('G')] = 4;
      _code_table[static_cast<int>('T')] = 5;
      _code_table[static_cast<int>('U')] = 5;
      _code_table[static_cast<int>('a')] = 2;
      _code_table[static_cast<int>('c')] = 3;
      _code_table[static_cast<int>('g')] = 4;
      _code_table[static_cast<int>('t')] = 5;
      _code_table[static_cast<int>('u')] = 5;
      
    }else{
      cerr << "Error: -r option must be 0, 1, or 2." << endl;
      exit(1);
    }
  }

// Assembly:
pushq %rbx
movw $0x100, 0xff(%rdi)      # imm = 0x100
testl %esi, %esi
je 0x7697
cmpl $0x1, %esi
je 0x7647
cmpl $0x2, %esi
jne 0x76e9
xorl %eax, %eax
movb 0x100(%rdi), %cl
movb %cl, (%rdi,%rax)
incq %rax
cmpq $0xff, %rax
jne 0x7628
movb $0x5, %al
movb $0x4, %cl
movb $0x3, %dl
movb $0x2, %sil
jmp 0x7666
xorl %eax, %eax
movb 0x100(%rdi), %cl
movb %cl, (%rdi,%rax)
incq %rax
cmpq $0xff, %rax
jne 0x7649
movb $0x9, %al
movb $0x8, %cl
movb $0x7, %dl
movb $0x6, %sil
movb $0x2, 0x41(%rdi)
movb $0x3, 0x43(%rdi)
movb $0x4, 0x47(%rdi)
movw $0x505, 0x54(%rdi)      # imm = 0x505
movl $0x75, %r8d
movl $0x74, %r9d
movl $0x67, %r10d
movl $0x63, %r11d
movl $0x61, %ebx
jmp 0x76d3
xorl %eax, %eax
movb 0x100(%rdi), %cl
movb %cl, (%rdi,%rax)
incq %rax
cmpq $0xff, %rax
jne 0x7699
movl $0x55, %r8d
movb $0x5, %al
movl $0x54, %r9d
movb $0x4, %cl
movl $0x47, %r10d
movb $0x3, %dl
movl $0x43, %r11d
movb $0x2, %sil
movl $0x41, %ebx
movb %sil, (%rdi,%rbx)
movb %dl, (%rdi,%r11)
movb %cl, (%rdi,%r10)
movb %al, (%rdi,%r9)
movb %al, (%rdi,%r8)
popq %rbx
retq
movq 0xde900(%rip), %rdi     # 0xe5ff0
leaq 0x141dd(%rip), %rsi     # 0x1b8d4
callq 0x3210
movq %rax, %rdi
callq 0x3120
movl $0x1, %edi
callq 0x32a0
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/encoder.cpp
// Function: Encoder::Encode(std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>>>&, std::vector<unsigned char, std::allocator<unsigned char>>&, int)
void Encoder::Encode(vector<string> &sequences, vector<unsigned char> &encoded_sequences, int r){
  for(int i = 0; i < sequences.size(); i++){
    if(r == 0){
      for(int j = 0; j<sequences[i].size();j++){
	encoded_sequences.push_back(_code_table[static_cast<int>(sequences[i][j])]);  
      }
    }else{
      for(int j = sequences[i].size()-1; j>= 0; j--){
	encoded_sequences.push_back(_code_table[static_cast<int>(sequences[i][j])]);  
      }
    }
    encoded_sequences.push_back(_sentinel_character);
  }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movl %ecx, 0xc(%rsp)
movq (%rsi), %rax
cmpq %rax, 0x8(%rsi)
je 0x7f9d
movq %rdx, %r14
movq %rsi, %r15
movq %rdi, %r12
leaq 0xff(%rdi), %rcx
movq %rcx, 0x10(%rsp)
xorl %ebx, %ebx
cmpl $0x0, 0xc(%rsp)
je 0x7f0d
movq %rbx, %rbp
shlq $0x5, %rbp
movl 0x8(%rax,%rbp), %eax
decl %eax
js 0x7f5d
movl %eax, %r13d
incq %r13
movq (%r15), %rax
movq (%rax,%rbp), %rax
movsbq -0x1(%rax,%r13), %rdx
addq %r12, %rdx
movq 0x8(%r14), %rsi
cmpq 0x10(%r14), %rsi
je 0x7efe
movb (%rdx), %al
movb %al, (%rsi)
incq 0x8(%r14)
jmp 0x7f06
movq %r14, %rdi
callq 0x8072
decq %r13
jg 0x7eda
jmp 0x7f5d
movq (%r15), %rax
movq %rbx, %rbp
shlq $0x5, %rbp
cmpq $0x0, 0x8(%rax,%rbp)
je 0x7f5d
addq %rbp, %rax
xorl %r13d, %r13d
movq (%rax), %rax
movsbq (%rax,%r13), %rdx
addq %r12, %rdx
movq 0x8(%r14), %rsi
cmpq 0x10(%r14), %rsi
je 0x7f44
movb (%rdx), %al
movb %al, (%rsi)
incq 0x8(%r14)
jmp 0x7f4c
movq %r14, %rdi
callq 0x8072
incq %r13
movq (%r15), %rcx
leaq (%rcx,%rbp), %rax
cmpq %r13, 0x8(%rcx,%rbp)
ja 0x7f25
movq 0x8(%r14), %rsi
cmpq 0x10(%r14), %rsi
je 0x7f76
movq 0x10(%rsp), %rax
movb (%rax), %al
movb %al, (%rsi)
incq 0x8(%r14)
jmp 0x7f83
movq %r14, %rdi
movq 0x10(%rsp), %rdx
callq 0x8072
incq %rbx
movq (%r15), %rax
movq 0x8(%r15), %rcx
subq %rax, %rcx
sarq $0x5, %rcx
cmpq %rbx, %rcx
ja 0x7eba
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/encoder.cpp
// Function: Encoder::Encode(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>&, std::vector<unsigned char, std::allocator<unsigned char>>&, int)
void Encoder::Encode(string &sequence, vector<unsigned char> &encoded_sequence, int r){
  if(r == 0){
    for(int i = 0; i<sequence.size();i++){
      encoded_sequence.push_back(_code_table[static_cast<int>(sequence[i])]);  
    }
  }else{
    for(int i = sequence.size()-1; i>= 0; i--){
      encoded_sequence.push_back(_code_table[static_cast<int>(sequence[i])]);  
    }
  }
  encoded_sequence.push_back(_sentinel_character);
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rdx, %rbx
movq %rsi, %r15
movq %rdi, %r14
movq 0x8(%rsi), %rax
testl %ecx, %ecx
je 0x7ffe
decl %eax
js 0x8036
movl %eax, %r12d
incq %r12
movq (%r15), %rax
movsbq -0x1(%rax,%r12), %rdx
addq %r14, %rdx
movq 0x8(%rbx), %rsi
cmpq 0x10(%rbx), %rsi
je 0x7fef
movb (%rdx), %al
movb %al, (%rsi)
incq 0x8(%rbx)
jmp 0x7ff7
movq %rbx, %rdi
callq 0x8072
decq %r12
jg 0x7fcf
jmp 0x8036
testq %rax, %rax
je 0x8036
xorl %r12d, %r12d
movq (%r15), %rax
movsbq (%rax,%r12), %rdx
addq %r14, %rdx
movq 0x8(%rbx), %rsi
cmpq 0x10(%rbx), %rsi
je 0x8025
movb (%rdx), %al
movb %al, (%rsi)
incq 0x8(%rbx)
jmp 0x802d
movq %rbx, %rdi
callq 0x8072
incq %r12
cmpq %r12, 0x8(%r15)
ja 0x8006
addq $0xff, %r14
movq 0x8(%rbx), %rsi
cmpq 0x10(%rbx), %rsi
je 0x805c
movb (%r14), %al
movb %al, (%rsi)
incq 0x8(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
movq %rbx, %rdi
movq %r14, %rdx
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
jmp 0x8072
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/raccess.cpp
// Function: Raccess::Run(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>&)
void Raccess::Run(string &sequence){
  clock_t start, end;
  Initiallize(sequence);
  CalcInsideVariable();
  CalcOutsideVariable();
  CalcAccessibility(sequence);
  Clear();
}

// Assembly:
pushq %rbx
movq %rdi, %rbx
callq 0x818e
movq %rbx, %rdi
callq 0x86f8
movq %rbx, %rdi
callq 0x8fd0
movq %rbx, %rdi
callq 0x9b4c
movq %rbx, %rdi
popq %rbx
jmp 0xa108
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/raccess.cpp
// Function: Raccess::Run(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>&, std::vector<float, std::allocator<float>>&, std::vector<float, std::allocator<float>>&)
void Raccess::Run(string &sequence, vector<float> &accessibility, vector<float> &conditional_accessibility){
  Initiallize(sequence);
  CalcInsideVariable();
  CalcOutsideVariable();
  CalcAccessibility(sequence, accessibility, conditional_accessibility);
  Clear();
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %rcx, %rbx
movq %rdx, %r14
movq %rdi, %r15
callq 0x818e
movq %r15, %rdi
callq 0x86f8
movq %r15, %rdi
callq 0x8fd0
movq %r15, %rdi
movq %r14, %rdx
movq %rbx, %rcx
callq 0xa3de
movq %r15, %rdi
popq %rbx
popq %r14
popq %r15
jmp 0xa108
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/raccess.cpp
// Function: Raccess::CalcDangleEnergy(int, int, int)
double Raccess::CalcDangleEnergy(int type, int a, int b){
  double x = 0;
  if (type != 0) {
    if (a>0) x += dangle5[type][_int_sequence[a]];
    if (b<_seq_length) x += dangle3[type][_int_sequence[b+1]];
    if( b == _seq_length && type>2){
      x += TermAU;
    }
  }
  return(x);
}

// Assembly:
testl %esi, %esi
je 0xad66
movslq %esi, %rax
testl %edx, %edx
jle 0xad6b
leaq (%rax,%rax,4), %r8
leaq (%rdi,%r8,8), %r8
movl %edx, %edx
movq 0x620f8(%rdi), %r9
movslq (%r9,%rdx,4), %rdx
xorpd %xmm0, %xmm0
addsd 0x61d80(%r8,%rdx,8), %xmm0
jmp 0xad6f
xorpd %xmm0, %xmm0
retq
xorpd %xmm0, %xmm0
movl 0x62110(%rdi), %edx
cmpl %ecx, %edx
jle 0xad9a
leaq (%rax,%rax,4), %rax
leaq (%rdi,%rax,8), %rax
movq 0x620f8(%rdi), %r8
movslq %ecx, %r9
movslq 0x4(%r8,%r9,4), %r8
addsd 0x61ec0(%rax,%r8,8), %xmm0
cmpl %ecx, %edx
setne %al
cmpl $0x3, %esi
setl %cl
orb %al, %cl
jne 0xad6a
addsd 0xe68(%rdi), %xmm0
retq
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/raccess.cpp
// Function: Raccess::HairpinEnergy(int, int, int)
double Raccess::HairpinEnergy(int type, int i, int j) {
  int d = j-i-1;
  double q = 0;

  q = d <= 30 ? hairpin[d] : hairpin[30] - lxc37*log( d/30.) *10./kT;  
  if(d!= 3){
    q += mismatchH[type][_int_sequence[i+1]][_int_sequence[j-1]];
  }else{
    if(type > 2){q += TermAU;}
  }
  return q;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x10, %rsp
movl %ecx, %ebx
movl %edx, %ebp
movl %esi, %r15d
movq %rdi, %r14
movl %edx, %r12d
notl %r12d
addl %ecx, %r12d
cmpl $0x1e, %r12d
jg 0xade2
movslq %r12d, %rax
movsd (%r14,%rax,8), %xmm0
jmp 0xae24
movsd 0xf0(%r14), %xmm0
movsd %xmm0, 0x8(%rsp)
xorps %xmm0, %xmm0
cvtsi2sd %r12d, %xmm0
divsd 0x41b4f(%rip), %xmm0    # 0x4c950
callq 0x31b0
mulsd 0x41b4a(%rip), %xmm0    # 0x4c958
mulsd 0x10a42(%rip), %xmm0    # 0x1b858
divsd 0xdb44a(%rip), %xmm0    # 0xe6268
addsd 0x8(%rsp), %xmm0
cmpl $0x3, %r12d
jne 0xae3b
cmpl $0x3, %r15d
jl 0xae70
addsd 0xe68(%r14), %xmm0
jmp 0xae70
movslq %r15d, %rax
imulq $0xc8, %rax, %rax
addq %r14, %rax
movq 0x620f8(%r14), %rcx
movslq %ebp, %rdx
movslq 0x4(%rcx,%rdx,4), %rdx
movslq %ebx, %rsi
movslq -0x4(%rcx,%rsi,4), %rcx
leaq (%rdx,%rdx,4), %rdx
leaq (%rax,%rdx,8), %rax
addsd 0xf8(%rax,%rcx,8), %xmm0
addq $0x10, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
nop
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/./fmath.hpp
// Function: fmath::local::ExpVar<10ul>::ExpVar()
ExpVar()
	{
		float log_2 = ::logf(2.0f);
		for (int i = 0; i < 8; i++) {
			maxX[i] = 88;
			minX[i] = -88;
			a[i] = n / log_2;
			b[i] = log_2 / n;
			f1[i] = 1.0f;
			i127s[i] = 127 << s;
			i7fffffff[i] = 0x7fffffff;
			mask_s[i] = mask(s);
		}

		for (int i = 0; i < n; i++) {
			float y = pow(2.0f, (float)i / n);
			fi fi;
			fi.f = y;
			tbl[i] = fi.i & mask(23);
		}
	}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq $-0x8, %rax
movl $0x42b00000, 0x40(%rbx,%rax,4) # imm = 0x42B00000
movl $0xc2b00000, 0x20(%rbx,%rax,4) # imm = 0xC2B00000
movl $0x44b8aa3b, 0x60(%rbx,%rax,4) # imm = 0x44B8AA3B
movl $0x3a317218, 0x80(%rbx,%rax,4) # imm = 0x3A317218
movl $0x3f800000, 0xa0(%rbx,%rax,4) # imm = 0x3F800000
movl $0x1fc00, 0xc0(%rbx,%rax,4) # imm = 0x1FC00
movl $0x7fffffff, 0x100(%rbx,%rax,4) # imm = 0x7FFFFFFF
movl $0x3ff, 0xe0(%rbx,%rax,4) # imm = 0x3FF
incq %rax
jne 0xcbe4
xorl %r14d, %r14d
xorps %xmm0, %xmm0
cvtsi2ss %r14d, %xmm0
mulss 0x3fd75(%rip), %xmm0    # 0x4c9c0
callq 0x3430
movd %xmm0, %eax
andl $0x7fffff, %eax         # imm = 0x7FFFFF
movl %eax, 0x100(%rbx,%r14,4)
incq %r14
cmpq $0x400, %r14            # imm = 0x400
jne 0xcc3b
addq $0x8, %rsp
popq %rbx
popq %r14
retq
nop
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/./fmath.hpp
// Function: fmath::local::LogVar<12ul>::LogVar()
LogVar()
		: c_log2(::logf(2.0f) / (1 << 23))
	{
		const double e = 1 / double(1 << 24);
		const double h = 1 / double(1 << LEN);
		const size_t n = 1U << LEN;
		for (size_t i = 0; i < n; i++) {
			double x = 1 + double(i) / n;
			double a = ::log(x);
			tbl[i].app = (float)a;
			if (i < n - 1) {
				double b = ::log(x + h - e);
				tbl[i].rev = (float)((b - a) / ((h - e) * (1 << 23)));
			} else {
				tbl[i].rev = (float)(1 / (x * (1 << 23)));
			}
		}
		for (int i = 0; i < 4; i++) {
			m1[i] = mask(8) << 23;
			m2[i] = mask(LEN) << (23 - LEN);
			m3[i] = mask(23 - LEN);
			m4[i] = c_log2;
			m5[i] = 127U << 23;
		}
	}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movl $0x33b17218, 0x4050(%rdi) # imm = 0x33B17218
xorl %r14d, %r14d
movsd 0x3fcfe(%rip), %xmm2    # 0x4c990
movsd 0x3fce6(%rip), %xmm1    # 0x4c980
xorps %xmm0, %xmm0
cvtsi2sd %r14, %xmm0
mulsd %xmm2, %xmm0
addsd %xmm1, %xmm0
movsd %xmm0, (%rsp)
callq 0x31b0
movapd %xmm0, %xmm1
cvtsd2ss %xmm0, %xmm0
movss %xmm0, 0x50(%rbx,%r14,8)
cmpq $0x7ff, %r14            # imm = 0x7FF
jne 0xcceb
movsd (%rsp), %xmm2
mulsd 0x3fccf(%rip), %xmm2    # 0x4c9a8
movsd 0x3fc9f(%rip), %xmm1    # 0x4c980
movapd %xmm1, %xmm0
divsd %xmm2, %xmm0
jmp 0xcd1f
movsd (%rsp), %xmm0
addsd 0x3fc98(%rip), %xmm0    # 0x4c990
addsd 0x3fc98(%rip), %xmm0    # 0x4c998
movsd %xmm1, (%rsp)
callq 0x31b0
subsd (%rsp), %xmm0
divsd 0x3fc89(%rip), %xmm0    # 0x4c9a0
movsd 0x3fc61(%rip), %xmm1    # 0x4c980
cvtsd2ss %xmm0, %xmm0
movss %xmm0, 0x54(%rbx,%r14,8)
incq %r14
cmpq $0x800, %r14            # imm = 0x800
movsd 0x3fc54(%rip), %xmm2    # 0x4c990
jne 0xcc9a
movq $-0x4, %rax
movl $0x7f800000, 0x10(%rbx,%rax,4) # imm = 0x7F800000
movl $0x7ff000, 0x20(%rbx,%rax,4) # imm = 0x7FF000
movl $0xfff, 0x30(%rbx,%rax,4) # imm = 0xFFF
movss 0x4050(%rbx), %xmm0
movss %xmm0, 0x40(%rbx,%rax,4)
movl $0x3f800000, 0x50(%rbx,%rax,4) # imm = 0x3F800000
incq %rax
jne 0xcd49
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/rna_interaction_search.cpp
// Function: RnaInteractionSearch::ConstructSuffixArray(RnaInteractionSearchParameters, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>&, std::vector<unsigned char, std::allocator<unsigned char>>&, std::vector<int, std::allocator<int>>&)
void RnaInteractionSearch::ConstructSuffixArray(const RnaInteractionSearchParameters parameters, string &query_sequence,  vector<unsigned char> &query_encoded_sequence, vector<int> &query_suffix_array){
  Encoder encoder(parameters.GetRepeatFlag());
  encoder.Encode(query_sequence, query_encoded_sequence, 0);
  query_suffix_array.resize(query_encoded_sequence.size());
  sais(&query_encoded_sequence[0], &query_suffix_array[0], query_encoded_sequence.size());
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x108, %rsp            # imm = 0x108
movq %r8, %rbx
movq %rcx, %r14
movq %rdx, %r15
movl 0x68(%rsi), %esi
leaq 0x7(%rsp), %r12
movq %r12, %rdi
callq 0x760a
movq %r12, %rdi
movq %r15, %rsi
movq %r14, %rdx
xorl %ecx, %ecx
callq 0x7fac
movq 0x8(%r14), %rsi
subq (%r14), %rsi
movq %rbx, %rdi
callq 0x770e
movq (%r14), %rdi
movq (%rbx), %rsi
movl 0x8(%r14), %edx
subl %edi, %edx
callq 0x183b4
addq $0x108, %rsp            # imm = 0x108
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/rna_interaction_search.cpp
// Function: RnaInteractionSearch::ExtendWithoutGap(RnaInteractionSearchParameters, std::vector<Hit, std::allocator<Hit>>&, std::vector<unsigned char, std::allocator<unsigned char>>&, std::vector<float, std::allocator<float>>&, std::vector<float, std::allocator<float>>&)
void RnaInteractionSearch::ExtendWithoutGap(const RnaInteractionSearchParameters parameters, vector<Hit> &hit_result, vector<unsigned char> &query_encoded_sequence, vector<float> &query_accessibility, vector<float> &query_conditional_accessibility){
  UngappedExtension ungapped_extension(parameters.GetMinAccessibleLength(), parameters.GetDropOutLengthWoGap());

  ungapped_extension.Run(hit_result, query_encoded_sequence, _db_seq, query_accessibility, query_conditional_accessibility, _db_accessibility, _db_conditional_accessibility);
  sort(hit_result.begin(), hit_result.end(), compare);
  CheckRedundancy(hit_result,parameters.GetInteractionEnergyThreshold());
  GetBasePair(hit_result, query_encoded_sequence);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rcx, %rbx
movq %rdx, %r14
movq %rsi, %r12
movq %rdi, %r15
movl 0x70(%rsi), %eax
movl 0x90(%rsi), %ecx
movq %rsp, %rdi
movl %eax, (%rdi)
movl %ecx, 0x4(%rdi)
leaq 0x60(%r15), %rcx
leaq 0x18(%r15), %rax
movq %rdx, %rsi
movq %rbx, %rdx
pushq %rax
pushq %r15
callq 0x13768
addq $0x10, %rsp
movq (%r14), %r13
movq 0x8(%r14), %rbp
cmpq %rbp, %r13
je 0xfd65
movq %rbp, %rax
subq %r13, %rax
sarq $0x4, %rax
movabsq $-0x3333333333333333, %rcx # imm = 0xCCCCCCCCCCCCCCCD
imulq %rax, %rcx
bsrq %rcx, %rdx
xorl $0x3f, %edx
addl %edx, %edx
xorq $0x7e, %rdx
leaq -0x1e80(%rip), %rcx     # 0xdec8
movq %r13, %rdi
movq %rbp, %rsi
callq 0x11ce6
movq %r13, %rdi
movq %rbp, %rsi
leaq -0x1e98(%rip), %rdx     # 0xdec8
callq 0x11dc1
movsd 0x78(%r12), %xmm0
movq %r14, %rsi
callq 0x10804
movq %r15, %rdi
movq %r14, %rsi
movq %rbx, %rdx
callq 0x10930
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
nop
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/rna_interaction_search.cpp
// Function: RnaInteractionSearch::ExtendWithGap(RnaInteractionSearchParameters, std::vector<Hit, std::allocator<Hit>>&, std::vector<unsigned char, std::allocator<unsigned char>>&, std::vector<float, std::allocator<float>>&, std::vector<float, std::allocator<float>>&)
void RnaInteractionSearch::ExtendWithGap(const RnaInteractionSearchParameters parameters, vector<Hit> &hit_result, vector<unsigned char> &query_encoded_sequence, vector<float> &query_accessibility, vector<float> &query_conditional_accessibility){
  GappedExtension gapped_extension(parameters.GetMinAccessibleLength(), parameters.GetDropOutLengthWGap(), parameters.GetMinHelixLength());
  gapped_extension.Run(hit_result, query_encoded_sequence, _db_seq, query_accessibility, query_conditional_accessibility, _db_accessibility, _db_conditional_accessibility, _db_seq_length);
  for(int i = 1; i<hit_result.size();i++){
    hit_result[i].SortBasePair();
  }
  sort(hit_result.begin(), hit_result.end(), compare);
  CheckRedundancy(hit_result,parameters.GetFinalThreshold());
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rdx, %rbx
movq %rdi, %rax
movl 0x70(%rsi), %edx
movl 0x94(%rsi), %r11d
movq %rsi, (%rsp)
movl 0x98(%rsi), %r10d
leaq 0xc(%rsp), %rdi
movl %edx, (%rdi)
movl %r11d, 0x4(%rdi)
movl %r10d, 0x8(%rdi)
leaq 0x60(%rax), %r10
leaq 0x18(%rax), %r11
leaq 0xc0(%rax), %r14
subq $0x8, %rsp
movq %rbx, %rsi
movq %rcx, %rdx
movq %r10, %rcx
pushq %r14
pushq %r11
pushq %rax
callq 0x15690
addq $0x20, %rsp
movq (%rbx), %r15
movq 0x8(%rbx), %r12
movq %r12, %rax
subq %r15, %rax
sarq $0x4, %rax
movabsq $-0x3333333333333333, %r13 # imm = 0xCCCCCCCCCCCCCCCD
imulq %r13, %rax
cmpq $0x2, %rax
jb 0xfe50
movl $0x1, %ebp
movl $0x50, %r14d
addq %r14, %r15
movq %r15, %rdi
callq 0x111b0
incq %rbp
movq (%rbx), %r15
movq 0x8(%rbx), %r12
movq %r12, %rax
subq %r15, %rax
sarq $0x4, %rax
imulq %r13, %rax
addq $0x50, %r14
cmpq %rbp, %rax
ja 0xfe24
cmpq %r12, %r15
je 0xfe85
bsrq %rax, %rdx
xorl $0x3f, %edx
addl %edx, %edx
xorq $0x7e, %rdx
leaq -0x1fa1(%rip), %r13     # 0xdec8
movq %r15, %rdi
movq %r12, %rsi
movq %r13, %rcx
callq 0x11ce6
movq %r15, %rdi
movq %r12, %rsi
movq %r13, %rdx
callq 0x11dc1
movq (%rsp), %rax
movsd 0x88(%rax), %xmm0
movq %rbx, %rsi
callq 0x10804
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/rna_interaction_search.cpp
// Function: RnaInteractionSearch::CheckRedundancy(std::vector<Hit, std::allocator<Hit>>&, double)
void RnaInteractionSearch::CheckRedundancy(vector<Hit> &hit_result, double energy_threshold){
  for(int i = 0; i<hit_result.size();i++){
    if(hit_result[i].GetEnergy() > energy_threshold){
      hit_result[i].SetFlag();
    }

    if(!hit_result[i].GetFlag()){
      int a_QSp = hit_result[i].GetQSp();
      int a_DbSp = hit_result[i].GetDbSp();
      int a_QEp = a_QSp+hit_result[i].GetQLength()-1;
      int a_DbEp = a_DbSp+hit_result[i].GetDbLength()-1;

      for(int j = i+1; j<hit_result.size();j++){
        if(!hit_result[j].GetFlag()){
          int b_DbSp = hit_result[j].GetDbSp();
          if(a_DbEp < b_DbSp){
            break;
          }

          int b_QSp = hit_result[j].GetQSp();
          int b_QEp = b_QSp+hit_result[j].GetQLength()-1;
          int b_DbEp = b_DbSp+hit_result[j].GetDbLength()-1;
          if(a_QEp>=b_QEp && a_QSp <= b_QSp && a_DbEp >= b_DbEp){
	    if(hit_result[i].GetEnergy() > hit_result[j].GetEnergy()){
	      hit_result[i].SetFlag();
	    }else{
	      hit_result[j].SetFlag();
	    }
          }
        }
      }
    }
  }
  hit_result.erase(remove_if(hit_result.begin(), hit_result.end(), CheckFlag()), hit_result.end());

}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq (%rsi), %rdi
movq %rsi, 0x10(%rsp)
movq 0x8(%rsi), %rcx
movq %rcx, 0x8(%rsp)
subq %rdi, %rcx
je 0x10906
sarq $0x4, %rcx
movabsq $-0x3333333333333333, %rax # imm = 0xCCCCCCCCCCCCCCCD
imulq %rcx, %rax
cmpq $0x1, %rax
movq %rax, %rsi
adcq $0x0, %rsi
leaq 0x80(%rdi), %rdx
movl $0x1, %r8d
xorl %r9d, %r9d
leaq (%r9,%r9,4), %r10
shlq $0x4, %r10
leaq (%rdi,%r10), %r15
movsd 0x28(%rdi,%r10), %xmm1
ucomisd %xmm0, %xmm1
jbe 0x10877
movb $0x1, 0x30(%r15)
cmpb $0x0, 0x30(%r15)
jne 0x108f3
leaq 0x1(%r9), %r10
cmpq %r10, %rax
jbe 0x108f3
leaq 0x30(%r15), %r10
movl 0x8(%r15), %r11d
movzwl 0x10(%r15), %ebp
addl %r11d, %ebp
movzwl 0x14(%r15), %r14d
addl 0xc(%r15), %r14d
movq %rdx, %r15
movq %r8, %r12
cmpb $0x0, (%r15)
jne 0x108e7
movl -0x24(%r15), %r13d
cmpl %r13d, %r14d
jle 0x108f3
movl -0x28(%r15), %ebx
cmpl %ebx, %r11d
jg 0x108e7
movzwl -0x20(%r15), %ecx
addl %ebx, %ecx
cmpl %ecx, %ebp
jl 0x108e7
movzwl -0x1c(%r15), %ecx
addl %r13d, %ecx
cmpl %ecx, %r14d
jl 0x108e7
ucomisd -0x8(%r15), %xmm1
movq %r10, %rbx
ja 0x108e4
movq %r15, %rbx
movb $0x1, (%rbx)
incq %r12
addq $0x50, %r15
cmpq %r12, %rax
ja 0x108a6
incq %r9
incq %r8
addq $0x50, %rdx
cmpq %rsi, %r9
jne 0x10859
movq 0x8(%rsp), %rsi
callq 0x12b3a
movq 0x10(%rsp), %rdi
movq 0x8(%rdi), %rdx
movq %rax, %rsi
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x12c66
nop
// File: /workspace/github_c_makefile_star2_O1/fukunagatsu[P]RIblast/rna_interaction_search_parameters.cpp
// Function: RnaInteractionSearchParameters::SetParameters(int, char**)
void RnaInteractionSearchParameters::SetParameters(int argc, char* argv[]) {
  int c;
  extern char *optarg;
  while ((c = getopt(argc, argv, "i:o:d:l:e:y:x:f:g:s:m:")) != -1) {
    switch (c) {
    case 'i':
      _input_filename = optarg;
      break;

    case 'o':
      _output_filename = optarg;
      break;
      
    case 'd':
      _db_filename = optarg;
      break;

    case 'l':
      _max_seed_length = atoi(optarg);
      break;

    case 'e':
      _hybrid_energy_threshold = atof(optarg);
      break;
   
    case 'f':
      _interaction_energy_threshold = atof(optarg);
      break;

    case 'g':
      _final_threshold = atof(optarg);
      break;

    case 's':
      _output_style = atoi(optarg);
      break;

    case 'x':
      _drop_out_length_w_gap = atoi(optarg);
      break;

    case 'y':
      _drop_out_length_wo_gap = atoi(optarg);
      break;

    case 'm':
      _min_helix_length = atoi(optarg);
      break;

    default:
      cerr << "Error: The argument is invalid command." << endl;
      exit(1);
    }
  }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rdx, %rbx
movl %esi, %ebp
movq %rdi, %r14
leaq 0x40(%rdi), %rax
movq %rax, 0x10(%rsp)
leaq 0x20(%rdi), %rax
movq %rax, 0x8(%rsp)
leaq 0x6a9e9(%rip), %r15     # 0x7dd98
leaq 0x6a98a(%rip), %r13     # 0x7dd40
movq 0xd2bf3(%rip), %r12     # 0xe5fb0
movl %ebp, %edi
movq %rbx, %rsi
movq %r15, %rdx
callq 0x3070
leal -0x64(%rax), %ecx
cmpl $0x15, %ecx
ja 0x134e3
movslq (%r13,%rcx,4), %rax
addq %r13, %rax
jmpq *%rax
movq (%r12), %r15
movq 0x8(%r14), %r12
movq %r15, %rdi
callq 0x3100
movq %r14, %rdi
jmp 0x1347d
movq (%r12), %rdi
callq 0x3370
movl %eax, 0x94(%r14)
jmp 0x133bd
movq (%r12), %rdi
callq 0x3370
movl %eax, 0x90(%r14)
jmp 0x133bd
movq (%r12), %rdi
callq 0x3370
movl %eax, 0x60(%r14)
jmp 0x133bd
movq (%r12), %r15
movq 0x28(%r14), %r12
movq %r15, %rdi
callq 0x3100
movq 0x8(%rsp), %rdi
jmp 0x1347d
movq (%r12), %rdi
callq 0x3370
movl %eax, 0x74(%r14)
jmp 0x133bd
movq (%r12), %rdi
callq 0x32c0
movsd %xmm0, 0x78(%r14)
jmp 0x133bd
movq (%r12), %r15
movq 0x48(%r14), %r12
movq %r15, %rdi
callq 0x3100
movq 0x10(%rsp), %rdi
xorl %esi, %esi
movq %r12, %rdx
movq 0xd2b27(%rip), %r12     # 0xe5fb0
movq %r15, %rcx
leaq 0x6a905(%rip), %r15     # 0x7dd98
movq %rax, %r8
callq 0x3360
jmp 0x133bd
movq (%r12), %rdi
callq 0x32c0
movsd %xmm0, 0x88(%r14)
jmp 0x133bd
movq (%r12), %rdi
callq 0x32c0
movsd %xmm0, 0x80(%r14)
jmp 0x133bd
movq (%r12), %rdi
callq 0x3370
movl %eax, 0x98(%r14)
jmp 0x133bd
cmpl $-0x1, %eax
jne 0x134f7
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0xd2af2(%rip), %rdi     # 0xe5ff0
leaq 0x6a8aa(%rip), %rsi     # 0x7ddaf
callq 0x3210
movq %rax, %rdi
callq 0x3120
movl $0x1, %edi
callq 0x32a0