LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/kmc_api/../kmc_api/mmer.h
// Function: CMmer::_si::init_norm(unsigned int*, unsigned int)
static void init_norm(uint32* norm, uint32 len)
		{
			uint32 special = 1 << len * 2;
			for(uint32 i = 0 ; i < special ; ++i)
			{				
				uint32 rev = get_rev(i, len);
				uint32 str_val = is_allowed(i, len) ? i : special;
				uint32 rev_val = is_allowed(rev, len) ? rev : special;
				norm[i] = MIN(str_val, rev_val);				
			}
		}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movl %esi, %ebx
leal (%rbx,%rbx), %ecx
movl $0x1, %r12d
shll %cl, %r12d
movq %rdi, %r14
leal -0x2(,%rbx,2), %eax
movl %eax, 0x4(%rsp)
xorl %r15d, %r15d
movl $0x0, %ebp
testl %ebx, %ebx
je 0x416359
xorl %ebp, %ebp
movl 0x4(%rsp), %ecx
movl %ebx, %eax
movl %r15d, %edx
movl %edx, %esi
notl %esi
andl $0x3, %esi
shll %cl, %esi
addl %esi, %ebp
shrl $0x2, %edx
addl $-0x2, %ecx
decl %eax
jne 0x416344
movl %r15d, %edi
movl %ebx, %esi
callq 0x41639e
testb %al, %al
movl %r12d, %r13d
cmovnel %r15d, %r13d
movl %ebp, %edi
movl %ebx, %esi
callq 0x41639e
testb %al, %al
cmovel %r12d, %ebp
cmpl %ebp, %r13d
cmovbl %r13d, %ebp
movl %ebp, (%r14,%r15,4)
incq %r15
cmpq %r12, %r15
jne 0x416330
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
nop
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/kmc_api/../kmc_api/mmer.h
// Function: CMmer::is_allowed(unsigned int, unsigned int)
static bool is_allowed(uint32 mmer, uint32 len)
	{
		if ((mmer & 0x3f) == 0x3f)            // TTT suffix
			return false;
		if ((mmer & 0x3f) == 0x3b)            // TGT suffix
			return false;
		if ((mmer & 0x3c) == 0x3c)            // TG* suffix
			return false;

		for (uint32 j = 0; j < len - 3; ++j)
		if ((mmer & 0xf) == 0)                // AA inside
			return false;
		else
			mmer >>= 2;

		if (mmer == 0)            // AAA prefix
			return false;
		if (mmer == 0x04)        // ACA prefix
			return false;
		if ((mmer & 0xf) == 0)    // *AA prefix
			return false;
	
		return true;
	}

// Assembly:
movl %edi, %eax
notl %eax
testb $0x3b, %al
jne 0x4163a9
xorl %eax, %eax
retq
testb $0x3c, %al
je 0x4163a6
addl $-0x3, %esi
setne %cl
sete %al
testb $0xf, %dil
sete %dl
orb %al, %dl
jne 0x4163df
movl $0x1, %edx
movl %edi, %eax
shrl $0x2, %eax
cmpl %esi, %edx
setb %cl
jae 0x4163e1
andl $0x3c, %edi
incl %edx
testl %edi, %edi
movl %eax, %edi
jne 0x4163c8
jmp 0x4163e1
movl %edi, %eax
testb %cl, %cl
jne 0x4163a6
testl $0xfffffffb, %eax       # imm = 0xFFFFFFFB
je 0x4163a6
testb $0xf, %al
setne %al
retq
nop
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/kmc_api/kmc_file.cpp
// Function: CKMCFile::OpenForRA(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&)
bool CKMCFile::OpenForRA(const std::string &file_name)
{
	uint64 size;
	size_t result;

	if (file_pre || file_suf)
		return false;

	if (!OpenASingleFile(file_name + ".kmc_pre", file_pre, size, (char *)"KMCP"))
		return false;

	ReadParamsFrom_prefix_file_buf(size);

	fclose(file_pre);
	file_pre = NULL;
		
	if (!OpenASingleFile(file_name + ".kmc_suf", file_suf, size, (char *)"KMCS"))
		return false;

	sufix_file_buf = new uchar[size];
	result = fread(sufix_file_buf, 1, size, file_suf);
	if (result != size)
		return false;

	fclose(file_suf);
	file_suf = NULL;

	is_opened = opened_for_RA;
	prefix_index = 0;
	sufix_number = 0;
	return true;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x30, %rsp
cmpq $0x0, 0x20(%rdi)
jne 0x41655b
movq %rdi, %rbx
cmpq $0x0, 0x28(%rdi)
jne 0x41655b
movq %rsi, %r14
leaq 0x20(%rsp), %r12
movq %r12, -0x10(%r12)
movq (%rsi), %rsi
movq 0x8(%r14), %rdx
addq %rsi, %rdx
leaq 0x10(%rsp), %r15
movq %r15, %rdi
callq 0x40805e
leaq 0x18ccba(%rip), %rsi    # 0x5a30fe
movq %r15, %rdi
callq 0x48d830
leaq 0x20(%rbx), %rdx
leaq 0x18da49(%rip), %r8     # 0x5a3ea0
leaq 0x10(%rsp), %r15
leaq 0x8(%rsp), %rcx
movq %r15, %rsi
callq 0x41658e
movl %eax, %ebp
movq (%r15), %rdi
cmpq %r12, %rdi
je 0x416480
movq 0x20(%rsp), %rsi
incq %rsi
callq 0x41b3a0
testb %bpl, %bpl
je 0x41655b
leaq 0x8(%rsp), %rsi
movq %rbx, %rdi
callq 0x416684
movq 0x20(%rbx), %rdi
callq 0x4ed8e0
movq $0x0, 0x20(%rbx)
leaq 0x20(%rsp), %r12
movq %r12, -0x10(%r12)
movq (%r14), %rsi
movq 0x8(%r14), %rdx
addq %rsi, %rdx
leaq 0x10(%rsp), %r14
movq %r14, %rdi
callq 0x40805e
leaq 0x18cbfa(%rip), %rsi    # 0x5a30c9
movq %r14, %rdi
callq 0x48d830
leaq 0x28(%rbx), %rdx
leaq 0x18d9c3(%rip), %r8     # 0x5a3ea5
leaq 0x10(%rsp), %r14
leaq 0x8(%rsp), %rcx
movq %r14, %rsi
callq 0x41658e
movl %eax, %ebp
movq (%r14), %rdi
cmpq %r12, %rdi
je 0x41650b
movq 0x20(%rsp), %rsi
incq %rsi
callq 0x41b3a0
testb %bpl, %bpl
je 0x41655b
movq 0x8(%rsp), %r14
movq %r14, %rdi
callq 0x41c2a0
movq %rax, 0x60(%rbx)
movq 0x28(%rbx), %rcx
movl $0x1, %esi
movq %rax, %rdi
movq %r14, %rdx
callq 0x4ee240
cmpq %r14, %rax
jne 0x41655b
movq 0x28(%rbx), %rdi
callq 0x4ed8e0
xorl %eax, %eax
movq %rax, 0x28(%rbx)
movl $0x1, (%rbx)
movq %rax, 0x40(%rbx)
movq %rax, 0x68(%rbx)
movb $0x1, %al
jmp 0x41655d
xorl %eax, %eax
addq $0x30, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
jmp 0x41656c
movq %rax, %rbx
movq 0x10(%rsp), %rdi
cmpq %r12, %rdi
je 0x416585
movq (%r12), %rsi
incq %rsi
callq 0x41b3a0
movq %rbx, %rdi
callq 0x4c0230
nop
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/kmc_api/kmc_file.cpp
// Function: CKMCFile::OpenASingleFile(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, _IO_FILE*&, unsigned long long&, char*)
bool CKMCFile::OpenASingleFile(const std::string &file_name, FILE *&file_handler, uint64 &size, char marker[])
{
	char _marker[4];
	size_t result;

	if ((file_handler = my_fopen(file_name.c_str(), "rb")) == NULL)
		return false;

	my_fseek(file_handler, 0, SEEK_END);
	size = my_ftell(file_handler);					//the size of a whole file

	my_fseek(file_handler, -4, SEEK_CUR);
	result = fread(_marker, 1, 4, file_handler);
	if (result == 0)
		return false;

	size = size - 4;							//the size of the file without the terminal marker
	if (strncmp(marker, _marker, 4) != 0)
	{
		fclose(file_handler);
		file_handler = NULL;
		return false;
	}

	rewind(file_handler);
	result = fread(_marker, 1, 4, file_handler);
	if (result == 0)
		return false;

	size = size - 4;							//the size of the file without initial and terminal markers 

	if (strncmp(marker, _marker, 4) != 0)
	{
		fclose(file_handler);
		file_handler = NULL;
		return false;
	}

	return true;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %r14
movq %rcx, %r15
movq %rdx, %rbx
movq (%rsi), %rdi
leaq 0x18d92e(%rip), %rsi    # 0x5a3ed7
callq 0x4ee010
movq %rax, (%rbx)
testq %rax, %rax
je 0x41662c
xorl %r12d, %r12d
movq %rax, %rdi
xorl %esi, %esi
movl $0x2, %edx
callq 0x4f2b30
movq (%rbx), %rdi
callq 0x4ee340
movq %rax, (%r15)
movq (%rbx), %rdi
movq $-0x4, %rsi
movl $0x1, %edx
callq 0x4f2b30
movq (%rbx), %rcx
leaq 0x4(%rsp), %rdi
movl $0x1, %esi
movl $0x4, %edx
callq 0x4ee240
testq %rax, %rax
je 0x41662f
addq $-0x4, (%r15)
leaq 0x4(%rsp), %rsi
movl $0x4, %edx
movq %r14, %rdi
callq 0x401048
movq (%rbx), %rdi
testl %eax, %eax
je 0x41663e
callq 0x4ed8e0
movq $0x0, (%rbx)
xorl %r12d, %r12d
movl %r12d, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0x4f2e70
movq (%rbx), %rcx
leaq 0x4(%rsp), %rdi
movl $0x1, %esi
movl $0x4, %edx
callq 0x4ee240
testq %rax, %rax
je 0x41662c
addq $-0x4, (%r15)
leaq 0x4(%rsp), %rsi
movl $0x4, %edx
movq %r14, %rdi
callq 0x401048
testl %eax, %eax
je 0x41667e
movq (%rbx), %rdi
jmp 0x416620
movb $0x1, %r12b
jmp 0x41662f
nop
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/kmc_api/kmc_file.cpp
// Function: CKMCFile::~CKMCFile()
CKMCFile::~CKMCFile()
{
	if (file_pre)
		fclose(file_pre);
	if (file_suf)
		fclose(file_suf);
	if (prefix_file_buf)
		delete[] prefix_file_buf;
	if (sufix_file_buf)
		delete[] sufix_file_buf;
	if (signature_map)
		delete[] signature_map;
}

// Assembly:
pushq %rbx
movq %rdi, %rbx
movq 0x20(%rdi), %rdi
testq %rdi, %rdi
je 0x416c88
callq 0x4ed8e0
movq 0x28(%rbx), %rdi
testq %rdi, %rdi
je 0x416c96
callq 0x4ed8e0
movq 0x30(%rbx), %rdi
testq %rdi, %rdi
je 0x416ca4
callq 0x41b3b0
movq 0x60(%rbx), %rdi
testq %rdi, %rdi
je 0x416cb2
callq 0x41b3b0
movq 0x50(%rbx), %rdi
testq %rdi, %rdi
je 0x416cc1
popq %rbx
jmp 0x41b3b0
popq %rbx
retq
nop
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/kmc_api/kmc_file.cpp
// Function: CKMCFile::CheckKmer(CKmerAPI&, float&)
bool CKMCFile::CheckKmer(CKmerAPI &kmer, float &count)
{
	uint32 int_counter;
	if (CheckKmer(kmer, int_counter))
	{
		if (mode == 0)
			count = (float)int_counter;
		else
			memcpy(&count, &int_counter, counter_size);
		return true;
	}
	return false;
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
subq $0x10, %rsp
movq %rdx, %rbx
movq %rdi, %r14
leaq 0xc(%rsp), %rdx
callq 0x416d18
movl %eax, %ebp
testb %al, %al
je 0x416d0c
cmpl $0x0, 0x7c(%r14)
je 0x416cff
movl 0x80(%r14), %edx
leaq 0xc(%rsp), %rsi
movq %rbx, %rdi
callq 0x401080
jmp 0x416d0c
movl 0xc(%rsp), %eax
cvtsi2ss %rax, %xmm0
movss %xmm0, (%rbx)
movl %ebp, %eax
addq $0x10, %rsp
popq %rbx
popq %r14
popq %rbp
retq
nop
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/kmc_api/kmc_file.cpp
// Function: CKMCFile::CheckKmer(CKmerAPI&, unsigned int&)
bool CKMCFile::CheckKmer(CKmerAPI &kmer, uint32 &count)
{
	if(is_opened != opened_for_RA)
		return false;
	if(end_of_file)
		return false;
	
	//recognize a prefix:
	uint64 pattern_prefix_value = kmer.kmer_data[0];

	uint32 pattern_offset = (sizeof(pattern_prefix_value)* 8) - (lut_prefix_length * 2) - (kmer.byte_alignment * 2);
	int64 index_start = 0, index_stop = 0;

	pattern_prefix_value = pattern_prefix_value >> pattern_offset;  //complements with 0
	if (pattern_prefix_value >= prefix_file_buf_size)
		return false;

	if (kmc_version == 0x200)
	{
		uint32 signature = kmer.get_signature(signature_len);
		uint32 bin_start_pos = signature_map[signature];
		bin_start_pos *= single_LUT_size;				
		//look into the array with data
		index_start = *(prefix_file_buf + bin_start_pos + pattern_prefix_value);
		index_stop = *(prefix_file_buf + bin_start_pos + pattern_prefix_value + 1) - 1;
	}
	else if (kmc_version == 0)
	{
		//look into the array with data
		index_start = prefix_file_buf[pattern_prefix_value];
		index_stop = prefix_file_buf[pattern_prefix_value + 1] - 1;
	}
	uint64 tmp_count ;
	bool res = BinarySearch(index_start, index_stop, kmer, tmp_count, pattern_offset);
	count = (uint32)tmp_count;
	return res;
}

// Assembly:
cmpl $0x1, (%rdi)
jne 0x416d8a
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rdi, %r15
cmpb $0x0, 0x18(%rdi)
jne 0x416d8d
movq %rsi, %r14
movq (%rsi), %rax
movq (%rax), %r12
movl 0x84(%r15), %ecx
addl 0xc(%rsi), %ecx
addl %ecx, %ecx
negb %cl
shrq %cl, %r12
cmpq 0x38(%r15), %r12
jae 0x416d8d
movq %rdx, %rbx
movl 0xa4(%r15), %eax
testl %eax, %eax
je 0x416d91
cmpl $0x200, %eax            # imm = 0x200
jne 0x416da3
movl 0x88(%r15), %esi
movq %r14, %rdi
callq 0x4197fe
movq 0x50(%r15), %rcx
movl %eax, %edx
movl 0x48(%r15), %eax
imull (%rcx,%rdx,4), %eax
shlq $0x3, %rax
addq 0x30(%r15), %rax
jmp 0x416d95
xorl %eax, %eax
retq
xorl %eax, %eax
jmp 0x416dbe
movq 0x30(%r15), %rax
movq (%rax,%r12,8), %rsi
movq 0x8(%rax,%r12,8), %rdx
decq %rdx
jmp 0x416da7
xorl %edx, %edx
xorl %esi, %esi
movq %rsp, %r12
movq %r15, %rdi
movq %r14, %rcx
movq %r12, %r8
callq 0x416dca
movl (%r12), %ecx
movl %ecx, (%rbx)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/kmc_api/kmc_file.cpp
// Function: CKMCFile::CheckKmer(CKmerAPI&, unsigned long long&)
bool CKMCFile::CheckKmer(CKmerAPI &kmer, uint64 &count)
{
	if (is_opened != opened_for_RA)
		return false;
	if (end_of_file)
		return false;

	//recognize a prefix:
	uint64 pattern_prefix_value = kmer.kmer_data[0];

	uint32 pattern_offset = (sizeof(pattern_prefix_value)* 8) - (lut_prefix_length * 2) - (kmer.byte_alignment * 2);
	int64 index_start = 0, index_stop = 0;

	pattern_prefix_value = pattern_prefix_value >> pattern_offset;  //complements with 0
	if (pattern_prefix_value >= prefix_file_buf_size)
		return false;

	if (kmc_version == 0x200)
	{
		uint32 signature = kmer.get_signature(signature_len);
		uint32 bin_start_pos = signature_map[signature];
		bin_start_pos *= single_LUT_size;
		//look into the array with data
		index_start = *(prefix_file_buf + bin_start_pos + pattern_prefix_value);
		index_stop = *(prefix_file_buf + bin_start_pos + pattern_prefix_value + 1) - 1;
	}
	else if (kmc_version == 0)
	{
		//look into the array with data
		index_start = prefix_file_buf[pattern_prefix_value];
		index_stop = prefix_file_buf[pattern_prefix_value + 1] - 1;
	}
	return BinarySearch(index_start, index_stop, kmer, count, pattern_offset);
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
cmpl $0x1, (%rdi)
jne 0x417040
movq %rdi, %r15
cmpb $0x0, 0x18(%rdi)
jne 0x417040
movq %rsi, %r14
movq (%rsi), %rax
movq (%rax), %r12
movl 0x84(%r15), %ecx
addl 0xc(%rsi), %ecx
addl %ecx, %ecx
negb %cl
shrq %cl, %r12
cmpq 0x38(%r15), %r12
jae 0x417040
movq %rdx, %rbx
movl 0xa4(%r15), %eax
testl %eax, %eax
je 0x41704e
cmpl $0x200, %eax            # imm = 0x200
jne 0x417060
movl 0x88(%r15), %esi
movq %r14, %rdi
callq 0x4197fe
movq 0x50(%r15), %rcx
movl %eax, %edx
movl 0x48(%r15), %eax
imull (%rcx,%rdx,4), %eax
shlq $0x3, %rax
addq 0x30(%r15), %rax
jmp 0x417052
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
movq 0x30(%r15), %rax
movq (%rax,%r12,8), %rsi
movq 0x8(%rax,%r12,8), %rdx
decq %rdx
jmp 0x417064
xorl %esi, %esi
xorl %edx, %edx
movq %r15, %rdi
movq %r14, %rcx
movq %rbx, %r8
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
jmp 0x416dca
nop
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/kmc_api/kmc_file.cpp
// Function: CKMCFile::ReadNextKmer(CKmerAPI&, float&)
bool CKMCFile::ReadNextKmer(CKmerAPI &kmer, float &count)
{
	uint32 int_counter;
	if (ReadNextKmer(kmer, int_counter))
	{
		if (mode == 0)
			count = (float)int_counter;
		else
			memcpy(&count, &int_counter, counter_size);
		return true;
	}
	return false;

}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
subq $0x10, %rsp
movq %rdx, %rbx
movq %rdi, %r14
leaq 0xc(%rsp), %rdx
callq 0x4170d6
movl %eax, %ebp
testb %al, %al
je 0x4170ca
cmpl $0x0, 0x7c(%r14)
je 0x4170bd
movl 0x80(%r14), %edx
leaq 0xc(%rsp), %rsi
movq %rbx, %rdi
callq 0x401080
jmp 0x4170ca
movl 0xc(%rsp), %eax
cvtsi2ss %rax, %xmm0
movss %xmm0, (%rbx)
movl %ebp, %eax
addq $0x10, %rsp
popq %rbx
popq %r14
popq %rbp
retq
nop
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/kmc_api/kmc_file.cpp
// Function: CKMCFile::Reload_sufix_file_buf()
void CKMCFile::Reload_sufix_file_buf()
{
	auto to_read = MIN(suf_file_left_to_read, part_size);
	auto readed = fread(sufix_file_buf, 1, (size_t)to_read, file_suf);
	suf_file_left_to_read -= readed;
	if (readed != to_read)
	{
		std::cerr << "Error: some error while reading suffix file\n";
		exit(1);
	}
	index_in_partial_buf = 0;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq 0x202e38(%rip), %r14    # 0x61a178
movq 0x8(%rdi), %rax
movq 0x28(%rdi), %rcx
cmpq %r14, %rax
cmovbq %rax, %r14
movq 0x60(%rdi), %rdi
movl $0x1, %esi
movq %r14, %rdx
callq 0x4ee240
subq %rax, 0x8(%rbx)
cmpq %r14, %rax
jne 0x417379
movq $0x0, 0x70(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r14
retq
movq $0x1b72840, %rdi        # imm = 0x1B72840
leaq 0x18cb23(%rip), %rsi    # 0x5a3eaa
callq 0x485cb0
movl $0x1, %edi
callq 0x4dbb10
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/kmc_api/kmc_file.cpp
// Function: CKMCFile::Close()
bool CKMCFile::Close()
{
	if(is_opened)
	{
		if(file_pre)
		{
			fclose(file_pre);	
			file_pre = NULL;
		}
		if(file_suf)
		{
			fclose(file_suf);
			file_suf = NULL;
		}
	
		is_opened = closed;
		end_of_file = false;
		delete [] prefix_file_buf;
		prefix_file_buf = NULL;
		delete [] sufix_file_buf;
		sufix_file_buf = NULL;
		delete[] signature_map;
		signature_map = NULL;

		return true;
	}
	else
		return false;
}

// Assembly:
pushq %rbp
pushq %rbx
pushq %rax
movl (%rdi), %ebp
testl %ebp, %ebp
je 0x417616
movq %rdi, %rbx
movq 0x20(%rdi), %rdi
testq %rdi, %rdi
je 0x4175b4
callq 0x4ed8e0
movq $0x0, 0x20(%rbx)
movq 0x28(%rbx), %rdi
testq %rdi, %rdi
je 0x4175ca
callq 0x4ed8e0
movq $0x0, 0x28(%rbx)
movl $0x0, (%rbx)
movb $0x0, 0x18(%rbx)
movq 0x30(%rbx), %rdi
testq %rdi, %rdi
je 0x4175e2
callq 0x41b3b0
movq $0x0, 0x30(%rbx)
movq 0x60(%rbx), %rdi
testq %rdi, %rdi
je 0x4175f8
callq 0x41b3b0
movq $0x0, 0x60(%rbx)
movq 0x50(%rbx), %rdi
testq %rdi, %rdi
je 0x41760e
callq 0x41b3b0
movq $0x0, 0x50(%rbx)
testl %ebp, %ebp
setne %al
addq $0x8, %rsp
popq %rbx
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/kmc_api/kmc_file.cpp
// Function: CKMCFile::RestartListing()
bool CKMCFile::RestartListing(void)
{
	if(is_opened == opened_for_listing)
	{
		my_fseek(file_suf , 4 , SEEK_SET);
		suf_file_left_to_read = suffix_file_total_to_read;
		auto to_read = MIN(suf_file_left_to_read, part_size);
		auto readed = fread(sufix_file_buf, 1, to_read, file_suf);
		if (readed != to_read)
		{
			std::cerr << "Error: some error while reading suffix file\n";
			return false;
		}

		suf_file_left_to_read -= readed;
		prefix_index = 0;
		sufix_number = 0;
		index_in_partial_buf = 0;

		end_of_file = total_kmers == 0;

		return true;
	}
	return false;
		
}

// Assembly:
cmpl $0x2, (%rdi)
jne 0x417691
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq 0x28(%rdi), %rdi
movl $0x4, %esi
xorl %edx, %edx
callq 0x4f2b30
movq 0x10(%rbx), %rax
movq 0x28(%rbx), %rcx
movq %rax, 0x8(%rbx)
movq 0x202b27(%rip), %r14    # 0x61a178
cmpq %r14, %rax
cmovbq %rax, %r14
movq 0x60(%rbx), %rdi
movl $0x1, %esi
movq %r14, %rdx
callq 0x4ee240
cmpq %r14, %rax
jne 0x417694
subq %rax, 0x8(%rbx)
movq $0x0, 0x40(%rbx)
xorps %xmm0, %xmm0
movups %xmm0, 0x68(%rbx)
cmpq $0x0, 0x98(%rbx)
sete 0x18(%rbx)
movb $0x1, %al
jmp 0x4176ae
xorl %eax, %eax
retq
movq $0x1b72840, %rdi        # imm = 0x1B72840
leaq 0x18c808(%rip), %rsi    # 0x5a3eaa
movl $0x2c, %edx
callq 0x485780
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/kmc_api/kmc_file.cpp
// Function: CKMCFile::Info(unsigned int&, unsigned int&, unsigned int&, unsigned int&, unsigned int&, unsigned int&, unsigned long long&, unsigned long long&)
bool CKMCFile::Info(uint32 &_kmer_length, uint32 &_mode, uint32 &_counter_size, uint32 &_lut_prefix_length, uint32 &_signature_len, uint32 &_min_count, uint64 &_max_count, uint64 &_total_kmers)
{
	if(is_opened)
	{
		_kmer_length = kmer_length;
		_mode = mode;
		_counter_size = counter_size;
		_lut_prefix_length = lut_prefix_length;
		if (kmc_version == 0x200)
			_signature_len = signature_len;
		else
			_signature_len = 0; //for kmc1 there is no signature_len
		_min_count = min_count;
		_max_count = max_count;
		_total_kmers = total_kmers;
		return true;
	}
	return false;
}

// Assembly:
movl (%rdi), %eax
testl %eax, %eax
je 0x417a47
pushq %rbp
pushq %rbx
movq 0x28(%rsp), %r10
movq 0x20(%rsp), %r11
movq 0x18(%rsp), %rbx
movl 0x78(%rdi), %ebp
movl %ebp, (%rsi)
movl 0x7c(%rdi), %esi
movl %esi, (%rdx)
movl 0x80(%rdi), %edx
movl %edx, (%rcx)
movl 0x84(%rdi), %ecx
movl %ecx, (%r8)
xorl %ecx, %ecx
cmpl $0x200, 0xa4(%rdi)      # imm = 0x200
jne 0x417a26
movl 0x88(%rdi), %ecx
movl %ecx, (%r9)
movl 0x8c(%rdi), %ecx
movl %ecx, (%rbx)
movq 0x90(%rdi), %rcx
movq %rcx, (%r11)
movq 0x98(%rdi), %rcx
movq %rcx, (%r10)
popq %rbx
popq %rbp
testl %eax, %eax
setne %al
retq
nop
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/kmc_api/kmc_file.cpp
// Function: CKMCFile::Info(CKMCFileInfo&)
bool CKMCFile::Info(CKMCFileInfo& info)
{
	if (is_opened)
	{
		info.kmer_length = kmer_length;
		info.mode = mode;
		info.counter_size = counter_size;
		info.lut_prefix_length = lut_prefix_length;
		if (kmc_version == 0x200)
			info.signature_len = signature_len;
		else
			info.signature_len = 0; //for kmc1 there is no signature_len
		info.min_count = min_count;
		info.max_count = max_count;
		info.total_kmers = total_kmers;
		info.both_strands = both_strands;
		return true;
	}
	return false;
}

// Assembly:
movl (%rdi), %eax
testl %eax, %eax
je 0x417ab0
movl 0x78(%rdi), %ecx
movl %ecx, (%rsi)
movl 0x7c(%rdi), %ecx
movl %ecx, 0x4(%rsi)
movl 0x80(%rdi), %ecx
movl %ecx, 0x8(%rsi)
movl 0x84(%rdi), %ecx
movl %ecx, 0xc(%rsi)
xorl %ecx, %ecx
cmpl $0x200, 0xa4(%rdi)      # imm = 0x200
jne 0x417a85
movl 0x88(%rdi), %ecx
movl %ecx, 0x10(%rsi)
movl 0x8c(%rdi), %ecx
movl %ecx, 0x14(%rsi)
movq 0x90(%rdi), %rcx
movq %rcx, 0x18(%rsi)
movq 0x98(%rdi), %rcx
movq %rcx, 0x28(%rsi)
movb 0xa0(%rdi), %cl
movb %cl, 0x20(%rsi)
testl %eax, %eax
setne %al
retq
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/kmc_api/kmc_file.cpp
// Function: CKMCFile::GetCountersForRead(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, std::vector<unsigned int, std::allocator<unsigned int>>&)
bool CKMCFile::GetCountersForRead(const std::string& read, std::vector<uint32>& counters)
{
	if (is_opened != opened_for_RA)
		return false;

	if (read.length() < kmer_length)
	{
		counters.clear();
		return false;
	}

	if (kmc_version == 0x200)
	{		
		if (both_strands)
			return GetCountersForRead_kmc2_both_strands(read, counters);
		else
			return GetCountersForRead_kmc2(read, counters);
	}
	else if (kmc_version == 0)
	{
		if (both_strands)
			return GetCountersForRead_kmc1_both_strands(read,counters);
		else
			return GetCountersForRead_kmc1(read, counters);
	}
	else
		return false; //never should be here
}

// Assembly:
pushq %rax
cmpl $0x1, (%rdi)
jne 0x417af5
movl 0x78(%rdi), %eax
cmpq %rax, 0x8(%rsi)
jae 0x417ad4
movq (%rdx), %rax
cmpq %rax, 0x8(%rdx)
je 0x417af5
movq %rax, 0x8(%rdx)
jmp 0x417af5
movl 0xa4(%rdi), %eax
testl %eax, %eax
je 0x417af9
cmpl $0x200, %eax            # imm = 0x200
jne 0x417af5
cmpb $0x1, 0xa0(%rdi)
jne 0x417b09
callq 0x417b1a
jmp 0x417b15
xorl %eax, %eax
popq %rcx
retq
cmpb $0x1, 0xa0(%rdi)
jne 0x417b10
callq 0x418724
jmp 0x417b15
callq 0x4182b0
jmp 0x417b15
callq 0x418f12
movb $0x1, %al
jmp 0x417af7
nop
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/kmc_api/kmc_file.cpp
// Function: CKMCFile::GetCountersForRead(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, std::vector<float, std::allocator<float>>&)
bool CKMCFile::GetCountersForRead(const std::string& read, std::vector<float>& counters)
{
	if (is_opened != opened_for_RA)
		return false;
	std::vector<uint32> uint32_v;
	if (GetCountersForRead(read, uint32_v))
	{
		counters.clear();
		counters.resize(uint32_v.size());
		if (mode == 0)
		{
			for (uint32 i = 0; i < uint32_v.size(); ++i)
				counters[i] = static_cast<float>(uint32_v[i]);
		}
		else
		{
			for (uint32 i = 0; i < uint32_v.size(); ++i)
				memcpy(&counters[i], &uint32_v[i], counter_size);
		}

		return true;
	}
	return false;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
subq $0x18, %rsp
cmpl $0x1, (%rdi)
jne 0x419407
movq %rdx, %r14
movq %rdi, %r15
xorps %xmm0, %xmm0
movq %rsp, %rdx
movaps %xmm0, (%rdx)
movq $0x0, 0x10(%rdx)
callq 0x417ab6
movl %eax, %ebx
testb %al, %al
je 0x419433
movq (%r14), %rax
cmpq %rax, 0x8(%r14)
je 0x4193a0
movq %rax, 0x8(%r14)
movq 0x8(%rsp), %rsi
subq (%rsp), %rsi
sarq $0x2, %rsi
movq %r14, %rdi
callq 0x419902
cmpl $0x0, 0x7c(%r15)
movq (%rsp), %rax
movq 0x8(%rsp), %rcx
je 0x41940b
cmpq %rax, %rcx
je 0x419433
movl $0x1, %ebp
xorl %ecx, %ecx
leaq (,%rcx,4), %rdi
addq (%r14), %rdi
leaq (%rax,%rcx,4), %rsi
movl 0x80(%r15), %edx
callq 0x401080
movl %ebp, %ecx
movq (%rsp), %rax
movq 0x8(%rsp), %rdx
subq %rax, %rdx
sarq $0x2, %rdx
incl %ebp
cmpq %rcx, %rdx
ja 0x4193d1
jmp 0x419433
xorl %ebx, %ebx
jmp 0x419449
subq %rax, %rcx
je 0x419433
sarq $0x2, %rcx
movq (%r14), %rdx
xorl %esi, %esi
movl (%rax,%rsi,4), %edi
xorps %xmm0, %xmm0
cvtsi2ss %rdi, %xmm0
movss %xmm0, (%rdx,%rsi,4)
incq %rsi
movl %esi, %edi
cmpq %rdi, %rcx
ja 0x419419
movq (%rsp), %rdi
testq %rdi, %rdi
je 0x419449
movq 0x10(%rsp), %rsi
subq %rdi, %rsi
callq 0x41b3a0
movl %ebx, %eax
addq $0x18, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %rbx
movq (%rsp), %rdi
testq %rdi, %rdi
je 0x41946f
movq 0x10(%rsp), %rsi
subq %rdi, %rsi
callq 0x41b3a0
movq %rbx, %rdi
callq 0x4c0230
nop
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/kmc_api/kmc_file.cpp
// Function: CKMCFile::count_for_kmer_kmc1(CKmerAPI&)
uint32 CKMCFile::count_for_kmer_kmc1(CKmerAPI& kmer)
{
	//recognize a prefix:

	uint64 pattern_prefix_value = kmer.kmer_data[0];

	uint32 pattern_offset = (sizeof(pattern_prefix_value)* 8) - (lut_prefix_length * 2) - (kmer.byte_alignment * 2);

	pattern_prefix_value = pattern_prefix_value >> pattern_offset;  //complements with 0
	if (pattern_prefix_value >= prefix_file_buf_size)
		return false;
	//look into the array with data

	int64 index_start = prefix_file_buf[pattern_prefix_value];
	int64 index_stop = prefix_file_buf[pattern_prefix_value + 1] - 1;

	uint64 counter = 0;
	if (BinarySearch(index_start, index_stop, kmer, counter, pattern_offset))
		return (uint32)counter;
	return 0;
}

// Assembly:
movq (%rsi), %rax
movq (%rax), %rdx
movl 0x84(%rdi), %ecx
addl 0xc(%rsi), %ecx
addl %ecx, %ecx
negb %cl
shrq %cl, %rdx
xorl %eax, %eax
cmpq 0x38(%rdi), %rdx
jae 0x4194cb
pushq %rax
movq %rsi, %r9
movq 0x30(%rdi), %rax
movq (%rax,%rdx,8), %rsi
movq 0x8(%rax,%rdx,8), %rdx
decq %rdx
movq %rsp, %r8
movq $0x0, (%r8)
movq %r9, %rcx
callq 0x416dca
movl %eax, %ecx
xorl %eax, %eax
testb %cl, %cl
je 0x4194c7
movl (%rsp), %eax
addq $0x8, %rsp
retq
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/kmc_api/kmc_file.cpp
// Function: CKMCFile::count_for_kmer_kmc2(CKmerAPI&, unsigned int)
uint32 CKMCFile::count_for_kmer_kmc2(CKmerAPI& kmer, uint32 bin_start_pos)
{
	//recognize a prefix:
	uint64 pattern_prefix_value = kmer.kmer_data[0];

	uint32 pattern_offset = (sizeof(pattern_prefix_value)* 8) - (lut_prefix_length * 2) - (kmer.byte_alignment * 2);

	pattern_prefix_value = pattern_prefix_value >> pattern_offset;  //complements with 0
	if (pattern_prefix_value >= prefix_file_buf_size)
		return false;
	//look into the array with data

	int64 index_start = *(prefix_file_buf + bin_start_pos + pattern_prefix_value);
	int64 index_stop = *(prefix_file_buf + bin_start_pos + pattern_prefix_value + 1) - 1;

	uint64 counter = 0;
	if (BinarySearch(index_start, index_stop, kmer, counter, pattern_offset))
		return (uint32)counter;
	return 0;
}

// Assembly:
movq (%rsi), %rax
movq (%rax), %r8
movl 0x84(%rdi), %ecx
addl 0xc(%rsi), %ecx
addl %ecx, %ecx
negb %cl
shrq %cl, %r8
xorl %eax, %eax
cmpq 0x38(%rdi), %r8
jae 0x419525
pushq %rax
movq %rsi, %r9
movl %edx, %eax
shlq $0x3, %rax
addq 0x30(%rdi), %rax
movq (%rax,%r8,8), %rsi
movq 0x8(%rax,%r8,8), %rdx
decq %rdx
movq %rsp, %r8
movq $0x0, (%r8)
movq %r9, %rcx
callq 0x416dca
movl %eax, %ecx
xorl %eax, %eax
testb %cl, %cl
je 0x419521
movl (%rsp), %eax
addq $0x8, %rsp
retq
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/kmc_api/kmer_api.h
// Function: CKmerAPI::get_signature(unsigned int)
uint32 get_signature(uint32 sig_len)
	 {
		 uchar symb;
		 CMmer cur_mmr(sig_len);
		 
		 for(uint32 i = 0; i < sig_len; ++i)
		 {
			 symb = get_num_symbol(i);
			 cur_mmr.insert(symb);
		 }
		 CMmer min_mmr(cur_mmr);
		 for (uint32 i = sig_len; i < kmer_length; ++i)
		 {
			 symb = get_num_symbol(i);
			 cur_mmr.insert(symb);
			 
			 if (cur_mmr < min_mmr)
				 min_mmr = cur_mmr;
		 }
		 return min_mmr.get();
	 }

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x20, %rsp
movl %esi, %ebx
movq %rdi, %r14
movabsq $-0x4000000000000000, %r15 # imm = 0xC000000000000000
movq %rsp, %rdi
callq 0x416258
testl %ebx, %ebx
je 0x41988d
movl (%rsp), %eax
movl 0x4(%rsp), %edx
movl 0x8(%r14), %esi
movzbl 0xc(%r14), %edi
movq (%r14), %r8
movq 0x10(%rsp), %r9
leal (%rdi,%rdi), %r10d
xorl %r11d, %r11d
movl $0x0, %ecx
cmpl %r11d, %esi
jbe 0x419871
leal (%rdi,%r11), %r12d
movl %r10d, %ecx
andb $0x3e, %cl
movq %r15, %r13
shrq %cl, %r13
shrl $0x5, %r12d
andq (%r8,%r12,8), %r13
xorb $0x3e, %cl
shrq %cl, %r13
movzbl %r13b, %ecx
leal (%rcx,%rax,4), %eax
andl %edx, %eax
movl %eax, (%rsp)
movl (%r9,%rax,4), %ecx
movl %ecx, 0x8(%rsp)
incl %r11d
addl $0x2, %r10d
cmpl %r11d, %ebx
jne 0x419845
movl 0x8(%rsp), %eax
movl 0x8(%r14), %edx
subl %ebx, %edx
jbe 0x4198f3
movl (%rsp), %esi
movl 0x4(%rsp), %edi
movzbl 0xc(%r14), %ecx
movq (%r14), %r8
movq 0x10(%rsp), %r9
addl %ecx, %ebx
leal (%rbx,%rbx), %r10d
movl %r10d, %ecx
andb $0x3e, %cl
movq %r15, %r11
shrq %cl, %r11
movl %ebx, %r14d
shrl $0x5, %r14d
andq (%r8,%r14,8), %r11
xorb $0x3e, %cl
shrq %cl, %r11
movzbl %r11b, %ecx
leal (%rcx,%rsi,4), %esi
andl %edi, %esi
movl %esi, (%rsp)
movl (%r9,%rsi,4), %ecx
cmpl %eax, %ecx
cmovbl %ecx, %eax
movl %ecx, 0x8(%rsp)
addl $0x2, %r10d
incl %ebx
decl %edx
jne 0x4198b3
addq $0x20, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
nop
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/stats_ml/stats.cpp
// Function: spearman_correlation_coefficient(std::vector<float, std::allocator<float>>, std::vector<float, std::allocator<float>>)
float spearman_correlation_coefficient(std::vector<float> group1, std::vector<float> group2)
{
	std::vector<float> ranked_data1, ranked_data2;
	float d2 = 0;
	uint32_t n = group1.size();

	getrank(group1, ranked_data1);
	getrank(group2, ranked_data2);

	for (uint32_t i = 0; i < n; i++) d2 += (group1[i] - group2[i]) * (group1[i] - group2[i]);

	return 1.0 - 6.0 * d2 / n / (n * n - 1);
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
subq $0x80, %rsp
movq %rsi, %rbx
movq %rdi, %r14
xorps %xmm0, %xmm0
movaps %xmm0, 0x30(%rsp)
xorl %eax, %eax
movq %rax, 0x40(%rsp)
movq %rax, 0x20(%rsp)
movaps %xmm0, 0x10(%rsp)
movq 0x8(%rdi), %r15
subq (%rdi), %r15
leaq 0x68(%rsp), %rdi
movq %r14, %rsi
callq 0x40c0a2
leaq 0x68(%rsp), %rdi
leaq 0x30(%rsp), %rsi
callq 0x419f48
movq 0x68(%rsp), %rdi
testq %rdi, %rdi
je 0x41a4da
movq 0x78(%rsp), %rsi
subq %rdi, %rsi
callq 0x41b3a0
leaq 0x50(%rsp), %rdi
movq %rbx, %rsi
callq 0x40c0a2
leaq 0x50(%rsp), %rdi
leaq 0x10(%rsp), %rsi
callq 0x419f48
shrq $0x2, %r15
movq 0x50(%rsp), %rdi
testq %rdi, %rdi
je 0x41a511
movq 0x60(%rsp), %rsi
subq %rdi, %rsi
callq 0x41b3a0
testl %r15d, %r15d
je 0x41a54c
movq (%r14), %rax
movq (%rbx), %rcx
movl %r15d, %edx
xorps %xmm0, %xmm0
xorl %esi, %esi
movss (%rax,%rsi,4), %xmm1
subss (%rcx,%rsi,4), %xmm1
mulss %xmm1, %xmm1
addss %xmm1, %xmm0
incq %rsi
cmpq %rsi, %rdx
jne 0x41a524
cvtss2sd %xmm0, %xmm0
mulsd 0x1899d6(%rip), %xmm0   # 0x5a3f20
jmp 0x41a54f
xorps %xmm0, %xmm0
movsd %xmm0, 0x8(%rsp)
movq 0x10(%rsp), %rdi
testq %rdi, %rdi
je 0x41a56c
movq 0x20(%rsp), %rsi
subq %rdi, %rsi
callq 0x41b3a0
movq 0x30(%rsp), %rdi
testq %rdi, %rdi
je 0x41a583
movq 0x40(%rsp), %rsi
subq %rdi, %rsi
callq 0x41b3a0
movl %r15d, %eax
xorps %xmm0, %xmm0
cvtsi2sd %rax, %xmm0
movsd 0x8(%rsp), %xmm1
divsd %xmm0, %xmm1
imull %r15d, %r15d
decl %r15d
xorps %xmm0, %xmm0
cvtsi2sd %r15, %xmm0
divsd %xmm0, %xmm1
movsd 0x189965(%rip), %xmm0   # 0x5a3f18
subsd %xmm1, %xmm0
cvtsd2ss %xmm0, %xmm0
addq $0x80, %rsp
popq %rbx
popq %r14
popq %r15
retq
movq %rax, %rbx
movq 0x50(%rsp), %rdi
testq %rdi, %rdi
je 0x41a5fb
movq 0x60(%rsp), %rsi
jmp 0x41a5ee
movq %rax, %rbx
movq 0x68(%rsp), %rdi
testq %rdi, %rdi
je 0x41a5fb
movq 0x78(%rsp), %rsi
subq %rdi, %rsi
callq 0x41b3a0
jmp 0x41a5fb
movq %rax, %rbx
movq 0x10(%rsp), %rdi
testq %rdi, %rdi
je 0x41a612
movq 0x20(%rsp), %rsi
subq %rdi, %rsi
callq 0x41b3a0
movq 0x30(%rsp), %rdi
testq %rdi, %rdi
je 0x41a629
movq 0x40(%rsp), %rsi
subq %rdi, %rsi
callq 0x41b3a0
movq %rbx, %rdi
callq 0x4c0230
nop
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/stats_ml/logistic_classifier.cpp
// Function: Logistic::gradient(double)
void Logistic::gradient(double lam) {
	for (uint32_t i = 0; i < param.w.size(); i++) {
		double tmp = 0.0L;
		for (uint32_t j = 0; j < dataSet.size(); j++) {
			tmp += (dataSet[j].cls - logiFun(param, dataSet[j])) * dataSet[j].features[i] * lam;
		}
		param.w[i] += (tmp);
	}
	double tmp = 0.0L;
	for (uint32_t j = 0; j < dataSet.size(); j++) {
		tmp += (dataSet[j].cls - logiFun(param, dataSet[j])) * lam;
	}
	param.d += tmp;

}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x20, %rsp
movsd %xmm0, 0x18(%rsp)
movq %rdi, %rbx
leaq 0x18(%rdi), %r14
movq 0x20(%rdi), %rax
cmpq 0x18(%rdi), %rax
je 0x41af5c
xorl %r15d, %r15d
movq (%rbx), %rdx
cmpq %rdx, 0x8(%rbx)
je 0x41af30
xorpd %xmm0, %xmm0
movl $0x1, %ebp
xorl %r12d, %r12d
movsd %xmm0, 0x8(%rsp)
shlq $0x5, %r12
xorps %xmm0, %xmm0
cvtsi2sdl 0x18(%rdx,%r12), %xmm0
movsd %xmm0, 0x10(%rsp)
addq %r12, %rdx
movq %rbx, %rdi
movq %r14, %rsi
callq 0x41b068
movsd 0x10(%rsp), %xmm1
subsd %xmm0, %xmm1
movq (%rbx), %rdx
movq 0x8(%rbx), %rax
movq (%rdx,%r12), %rcx
xorps %xmm0, %xmm0
cvtss2sd (%rcx,%r15,4), %xmm0
mulsd %xmm1, %xmm0
mulsd 0x18(%rsp), %xmm0
movsd 0x8(%rsp), %xmm1
addsd %xmm0, %xmm1
movsd %xmm1, 0x8(%rsp)
movsd 0x8(%rsp), %xmm0
movl %ebp, %r12d
subq %rdx, %rax
sarq $0x5, %rax
incl %ebp
cmpq %r12, %rax
ja 0x41aeb7
jmp 0x41af34
xorpd %xmm0, %xmm0
movq 0x18(%rbx), %rax
addsd (%rax,%r15,8), %xmm0
movsd %xmm0, (%rax,%r15,8)
incl %r15d
movq 0x20(%rbx), %rax
subq 0x18(%rbx), %rax
sarq $0x3, %rax
cmpq %r15, %rax
ja 0x41ae9e
movq (%rbx), %rax
cmpq %rax, 0x8(%rbx)
je 0x41afcb
xorpd %xmm0, %xmm0
movl $0x1, %ebp
xorl %ecx, %ecx
movsd %xmm0, 0x8(%rsp)
shlq $0x5, %rcx
leaq (%rax,%rcx), %rdx
xorps %xmm0, %xmm0
cvtsi2sdl 0x18(%rax,%rcx), %xmm0
movsd %xmm0, 0x10(%rsp)
movq %rbx, %rdi
movq %r14, %rsi
callq 0x41b068
movsd 0x10(%rsp), %xmm1
subsd %xmm0, %xmm1
movsd 0x8(%rsp), %xmm0
mulsd 0x18(%rsp), %xmm1
addsd %xmm1, %xmm0
movl %ebp, %ecx
movq (%rbx), %rax
movq 0x8(%rbx), %rdx
subq %rax, %rdx
sarq $0x5, %rdx
incl %ebp
cmpq %rcx, %rdx
ja 0x41af70
jmp 0x41afcf
xorpd %xmm0, %xmm0
addsd 0x30(%rbx), %xmm0
movsd %xmm0, 0x30(%rbx)
addq $0x20, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/stats_ml/logistic_classifier.cpp
// Function: Logistic::samewb(Logistic_Param const&, Logistic_Param const&, double)
bool Logistic::samewb(const Logistic_Param& tparam, const Logistic_Param& param, double delta) {
	for (uint32_t i = 0; i < tparam.w.size(); i++) {
		if (fabs(tparam.w[i] - param.w[i]) > delta) {
			return false;
		}
	}
	if (fabs(tparam.d - param.d) > delta) {
		return false;
	}
	return true;
}

// Assembly:
movq (%rsi), %rax
movq 0x8(%rsi), %rcx
subq %rax, %rcx
setne %r8b
je 0x41b04e
movq (%rdx), %rdi
movsd (%rax), %xmm1
subsd (%rdi), %xmm1
andpd 0x189ee7(%rip), %xmm1   # 0x5a4ef0
ucomisd %xmm0, %xmm1
ja 0x41b046
sarq $0x3, %rcx
movl $0x1, %r9d
movapd 0x189ecf(%rip), %xmm1   # 0x5a4ef0
movl %r9d, %r9d
cmpq %r9, %rcx
seta %r8b
jbe 0x41b04e
movsd (%rax,%r9,8), %xmm2
subsd (%rdi,%r9,8), %xmm2
andpd %xmm1, %xmm2
incl %r9d
ucomisd %xmm0, %xmm2
jbe 0x41b021
testb %r8b, %r8b
je 0x41b04e
xorl %eax, %eax
retq
movsd 0x18(%rsi), %xmm1
subsd 0x18(%rdx), %xmm1
andpd 0x189e90(%rip), %xmm1   # 0x5a4ef0
ucomisd %xmm0, %xmm1
setbe %al
retq
// File: /workspace/github_cpp_makefile_star2_O1/ChnMasterOG[P]KmerGO2/stats_ml/logistic_classifier.cpp
// Function: Logistic::innerWX(Logistic_Param const&, Logistic_Data const&)
double Logistic::innerWX(const Logistic_Param& p, const Logistic_Data& data) {
	if (p.w.size() != data.features.size()) {
		exit(0);
	}
	double innerP = 0.0L;
	for (uint32_t i = 0; i < p.w.size(); i++) {
		innerP += (p.w[i] * data.features[i]);
	}
	innerP += p.d;
	return innerP;
}

// Assembly:
pushq %rax
movq (%rsi), %rax
movq 0x8(%rsi), %r8
movq %r8, %rcx
subq %rax, %rcx
sarq $0x3, %rcx
movq (%rdx), %rdi
movq 0x8(%rdx), %rdx
subq %rdi, %rdx
sarq $0x2, %rdx
cmpq %rdx, %rcx
jne 0x41b0fb
xorpd %xmm0, %xmm0
cmpq %rax, %r8
je 0x41b0f4
xorl %edx, %edx
xorps %xmm1, %xmm1
cvtss2sd (%rdi,%rdx,4), %xmm1
mulsd (%rax,%rdx,8), %xmm1
addsd %xmm1, %xmm0
incq %rdx
movl %edx, %r8d
cmpq %r8, %rcx
ja 0x41b0d8
addsd 0x18(%rsi), %xmm0
popq %rax
retq
xorl %edi, %edi
callq 0x4dbb10
// File: /workspace/github_cpp_makefile_star2_O1/williewillus[P]panda_scratchpad/src/communication/ClientSocket.cpp
// Function: communication::ClientSocket::Init()
int ClientSocket::Init() {
    	struct sockaddr_in server_addr; 

	// Communicate over TCP, IPv4
	if (( sockfd = socket( AF_INET, SOCK_STREAM, 0 )) < 0) 
    	{	 
        	cout << "Socket creation error" << endl; 
        	return -1; 
    	} 
   
    	memset(&server_addr, '0', sizeof(server_addr)); 
   	server_addr.sin_family = AF_INET; 
    	server_addr.sin_port = htons(sockport); 

    	// Convert IPv4 addresses from string to address struct in af family 
    	if ( inet_pton( AF_INET, sockaddr.c_str(), &server_addr.sin_addr ) <=0 )  
    	{ 
        	cout << "Invalid address" << endl; 
        	return -1; 
    	} 

	// Now that we've populated address and port, let's connect to the Qemu
	// socket listening on port *sockport*
	// TODO (jaya) : This is a blocking connect operation. The current timeout is too large
	// Need to use select() in non-blocking mode to reduce the timeout.
    	if ( connect(sockfd, (struct sockaddr*) &server_addr, sizeof(server_addr) ) < 0 ) 
    	{ 
        	cout << "Connection Failed" << endl;; 
        	return -1; 
    	} 
	return 0;
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %rbx
subq $0x18, %rsp
movq %rdi, %rbx
movl $0x2, %edi
movl $0x1, %esi
xorl %edx, %edx
callq 0x50f0
movl %eax, (%rbx)
testl %eax, %eax
js 0x829d
movaps 0xc28c(%rip), %xmm0     # 0x144d0
leaq -0x1c(%rbp), %rdx
movaps %xmm0, -0x4(%rdx)
movw $0x2, -0x4(%rdx)
movzwl 0x28(%rbx), %eax
rolw $0x8, %ax
movw %ax, -0x2(%rdx)
movq 0x8(%rbx), %rsi
movl $0x2, %edi
callq 0x5850
testl %eax, %eax
jle 0x82b2
movl (%rbx), %edi
leaq -0x20(%rbp), %rsi
movl $0x10, %edx
callq 0x53c0
movl %eax, %ecx
xorl %eax, %eax
testl %ecx, %ecx
jns 0x82fd
movq 0x13d39(%rip), %rdi     # 0x1bfc8
leaq 0xc270(%rip), %rsi      # 0x14506
movl $0x11, %edx
jmp 0x82c5
movq 0x13d24(%rip), %rdi     # 0x1bfc8
leaq 0xc235(%rip), %rsi      # 0x144e0
movl $0x15, %edx
jmp 0x82c5
movq 0x13d0f(%rip), %rdi     # 0x1bfc8
leaq 0xc236(%rip), %rsi      # 0x144f6
movl $0xf, %edx
callq 0x54f0
movq 0x13cf7(%rip), %rbx     # 0x1bfc8
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x5470
movsbl %al, %esi
movq %rbx, %rdi
callq 0x5040
movq %rax, %rdi
callq 0x5300
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
addq $0x18, %rsp
popq %rbx
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O1/williewillus[P]panda_scratchpad/src/communication/ClientSocket.cpp
// Function: communication::ClientSocket::BuildLoadPluginMsg(communication::SockMessage&, communication::Plugins, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>)
void ClientSocket::BuildLoadPluginMsg(SockMessage& msg, Plugins plugin_name, string start, string end ) {
	msg.q_cmd = cLoadPlugin;
	msg.need_response = false;
	msg.q_cmd_options->plugin_name =plugin_name;
	msg.q_cmd_options->start = start;
	msg.q_cmd_options->end = end;
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %r14
pushq %rbx
movq %r8, %rbx
movq %rsi, %r14
movl $0x1, (%rsi)
movb $0x0, 0x4(%rsi)
movq 0x8(%rsi), %rdi
movl %edx, (%rdi)
addq $0x8, %rdi
movq %rcx, %rsi
callq 0x5280
movq 0x8(%r14), %rdi
addq $0x28, %rdi
movq %rbx, %rsi
popq %rbx
popq %r14
popq %rbp
jmp 0x5280
nop
// File: /workspace/github_cpp_makefile_star2_O1/williewillus[P]panda_scratchpad/src/communication/ClientSocket.cpp
// Function: communication::ClientSocket::ReceiveReply(communication::SockMessage&)
SockError ClientSocket::ReceiveReply(SockMessage& msg) {
	SockError err = eNone;
	int valread;
	char buffer[BUFLEN];
	int bytes_read = 0;
	while(1) {
		valread = recv( sockfd, buffer, BUFLEN, 0);
    		if (valread <= 0){
			err = eOther;
			return err;
		}
		bytes_read += valread;
		string compare(buffer);
		//cout  << "Reply : " << buffer << " Bytes read = " << compare.find("cmEOF") << endl;
		string::size_type n = compare.find("cmEOF");
		if (n != string::npos){
			break;
		}
	}
	return err;
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x1028, %rsp           # imm = 0x1028
movq %rdi, %rbx
leaq -0x38(%rbp), %r12
leaq -0x1050(%rbp), %r14
leaq -0x48(%rbp), %r15
movl (%rbx), %edi
movl $0x1000, %edx           # imm = 0x1000
movq %r14, %rsi
xorl %ecx, %ecx
callq 0x5170
testl %eax, %eax
jle 0x8849
movq %r12, -0x48(%rbp)
movq %r14, %rdi
callq 0x51f0
leaq (%rax,%rbp), %rdx
addq $-0x1050, %rdx          # imm = 0xEFB0
movq %r15, %rdi
movq %r14, %rsi
callq 0x80ec
movl $0x5, %ecx
movq %r15, %rdi
leaq 0xbd92(%rip), %rsi      # 0x145b6
xorl %edx, %edx
callq 0x57b0
movq %rax, %r13
movq -0x48(%rbp), %rdi
cmpq %r12, %rdi
je 0x883c
callq 0x5460
cmpq $-0x1, %r13
je 0x87de
movl $0x3, %eax
jmp 0x884e
movl $0x2, %eax
addq $0x1028, %rsp           # imm = 0x1028
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O1/williewillus[P]panda_scratchpad/src/tests/BaseTestCase.cpp
// Function: tests::BaseTestCase::Run(int, int)
int BaseTestCase::Run(const int change_fd, const int checkpoint) {
  DefaultFsFns default_fns;
  RecordCmFsOps cm(&default_fns);
  PassthroughCmFsOps pcm(&default_fns);
  if (checkpoint == 0) {
    cm_ = &cm;
  } else {
    cm_ = &pcm;
  }

  int res_1 = run(checkpoint);
  if (res_1 < 0) {
    return res_1;
  }

  if (checkpoint == 0) {
    int res_2 = cm.Serialize(change_fd);
    if (res_2 < 0) {
      return res_2;
    }
  }
  return res_1;
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0xb8, %rsp
movl %edx, %r14d
movl %esi, -0x2c(%rbp)
movq %rdi, %r15
leaq 0x1310a(%rip), %rax     # 0x1ba60
addq $0x10, %rax
leaq -0x38(%rbp), %rbx
movq %rax, (%rbx)
leaq -0xe0(%rbp), %r12
movq %r12, %rdi
movq %rbx, %rsi
callq 0xa0cc
leaq -0x48(%rbp), %r13
movq %r13, %rdi
movq %rbx, %rsi
callq 0xba74
testl %r14d, %r14d
cmoveq %r12, %r13
movq %r13, 0x30(%r15)
movq (%r15), %rax
movq %r15, %rdi
movl %r14d, %esi
callq *0x18(%rax)
movl %eax, %r15d
testl %eax, %eax
js 0x89bb
testl %r14d, %r14d
jne 0x89bb
leaq -0xe0(%rbp), %rdi
movl -0x2c(%rbp), %esi
callq 0xb93c
testl %eax, %eax
jns 0x89bb
movl %eax, %r15d
leaq -0xe0(%rbp), %rdi
callq 0x89f8
movl %r15d, %eax
addq $0xb8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
jmp 0x89e0
jmp 0x89e0
movq %rax, %rbx
leaq -0xe0(%rbp), %rdi
callq 0x89f8
movq %rbx, %rdi
callq 0x57c0
nop
// File: /workspace/github_cpp_makefile_star2_O1/williewillus[P]panda_scratchpad/src/results/DataTestResult.cpp
// Function: tests::DataTestResult::PrintErrors(std::ostream&) const
ostream& DataTestResult::PrintErrors(ostream& os) const {
  unsigned int noted_errors = error_summary_;
  unsigned int shift = 0;
  while (noted_errors != 0) {
    if (noted_errors & 1) {
      os << (DataTestResult::ErrorType) (1 << shift);
    }
    ++shift;
    noted_errors >>= 1;
  }

  return os;
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movl 0x20(%rdi), %r15d
testl %r15d, %r15d
je 0x8d20
xorl %r14d, %r14d
testb $0x1, %r15b
je 0x8d0f
movl $0x1, %esi
movl %r14d, %ecx
shll %cl, %esi
movq %rbx, %rdi
callq 0x8d2e
incl %r14d
movl %r15d, %eax
shrl %eax
cmpl $0x1, %r15d
movl %eax, %r15d
ja 0x8cf7
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O1/williewillus[P]panda_scratchpad/src/results/DataTestResult.cpp
// Function: tests::operator<<(std::ostream&, tests::DataTestResult::ErrorType)
ostream& operator<<(ostream& os, DataTestResult::ErrorType err) {
  switch (err) {
    case DataTestResult::kClean:
      break;
    case DataTestResult::kOldFilePersisted:
      os << "old_file_persisted";
      break;
    case DataTestResult::kFileMissing:
      os << "file_missing";
      break;
    case DataTestResult::kFileDataCorrupted:
      os << "file_data_corrupted";
      break;
    case DataTestResult::kFileMetadataCorrupted:
      os << "file_metadata_corrupted";
      break;
    case DataTestResult::kIncorrectBlockCount:
      os << "incorrect_block_count";
      break;      
    case DataTestResult::kOther:
      os << "other_error";
      break;
    case DataTestResult::kAutoCheckFailed:
      os << "auto_check_test_failed";
      break;
    default:
      os.setstate(std::ios_base::failbit);
  }
  return os;
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %rbx
pushq %rax
movq %rdi, %rbx
cmpl $0xf, %esi
jg 0x8d65
cmpl $0x8, %esi
ja 0x8dd8
movl %esi, %eax
leaq 0xb952(%rip), %rcx      # 0x146a0
movslq (%rcx,%rax,4), %rax
addq %rcx, %rax
jmpq *%rax
leaq 0xb966(%rip), %rsi      # 0x146c4
movl $0x12, %edx
jmp 0x8dc6
cmpl $0x10, %esi
je 0x8dac
cmpl $0x20, %esi
je 0x8dba
cmpl $0x40, %esi
jne 0x8dd8
leaq 0xb9b7(%rip), %rsi      # 0x14732
movl $0x16, %edx
jmp 0x8dc6
leaq 0xb95b(%rip), %rsi      # 0x146e4
movl $0x13, %edx
jmp 0x8dc6
leaq 0xb940(%rip), %rsi      # 0x146d7
movl $0xc, %edx
jmp 0x8dc6
leaq 0xb953(%rip), %rsi      # 0x146f8
movl $0x17, %edx
jmp 0x8dc6
leaq 0xb95d(%rip), %rsi      # 0x14710
movl $0x15, %edx
jmp 0x8dc6
leaq 0xb965(%rip), %rsi      # 0x14726
movl $0xb, %edx
movq %rbx, %rdi
callq 0x54f0
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %rbp
retq
movq (%rbx), %rax
movq -0x18(%rax), %rax
leaq (%rbx,%rax), %rdi
movl 0x20(%rbx,%rax), %esi
orl $0x4, %esi
callq 0x5770
jmp 0x8dce
nopl (%rax)
// File: /workspace/github_cpp_makefile_star2_O1/williewillus[P]panda_scratchpad/src/results/FileSystemTestResult.cpp
// Function: FileSystemTestResult::PrintErrors(std::ostream&) const
void FileSystemTestResult::PrintErrors(ostream& os) const {
  if (error_summary_ == 0) {
    os << FileSystemTestResult::kCheckNotRun;
    return;
  }

  unsigned int noted_errors = error_summary_;
  unsigned int shift = 0;
  while (noted_errors != 0) {
    if (noted_errors & 1) {
      os << (FileSystemTestResult::ErrorType) (1 << shift) << " ";
    }
    ++shift;
    noted_errors >>= 1;
  }
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movq %rsi, %rbx
movl 0x44(%rdi), %r12d
testl %r12d, %r12d
je 0x8ea5
xorl %r14d, %r14d
leaq 0xc804(%rip), %r15      # 0x15667
testb $0x1, %r12b
je 0x8e8b
movl $0x1, %esi
movl %r14d, %ecx
shll %cl, %esi
movq %rbx, %rdi
callq 0x8ec1
movl $0x1, %edx
movq %rbx, %rdi
movq %r15, %rsi
callq 0x54f0
incl %r14d
movl %r12d, %eax
shrl %eax
cmpl $0x1, %r12d
movl %eax, %r12d
ja 0x8e63
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
leaq 0xb8c4(%rip), %rsi      # 0x14770
movl $0xc, %edx
movq %rbx, %rdi
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
jmp 0x54f0