LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_cpp_makefile_star2_O3/biotomas[P]ipasir/app/genipareach/genipareach.cpp
// Function: loadReachabilityProblem(char const*, Formula*, Formula*, Formula*, Formula*)
bool loadReachabilityProblem(const char* filename, Formula* initial, Formula* universal, Formula* goal, Formula* transition) {
	FILE* f = fopen(filename, "r");
	if (f == NULL) {
		return false;
	}
	int c = 0;
	bool neg = false;
	Formula* current = goal;
	while (c != EOF) {
		c = fgetc(f);

		// comment line
		if (c == 'c') {
			readLine(f);
			continue;
		}
		// problem lines
		if (c == 'i' || c == 'u' || c == 'g' || c == 't') {
			switch (c) {
			case 'i':
				current = initial;
				break;
			case 'u':
				current = universal;
				break;
			case 'g':
				current = goal;
				break;
			case 't':
				current = transition;
				break;
			default:
				printf("Invalid character: \"%c\"\n", c);
				return false;
			}
			current->variables = readNextNumber(f, 0);
			readLine(f);
			continue;
		}
		// whitespace
		if (isspace(c)) {
			continue;
		}
		// negative
		if (c == '-') {
			neg = true;
			continue;
		}

		// number
		if (isdigit(c)) {
			int num = readNextNumber(f, c);
			if (neg) {
				num *= -1;
			}
			neg = false;
			current->addLit(num);
		}
	}
	fclose(f);

	return true;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %r8, %rbx
movq %rcx, %r14
movq %rdx, %r15
movq %rsi, %r12
leaq 0x112cd(%rip), %rsi     # 0x12ad9
callq 0x1170
movq %rax, %r13
testq %rax, %rax
je 0x18e3
movq %r15, 0x8(%rsp)
movq %rbx, 0x10(%rsp)
xorl %r15d, %r15d
movq %r14, %rbp
movq %r13, %rdi
callq 0x1200
movl %eax, %ebx
cmpl $0x66, %eax
jg 0x184b
cmpl $0x63, %ebx
jne 0x1869
movq %r13, %rdi
callq 0x17d6
jmp 0x1874
cmpl $0x73, %ebx
jg 0x185f
cmpl $0x67, %ebx
je 0x1882
cmpl $0x69, %ebx
jne 0x1869
movq %r12, %rbp
jmp 0x188c
cmpl $0x74, %ebx
je 0x1887
cmpl $0x75, %ebx
je 0x187b
movl %ebx, %edi
callq 0x1040
testl %eax, %eax
je 0x18a3
cmpl $-0x1, %ebx
jne 0x182d
jmp 0x18db
movq 0x8(%rsp), %rbp
jmp 0x188c
movq %r14, %rbp
jmp 0x188c
movq 0x10(%rsp), %rbp
movq %r13, %rdi
xorl %esi, %esi
callq 0x178c
movl %eax, (%rbp)
movq %r13, %rdi
callq 0x17d6
jmp 0x182d
movb $0x1, %al
cmpl $0x2d, %ebx
je 0x18d6
leal -0x30(%rbx), %eax
cmpl $0x9, %eax
ja 0x18d3
movq %r13, %rdi
movl %ebx, %esi
callq 0x178c
movl %eax, %esi
negl %esi
testb $0x1, %r15b
cmovel %eax, %esi
movq %rbp, %rdi
callq 0x1e06
xorl %eax, %eax
jmp 0x18d6
movl %r15d, %eax
movl %eax, %r15d
jmp 0x1874
movq %r13, %rdi
callq 0x1110
testq %r13, %r13
setne %al
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O3/biotomas[P]ipasir/app/genipareach/genipareach.cpp
// Function: Formula::addLit(int)
void addLit(int lit) {
		if (lit == 0) {
			clausesCount++;
			clauses.push_back(tmpClause);
			tmpClause.clear();
		} else {
			tmpClause.push_back(lit);
		}
	}

// Assembly:
pushq %rbx
subq $0x10, %rsp
movq %rdi, %rbx
movl %esi, 0xc(%rsp)
testl %esi, %esi
je 0x1e2e
movl %esi, %eax
movq 0x28(%rbx), %rsi
cmpq 0x30(%rbx), %rsi
je 0x1e4e
movl %eax, (%rsi)
addq $0x4, %rsi
movq %rsi, 0x28(%rbx)
jmp 0x1e5f
incl 0x4(%rbx)
leaq 0x8(%rbx), %rdi
leaq 0x20(%rbx), %rsi
callq 0x1e8c
movq 0x20(%rbx), %rax
cmpq %rax, 0x28(%rbx)
je 0x1e5f
movq %rax, 0x28(%rbx)
jmp 0x1e5f
addq $0x20, %rbx
leaq 0xc(%rsp), %rdx
movq %rbx, %rdi
callq 0x2198
addq $0x10, %rsp
popq %rbx
retq
nop
// File: /workspace/github_cpp_makefile_star2_O3/biotomas[P]ipasir/sat/picosat961/ipasirpicosatglue.c
// Function: ipasir_init
void * ipasir_init () { 
  char prefix[80];
  void * res = picosat_init ();
  sprintf (prefix, "c [%s] ", sig);
  picosat_set_prefix (res, prefix);
  picosat_set_verbosity (res, 1);
  picosat_set_output (res, stdout);
  return res;
}

// Assembly:
pushq %r14
pushq %rbx
subq $0x58, %rsp
callq 0x2519
movq %rax, %rbx
leaq 0xdef5(%rip), %rsi      # 0x101cb
leaq 0xdef6(%rip), %rdx      # 0x101d3
movq %rsp, %r14
movq %r14, %rdi
xorl %eax, %eax
callq 0x1050
movq %rbx, %rdi
movq %r14, %rsi
callq 0x5208
movq %rbx, %rdi
movl $0x1, %esi
callq 0x513b
movq 0x14cbf(%rip), %rax     # 0x16fc8
movq (%rax), %rsi
movq %rbx, %rdi
callq 0x51d8
movq %rbx, %rax
addq $0x58, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/./timer.h
// Function: logTime(std::ostream&, bool)
static inline void logTime(std::ostream& os, bool nl = true) {
	struct tm *current;
	time_t now;
	time(&now);
	current = localtime(&now);
	std::ostringstream oss;
	oss << setfill('0') << setw(2)
	    << current->tm_hour << ":"
	    << setfill('0') << setw(2)
	    << current->tm_min << ":"
	    << setfill('0') << setw(2)
	    << current->tm_sec;
	if(nl) oss << std::endl;
	os << oss.str().c_str();
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x1a8, %rsp            # imm = 0x1A8
leaq 0x28(%rsp), %rbx
movq %rbx, %rdi
callq 0x42d0
movq %rbx, %rdi
callq 0x4230
movq %rax, %rbx
leaq 0x30(%rsp), %r14
movq %r14, %rdi
callq 0x4450
movq (%r14), %rax
movq -0x18(%rax), %rax
leaq (%rsp,%rax), %r14
addq $0x30, %r14
cmpb $0x0, 0xe1(%r14)
jne 0xa8a1
movq %r14, %rdi
movl $0x20, %esi
callq 0x4300
movb $0x1, 0xe1(%r14)
movb $0x30, 0xe0(%r14)
leaq 0x30(%rsp), %r14
movq (%r14), %rax
movq -0x18(%rax), %rax
movq $0x2, 0x40(%rsp,%rax)
movl 0x8(%rbx), %esi
movq %r14, %rdi
callq 0x4610
movq %rax, %r15
leaq 0x22ed5(%rip), %rsi     # 0x2d7a8
movl $0x1, %edx
movq %rax, %rdi
callq 0x43b0
movq (%r15), %rax
movq -0x18(%rax), %rax
movq %r15, %r12
addq %rax, %r12
cmpb $0x0, 0xe1(%r15,%rax)
jne 0xa90e
movq %r12, %rdi
movl $0x20, %esi
callq 0x4300
movb $0x1, 0xe1(%r12)
movb $0x30, 0xe0(%r12)
movq (%r15), %rax
movq -0x18(%rax), %rax
movq $0x2, 0x10(%r15,%rax)
movl 0x4(%rbx), %esi
movq %r15, %rdi
callq 0x4610
movq %rax, %r15
leaq 0x22e6c(%rip), %rsi     # 0x2d7a8
movl $0x1, %edx
movq %rax, %rdi
callq 0x43b0
movq (%r15), %rax
movq -0x18(%rax), %rax
movq %r15, %r12
addq %rax, %r12
cmpb $0x0, 0xe1(%r15,%rax)
jne 0xa977
movq %r12, %rdi
movl $0x20, %esi
callq 0x4300
movb $0x1, 0xe1(%r12)
movb $0x30, 0xe0(%r12)
movq (%r15), %rax
movq -0x18(%rax), %rax
movq $0x2, 0x10(%r15,%rax)
movl (%rbx), %esi
movq %r15, %rdi
callq 0x4610
movq 0x30(%rsp), %rax
addq -0x18(%rax), %r14
movq %r14, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
leaq 0x30(%rsp), %rdi
callq 0x4040
movq %rax, %rdi
callq 0x41e0
leaq 0x38(%rsp), %rsi
leaq 0x8(%rsp), %rdi
callq 0x4560
movq 0x8(%rsp), %rbx
testq %rbx, %rbx
je 0xa9fa
movq %rbx, %rdi
callq 0x4140
movq 0x2c603(%rip), %rdi     # 0x36ff0
movq %rbx, %rsi
movq %rax, %rdx
callq 0x43b0
jmp 0xaa18
movq 0x2c5ef(%rip), %rax     # 0x36ff0
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
leaq (%rax,%rcx), %rdi
movl 0x20(%rax,%rcx), %esi
orl $0x1, %esi
callq 0x45e0
leaq 0x18(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0xaa33
movq 0x18(%rsp), %rsi
incq %rsi
callq 0x4340
movq 0x2c56e(%rip), %rsi     # 0x36fa8
leaq 0x30(%rsp), %rdi
callq 0x4170
leaq 0xa0(%rsp), %rdi
callq 0x4120
addq $0x1a8, %rsp            # imm = 0x1A8
popq %rbx
popq %r12
popq %r14
popq %r15
retq
movq %rax, %rbx
leaq 0x18(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0xaa85
movq 0x18(%rsp), %rsi
incq %rsi
callq 0x4340
jmp 0xaa85
jmp 0xaa82
movq %rax, %rbx
movq 0x2c51c(%rip), %rsi     # 0x36fa8
leaq 0x30(%rsp), %rdi
callq 0x4170
leaq 0xa0(%rsp), %rdi
callq 0x4120
movq %rbx, %rdi
callq 0x4620
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/./word_io.h
// Function: unsigned int readU<unsigned int>(_IO_FILE*, bool)
static inline T readU(FILE* in, bool swap) {
	T x;
	if(fread((void *)&x, 1, sizeof(T), in) != sizeof(T)) {
		assert(false);
	}
	if(swap) {
		if(sizeof(T) == 4) {
			return endianSwapU32(x);
		} else if(sizeof(T) == 8) {
			return endianSwapU64(x);
		} else {
			assert(false);
		}
	} else {
		return x;
	}
}

// Assembly:
pushq %rax
movq %rdi, %rcx
leaq 0x4(%rsp), %rdi
movl $0x1, %esi
movl $0x4, %edx
callq 0x44e0
cmpq $0x4, %rax
jne 0xaacf
movl 0x4(%rsp), %eax
popq %rcx
retq
leaq 0x23230(%rip), %rdi     # 0x2dd06
leaq 0x2322f(%rip), %rsi     # 0x2dd0c
leaq 0x25470(%rip), %rcx     # 0x2ff54
movl $0x4a, %edx
callq 0x41c0
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/bowtie_inspect.cpp
// Function: print_fasta_record(std::ostream&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&)
void print_fasta_record(ostream& fout,
						const string& defline,
						const string& seq)
{
	fout << ">";
	fout << defline << endl;

	if(across > 0) {
		size_t i = 0;
		while (i + across < seq.length())
		{
			fout << seq.substr(i, across) << endl;
			i += across;
		}
		if (i < seq.length())
			fout << seq.substr(i) << endl;
	} else {
		fout << seq << endl;
	}
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %rdx, %r14
movq %rsi, %r15
movq %rdi, %rbx
leaq 0x234ae(%rip), %rsi     # 0x2e6a3
movl $0x1, %edx
callq 0x43b0
movq (%r15), %rsi
movq 0x8(%r15), %rdx
movq %rbx, %rdi
callq 0x43b0
movq %rax, %r15
movq (%rax), %rax
movq -0x18(%rax), %rdi
addq %r15, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %r15, %rdi
callq 0x4040
movq %rax, %rdi
callq 0x41e0
movslq 0x2c141(%rip), %rcx     # 0x37380
testq %rcx, %rcx
jle 0xb2dc
movq 0x8(%r14), %rax
cmpq %rcx, %rax
jbe 0xb323
leaq 0x18(%rsp), %rbp
xorl %r15d, %r15d
leaq 0x8(%rsp), %r12
movq %r12, %rdi
movq %r14, %rsi
movq %r15, %rdx
callq 0x4350
movq 0x8(%rsp), %rsi
movq 0x10(%rsp), %rdx
movq %rbx, %rdi
callq 0x43b0
movq %rax, %r13
movq (%rax), %rax
movq -0x18(%rax), %rdi
addq %r13, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %r13, %rdi
callq 0x4040
movq %rax, %rdi
callq 0x41e0
movq 0x8(%rsp), %rdi
cmpq %rbp, %rdi
je 0xb2c3
movq 0x18(%rsp), %rsi
incq %rsi
callq 0x4340
movslq 0x2c0b6(%rip), %rcx     # 0x37380
addq %rcx, %r15
leaq (%r15,%rcx), %rdx
movq 0x8(%r14), %rax
cmpq %rax, %rdx
jb 0xb262
jmp 0xb326
movq (%r14), %rsi
movq 0x8(%r14), %rdx
movq %rbx, %rdi
callq 0x43b0
movq %rax, %rbx
movq (%rax), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4040
movq %rax, %rdi
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0x41e0
xorl %r15d, %r15d
cmpq %rax, %r15
jae 0xb39b
leaq 0x8(%rsp), %r12
movq %r12, %rdi
movq %r14, %rsi
movq %r15, %rdx
movq $-0x1, %rcx
callq 0x4350
movq (%r12), %rsi
movq 0x8(%r12), %rdx
movq %rbx, %rdi
callq 0x43b0
movq %rax, %rbx
movq (%rax), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %rbx, %rdi
callq 0x4040
movq %rax, %rdi
callq 0x41e0
leaq 0x18(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0xb39b
movq 0x18(%rsp), %rsi
incq %rsi
callq 0x4340
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %rbx
leaq 0x18(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
jne 0xb3ca
jmp 0xb3d7
movq %rax, %rbx
movq 0x8(%rsp), %rdi
cmpq %rbp, %rdi
je 0xb3d7
movq 0x18(%rsp), %rsi
incq %rsi
callq 0x4340
movq %rbx, %rdi
callq 0x4620
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/bowtie_inspect.cpp
// Function: print_alln_ref_sequence(std::ostream&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, unsigned long)
void print_alln_ref_sequence(
	ostream& fout,
	const string& name,
	size_t len)
{
	fout << ">" << name << "\n";
	size_t j = 0;
	for(size_t i = 0; i < len; i += across) {
		while(j < len && j < i+across) {
			fout << 'N';
			j++;
		}
		fout << "\n";
	}
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rdx, %rbx
movq %rsi, %r15
movq %rdi, %r14
leaq 0x232a9(%rip), %rsi     # 0x2e6a3
movl $0x1, %edx
callq 0x43b0
movq (%r15), %rsi
movq 0x8(%r15), %rdx
movq %r14, %rdi
callq 0x43b0
leaq 0x219ff(%rip), %rsi     # 0x2ce19
movl $0x1, %edx
movq %rax, %rdi
callq 0x43b0
testq %rbx, %rbx
je 0xb490
xorl %r13d, %r13d
leaq 0x7(%rsp), %r15
leaq 0x219de(%rip), %r12     # 0x2ce19
xorl %ebp, %ebp
cmpq %rbx, %rbp
jae 0xb471
movslq 0x2bf37(%rip), %rax     # 0x37380
addq %r13, %rax
cmpq %rax, %rbp
jae 0xb471
movb $0x4e, 0x7(%rsp)
movl $0x1, %edx
movq %r14, %rdi
movq %r15, %rsi
callq 0x43b0
incq %rbp
cmpq %rbp, %rbx
jne 0xb442
movq %rbx, %rbp
movl $0x1, %edx
movq %r14, %rdi
movq %r12, %rsi
callq 0x43b0
movslq 0x2bef8(%rip), %rax     # 0x37380
addq %rax, %r13
cmpq %rbx, %r13
jb 0xb43d
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/bowtie_inspect.cpp
// Function: print_ref_sequence(std::ostream&, BitPairReference&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, unsigned long, unsigned long)
void print_ref_sequence(
	ostream& fout,
	BitPairReference& ref,
	const string& name,
	size_t refi,
	size_t len)
{
	bool newlines = across > 0;
	int myacross = across > 0 ? across : 60;
	size_t incr = myacross * 1000;
	uint32_t *buf = new uint32_t[(incr + 128)/4];
	fout << ">" << name << "\n";
	for(size_t i = 0; i < len; i += incr) {
		size_t amt = min(incr, len-i);
		assert_leq(amt, incr);
		int off = ref.getStretch(buf, refi, i, amt);
		uint8_t *cb = ((uint8_t*)buf) + off;
		for(size_t j = 0; j < amt; j++) {
			if(newlines && j > 0 && (j % myacross) == 0) fout << "\n";
			assert_range(0, 4, (int)cb[j]);
			fout << "ACGTN"[(int)cb[j]];
		}
		fout << "\n";
	}
	delete[] buf;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x58, %rsp
movq %r8, %r15
movq %rcx, 0x40(%rsp)
movq %rdx, %rbx
movq %rsi, 0x38(%rsp)
movq %rdi, %r12
movslq 0x2beb9(%rip), %r13     # 0x37380
imull $0x3e8, %r13d, %eax     # imm = 0x3E8
testq %r13, %r13
movl $0xea60, %ecx           # imm = 0xEA60
cmovgl %eax, %ecx
movslq %ecx, %r14
leaq 0x80(%r14), %rdi
callq 0x4030
movq %rax, 0x10(%rsp)
leaq 0x231af(%rip), %rsi     # 0x2e6a3
movl $0x1, %edx
movq %r12, %rdi
callq 0x43b0
movq (%rbx), %rsi
movq 0x8(%rbx), %rdx
movq %r12, %rdi
callq 0x43b0
leaq 0x21902(%rip), %rsi     # 0x2ce19
movl $0x1, %edx
movq %rax, %rdi
callq 0x43b0
testq %r15, %r15
je 0xb65b
movq %r14, %rax
xorl %ecx, %ecx
leaq 0xf(%rsp), %rbp
movq %r15, %rdx
movq %r15, 0x30(%rsp)
movq %r14, 0x28(%rsp)
movq %rdx, %r14
subq %rax, %rdx
movq %rdx, 0x48(%rsp)
cmovaeq %rax, %r14
subq %rcx, %r15
cmpq %rax, %r15
cmovaeq %rax, %r15
movq 0x38(%rsp), %rdi
movq 0x10(%rsp), %rsi
movq 0x40(%rsp), %rdx
movq %rcx, 0x50(%rsp)
movq %r15, %r8
callq 0x134e4
testq %r15, %r15
je 0xb627
movslq %eax, %rbx
addq 0x10(%rsp), %rbx
xorl %r15d, %r15d
testl %r13d, %r13d
setle %al
testq %r15, %r15
sete %cl
orb %al, %cl
jne 0xb5be
movq %r15, %rax
xorl %edx, %edx
divq %r13
testq %rdx, %rdx
jne 0xb5be
movl $0x1, %edx
movq %r12, %rdi
leaq 0x21860(%rip), %rsi     # 0x2ce19
callq 0x43b0
movl $0x0, 0x24(%rsp)
movl $0x4, 0x20(%rsp)
movzbl (%rbx,%r15), %eax
movl %eax, 0x1c(%rsp)
leaq 0x24(%rsp), %rdi
leaq 0x20(%rsp), %rsi
leaq 0x1c(%rsp), %rdx
leaq 0x21709(%rip), %rcx     # 0x2ccf6
movl $0xcf, %r8d
callq 0xb674
movzbl (%rbx,%r15), %eax
leaq 0x21705(%rip), %rcx     # 0x2cd09
movb (%rax,%rcx), %al
movb %al, 0xf(%rsp)
movl $0x1, %edx
movq %r12, %rdi
movq %rbp, %rsi
callq 0x43b0
incq %r15
cmpq %r15, %r14
jne 0xb58d
movl $0x1, %edx
movq %r12, %rdi
leaq 0x217e3(%rip), %rsi     # 0x2ce19
callq 0x43b0
movq 0x28(%rsp), %rax
movq 0x50(%rsp), %rcx
addq %rax, %rcx
movq 0x30(%rsp), %r15
cmpq %r15, %rcx
movq 0x48(%rsp), %rdx
jb 0xb544
movq 0x10(%rsp), %rdi
callq 0x4420
addq $0x58, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/./assert_helpers.h
// Function: void assert_range_helper<int>(int const&, int const&, int const&, char const*, int)
inline static void assert_range_helper(const T& begin,
                                       const T& end,
                                       const T& val,
                                       const char *file,
                                       int line)
{
	if(val < begin || val > end) {
		std::cout << "assert_range: (" << val << ") not in  ["
		          << begin << ", " << end << "]" << std::endl;
		std::cout << file << ":" << line << std::endl;
		assert(0);
	}
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movl %r8d, %ebx
movq %rcx, %r14
movq %rdx, %rbp
movq %rsi, %r12
movq %rdi, %r13
movl (%rdx), %eax
cmpl (%rdi), %eax
jl 0xb6a9
cmpl (%r12), %eax
jg 0xb6a9
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x2b908(%rip), %r15     # 0x36fb8
leaq 0x23416(%rip), %rsi     # 0x2eacd
movq %r15, %rdi
callq 0x4310
movl (%rbp), %esi
movq %rax, %rdi
callq 0x4610
leaq 0x2340c(%rip), %rsi     # 0x2eadd
movq %rax, %rdi
callq 0x4310
movl (%r13), %esi
movq %rax, %rdi
callq 0x4610
leaq 0x2107b(%rip), %rsi     # 0x2c767
movq %rax, %rdi
callq 0x4310
movl (%r12), %esi
movq %rax, %rdi
callq 0x4610
leaq 0x20c75(%rip), %rsi     # 0x2c37c
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
callq 0x4150
movq %r15, %rdi
movq %r14, %rsi
callq 0x4310
leaq 0x2207f(%rip), %rsi     # 0x2d7a8
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movl %ebx, %esi
callq 0x4610
movq %rax, %rdi
callq 0x4150
leaq 0x21f3e(%rip), %rdi     # 0x2d688
leaq 0x23398(%rip), %rsi     # 0x2eae9
leaq 0x233a4(%rip), %rcx     # 0x2eafc
movl $0xfd, %edx
callq 0x41c0
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/bowtie_inspect.cpp
// Function: print_index_sequence_names(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, std::ostream&)
void print_index_sequence_names(const string& fname, ostream& fout)
{
	EList<string> p_refnames;
	readEbwtRefnames(fname, p_refnames);
	for(size_t i = 0; i < p_refnames.size(); i++) {
		cout << p_refnames[i] << endl;
	}
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x28, %rsp
movabsq $-0x100000000, %rax     # imm = 0xFFFFFFFF00000000
leaq 0x8(%rsp), %rsi
movq %rax, (%rsi)
xorl %eax, %eax
movq %rax, 0x8(%rsi)
movq $0x80, 0x10(%rsi)
movq %rax, 0x18(%rsi)
callq 0xba6f
cmpq $0x0, 0x20(%rsp)
je 0xba38
xorl %ebx, %ebx
leaq 0x8(%rsp), %r14
movq 0x2b5ce(%rip), %r15     # 0x36fb8
movq %r14, %rdi
movq %rbx, %rsi
callq 0x179c4
movq (%rax), %rsi
movq 0x8(%rax), %rdx
movq %r15, %rdi
callq 0x43b0
movq %rax, %r12
movq (%rax), %rax
movq -0x18(%rax), %rdi
addq %r12, %rdi
movl $0xa, %esi
callq 0x4300
movsbl %al, %esi
movq %r12, %rdi
callq 0x4040
movq %rax, %rdi
callq 0x41e0
incq %rbx
cmpq 0x20(%rsp), %rbx
jb 0xb9ea
leaq 0x8(%rsp), %rdi
callq 0x21874
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
jmp 0xba67
jmp 0xba52
movq %rax, %rbx
leaq 0x8(%rsp), %rdi
callq 0x21874
movq %rbx, %rdi
callq 0x4620
movq %rax, %rdi
callq 0x100de
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/./word_io.h
// Function: int readI<int>(std::istream&, bool)
static inline T readI(std::istream& in, bool swap) {
	T x;
	in.read((char *)&x, sizeof(T));
	assert_eq(sizeof(T), in.gcount());
	if(swap) {
		if(sizeof(T) == 4) {
			return endianSwapI32(x);
		} else if(sizeof(T) == 8) {
			return endianSwapI64(x);
		} else {
			assert(false);
		}
	} else {
		return x;
	}
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
subq $0x10, %rsp
movl %esi, %ebx
movq %rdi, %r14
leaq 0xc(%rsp), %rsi
movl $0x4, %edx
callq 0x4410
cmpq $0x4, 0x8(%r14)
jne 0xe755
movl 0xc(%rsp), %ecx
movl %ecx, %eax
bswapl %eax
testb %bl, %bl
cmovel %ecx, %eax
addq $0x10, %rsp
popq %rbx
popq %r14
popq %r15
retq
movq 0x2885c(%rip), %rbx     # 0x36fb8
leaq 0x1da63(%rip), %rsi     # 0x2c1c6
movq %rbx, %rdi
callq 0x4310
movl $0x4, %esi
movq %rax, %rdi
callq 0x40c0
leaq 0x1da5d(%rip), %r15     # 0x2c1dc
movq %rax, %rdi
movq %r15, %rsi
callq 0x4310
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
movl 0x18(%rax,%rcx), %edx
andl $-0x4b, %edx
orl $0x8, %edx
movl %edx, 0x18(%rax,%rcx)
movl $0x4, %esi
movq %rax, %rdi
callq 0x40c0
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
movl 0x18(%rax,%rcx), %edx
andl $-0x4b, %edx
orl $0x2, %edx
movl %edx, 0x18(%rax,%rcx)
leaq 0x1da19(%rip), %rsi     # 0x2c1e1
movq %rax, %rdi
callq 0x4310
movq 0x8(%r14), %rsi
movq %rax, %rdi
callq 0x4650
movq %rax, %rdi
movq %r15, %rsi
callq 0x4310
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
movl 0x18(%rax,%rcx), %edx
andl $-0x4b, %edx
orl $0x8, %edx
movl %edx, 0x18(%rax,%rcx)
movq 0x8(%r14), %rsi
movq %rax, %rdi
callq 0x4650
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
movl 0x18(%rax,%rcx), %edx
andl $-0x4b, %edx
orl $0x2, %edx
movl %edx, 0x18(%rax,%rcx)
leaq 0x1fb81(%rip), %rsi     # 0x2e3a5
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
callq 0x4150
leaq 0x1f4d1(%rip), %r14     # 0x2dd0c
movq %rbx, %rdi
movq %r14, %rsi
callq 0x4310
leaq 0x1ef5b(%rip), %rsi     # 0x2d7a8
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movl $0x5d, %esi
callq 0x4610
movq %rax, %rdi
callq 0x4150
leaq 0x1ee17(%rip), %rdi     # 0x2d688
leaq 0x1fc59(%rip), %rcx     # 0x2e4d1
movq %r14, %rsi
movl $0x5d, %edx
callq 0x41c0
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/./multikey_qsort.h
// Function: void swap<unsigned long, unsigned long>(unsigned long*, unsigned long, unsigned long, unsigned long)
static inline void swap(TVal* s, size_t slen, TPos a, TPos b) {
	assert_lt(a, slen);
	assert_lt(b, slen);
	TVal tmp = s[a];
	s[a] = s[b];
	s[b] = tmp;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rdx, %r12
movq %rsi, %rbx
cmpq %rsi, %rdx
jae 0xeca1
movq %rcx, %r15
cmpq %rbx, %rcx
jae 0xed44
movq (%rdi,%r12,8), %rax
movq (%rdi,%r15,8), %rcx
movq %rcx, (%rdi,%r12,8)
movq %rax, (%rdi,%r15,8)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
movq 0x28310(%rip), %r14     # 0x36fb8
leaq 0x1d645(%rip), %rsi     # 0x2c2f4
movq %r14, %rdi
callq 0x4310
movq %rax, %rdi
movq %r12, %rsi
callq 0x40c0
leaq 0x1d641(%rip), %rsi     # 0x2c30a
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movq %rbx, %rsi
callq 0x40c0
leaq 0x1f6c2(%rip), %rsi     # 0x2e3a5
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
callq 0x4150
leaq 0x1ffb0(%rip), %rbx     # 0x2ecaa
movq %r14, %rdi
movq %rbx, %rsi
callq 0x4310
leaq 0x1ea9c(%rip), %rsi     # 0x2d7a8
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movl $0x21, %esi
callq 0x4610
movq %rax, %rdi
callq 0x4150
leaq 0x1e958(%rip), %rdi     # 0x2d688
leaq 0x209d9(%rip), %rcx     # 0x2f710
movq %rbx, %rsi
movl $0x21, %edx
callq 0x41c0
movq 0x2826d(%rip), %r14     # 0x36fb8
leaq 0x1d5a2(%rip), %rsi     # 0x2c2f4
movq %r14, %rdi
callq 0x4310
movq %rax, %rdi
movq %r15, %rsi
callq 0x40c0
leaq 0x1d59e(%rip), %rsi     # 0x2c30a
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movq %rbx, %rsi
callq 0x40c0
leaq 0x1f61f(%rip), %rsi     # 0x2e3a5
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
callq 0x4150
leaq 0x1ff0d(%rip), %rbx     # 0x2ecaa
movq %r14, %rdi
movq %rbx, %rsi
callq 0x4310
leaq 0x1e9f9(%rip), %rsi     # 0x2d7a8
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movl $0x22, %esi
callq 0x4610
movq %rax, %rdi
callq 0x4150
leaq 0x1e8b5(%rip), %rdi     # 0x2d688
leaq 0x20936(%rip), %rcx     # 0x2f710
movq %rbx, %rsi
movl $0x22, %edx
callq 0x41c0
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/./sstring.h
// Function: bool sstr_suf_lt<S2bDnaString, S2bDnaString>(S2bDnaString const&, unsigned long, unsigned long, S2bDnaString const&, unsigned long, unsigned long, bool)
static inline bool sstr_suf_lt(
	const T1& s1, size_t suf1, size_t len1,
	const T2& s2, size_t suf2, size_t len2,
	bool endlt = true)
{
	assert_leq(suf1, len1);
	assert_leq(suf2, len2);
	size_t left1 = len1 - suf1;
	size_t left2 = len2 - suf2;
	size_t minleft = (left1 < left2 ? left1 : left2);
	for(size_t i = 0; i < minleft; i++) {
		if(s1[suf1+i] < s2[suf2+i]) {
			return true;
		} else if(s1[suf1+i] > s2[suf2+i]) {
			return false;
		}
	}
	if(left1 == left2) return false;
	return (left1 < left2) == endlt;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rcx, 0x10(%rsp)
movq %rsi, %r14
movq %rdx, %rax
subq %rsi, %rax
jb 0xf4a1
movq %r9, %r13
movq %r8, %rbx
movq %r9, %r15
subq %r8, %r15
jb 0xf547
cmpq %r15, %rax
movq %r15, (%rsp)
movq %rax, 0x8(%rsp)
cmovbq %rax, %r15
testq %r15, %r15
je 0xf483
movq %rdi, %r12
movq %r12, %rdi
movq %r14, %rsi
callq 0x25e5e
movl %eax, %ebp
movq 0x10(%rsp), %r13
movq %r13, %rdi
movq %rbx, %rsi
callq 0x25e5e
cmpb %al, %bpl
setl %bpl
jl 0xf490
movq %r12, %rdi
movq %r14, %rsi
callq 0x25e5e
movq %r13, %rdi
movl %eax, %r13d
movq %rbx, %rsi
callq 0x25e5e
cmpb %al, %r13b
jg 0xf490
incq %rbx
incq %r14
decq %r15
jne 0xf434
movq (%rsp), %rax
cmpq %rax, 0x8(%rsp)
seta %bpl
movl %ebp, %eax
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rdx, %rbp
movq 0x27b0d(%rip), %rbx     # 0x36fb8
leaq 0x1cd9e(%rip), %rsi     # 0x2c250
movq %rbx, %rdi
callq 0x4310
movq %rax, %rdi
movq %r14, %rsi
callq 0x40c0
leaq 0x1cd9b(%rip), %rsi     # 0x2c267
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movq %rbp, %rsi
callq 0x40c0
leaq 0x1eebf(%rip), %rsi     # 0x2e3a5
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
callq 0x4150
leaq 0x1fcb1(%rip), %r14     # 0x2f1ae
movq %rbx, %rdi
movq %r14, %rsi
callq 0x4310
leaq 0x1e299(%rip), %rsi     # 0x2d7a8
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movl $0xcc, %esi
callq 0x4610
movq %rax, %rdi
callq 0x4150
leaq 0x1e155(%rip), %rdi     # 0x2d688
leaq 0x1fd3b(%rip), %rcx     # 0x2f275
movq %r14, %rsi
movl $0xcc, %edx
callq 0x41c0
movq 0x27a6a(%rip), %r14     # 0x36fb8
leaq 0x1ccfb(%rip), %rsi     # 0x2c250
movq %r14, %rdi
callq 0x4310
movq %rax, %rdi
movq %rbx, %rsi
callq 0x40c0
leaq 0x1ccf8(%rip), %rsi     # 0x2c267
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movq %r13, %rsi
callq 0x40c0
leaq 0x1ee1c(%rip), %rsi     # 0x2e3a5
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
callq 0x4150
leaq 0x1fc0e(%rip), %rbx     # 0x2f1ae
movq %r14, %rdi
movq %rbx, %rsi
callq 0x4310
leaq 0x1e1f6(%rip), %rsi     # 0x2d7a8
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movl $0xcd, %esi
callq 0x4610
movq %rax, %rdi
callq 0x4150
leaq 0x1e0b2(%rip), %rdi     # 0x2d688
leaq 0x1fc98(%rip), %rcx     # 0x2f275
movq %rbx, %rsi
movl $0xcd, %edx
callq 0x41c0
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/./multikey_qsort.h
// Function: void mkeyQSortSuf<S2bDnaString>(S2bDnaString const&, unsigned long*, unsigned long, int, bool, bool, unsigned long)
void mkeyQSortSuf(
	const T& host,
	TIndexOffU *s,
	size_t slen,
	int hi,
	bool verbose = false,
	bool sanityCheck = false,
	size_t upto = OFF_MASK)
{
	size_t hlen = host.length();
	assert_gt(slen, 0);
	if(sanityCheck) sanityCheckInputSufs(s, slen);
	mkeyQSortSuf(host, hlen, s, slen, hi, (size_t)0, slen, (size_t)0, upto);
	if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
testq %rdx, %rdx
je 0xf868
movl %ecx, %ebp
movq %rdx, %rbx
movq %rsi, %r14
movq %rdi, %r12
movq 0x40(%rsp), %r15
movq 0x18(%rdi), %r13
testb %r9b, %r9b
je 0xf839
movq %r14, %rdi
movq %rbx, %rsi
callq 0xe885
subq $0x8, %rsp
movq %r12, %rdi
movq %r13, %rsi
movq %r14, %rdx
movq %rbx, %rcx
movl %ebp, %r8d
xorl %r9d, %r9d
pushq %r15
pushq $0x0
pushq %rbx
callq 0x27941
addq $0x18, %rsp
movq %r12, %rdi
movq %r13, %rsi
movq %r14, %rdx
movq %rbx, %rcx
movq %r15, %r8
xorl %r9d, %r9d
pushq $-0x1
callq 0x2413a
addq $0x18, %rsp
jmp 0xf85d
subq $0x8, %rsp
movq %r12, %rdi
movq %r13, %rsi
movq %r14, %rdx
movq %rbx, %rcx
movl %ebp, %r8d
xorl %r9d, %r9d
pushq %r15
pushq $0x0
pushq %rbx
callq 0x27941
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x27749(%rip), %rbx     # 0x36fb8
leaq 0x1c92f(%rip), %rsi     # 0x2c1a5
movq %rbx, %rdi
callq 0x4310
movq %rax, %rdi
xorl %esi, %esi
callq 0x40c0
leaq 0x1c92c(%rip), %rsi     # 0x2c1bb
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
xorl %esi, %esi
callq 0x4610
leaq 0x1eafd(%rip), %rsi     # 0x2e3a5
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
callq 0x4150
leaq 0x1f3eb(%rip), %r14     # 0x2ecaa
movq %rbx, %rdi
movq %r14, %rsi
callq 0x4310
leaq 0x1ded7(%rip), %rsi     # 0x2d7a8
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movl $0x1e1, %esi            # imm = 0x1E1
callq 0x4610
movq %rax, %rdi
callq 0x4150
leaq 0x1dd93(%rip), %rdi     # 0x2d688
leaq 0x1ffeb(%rip), %rcx     # 0x2f8e7
movq %r14, %rsi
movl $0x1e1, %edx            # imm = 0x1E1
callq 0x41c0
nop
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/./sstring.h
// Function: SString<char>::resize(unsigned long)
void resize(size_t sz) {
		if(cs_ != NULL) {
			delete cs_;
			cs_ = NULL;
		}
		if(printcs_ != NULL) {
			delete printcs_;
			printcs_ = NULL;
		}
		if(sz != 0) {
			cs_ = new T[sz+1];
		}
		len_ = sz;
	}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
movq 0x8(%rdi), %rdi
testq %rdi, %rdi
je 0x10139
movl $0x1, %esi
callq 0x4340
movq $0x0, 0x8(%r14)
movq 0x10(%r14), %rdi
testq %rdi, %rdi
je 0x10154
movl $0x1, %esi
callq 0x4340
movq $0x0, 0x10(%r14)
testq %rbx, %rbx
je 0x10166
leaq 0x1(%rbx), %rdi
callq 0x4030
movq %rax, 0x8(%r14)
movq %rbx, 0x18(%r14)
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/./sstring.h
// Function: SString<char>::~SString()
virtual ~SString() {
		if(cs_ != NULL) {
			delete[] cs_;
			cs_ = NULL;
		}
		if(printcs_ != NULL) {
			delete[] printcs_;
			printcs_ = NULL;
		}
		len_ = 0;
	}

// Assembly:
pushq %rbx
movq %rdi, %rbx
leaq 0x26377(%rip), %rax     # 0x36cb0
movq %rax, (%rdi)
movq 0x8(%rdi), %rdi
testq %rdi, %rdi
je 0x10952
callq 0x4420
movq $0x0, 0x8(%rbx)
movq 0x10(%rbx), %rdi
testq %rdi, %rdi
je 0x10968
callq 0x4420
movq $0x0, 0x10(%rbx)
movq $0x0, 0x18(%rbx)
popq %rbx
retq
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/./bitset.h
// Function: Bitset::Bitset(unsigned long, char const*)
Bitset(TIndexOffU sz, const char *errmsg = NULL) : _errmsg(errmsg) {
		TIndexOffU nwords = (sz / WORD_SIZE)+1;
		try {
			_words = new TIndexOffU[nwords];
		} catch(std::bad_alloc& ba) {
			if(_errmsg != NULL) {
				std::cerr << _errmsg;
			}
			throw 1;
		}
		assert(_words != NULL);
		memset(_words, 0, nwords * OFF_SIZE);
		_sz = nwords * WORD_SIZE;
		_cnt = 0;
	}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %rsi, %r14
movq %rdi, %rbx
movq %rdx, 0x8(%rdi)
shrq $0x6, %r14
leaq 0x8(,%r14,8), %r15
movq %r15, %rdi
callq 0x4030
incq %r14
movq %rax, 0x18(%rbx)
movq %rax, %rdi
xorl %esi, %esi
movq %r15, %rdx
callq 0x4190
shlq $0x6, %r14
movq %r14, 0x10(%rbx)
movq $0x0, (%rbx)
popq %rbx
popq %r14
popq %r15
retq
movq %rax, %r14
cmpl $0x1, %edx
jne 0x1264a
movq %r14, %rdi
callq 0x4130
movq 0x8(%rbx), %rbx
testq %rbx, %rbx
je 0x12621
movq %rbx, %rdi
callq 0x4140
movq 0x249da(%rip), %rdi     # 0x36ff0
movq %rbx, %rsi
movq %rax, %rdx
callq 0x43b0
movl $0x4, %edi
callq 0x4160
movl $0x1, (%rax)
movq 0x24920(%rip), %rsi     # 0x36f58
movq %rax, %rdi
xorl %edx, %edx
callq 0x45f0
movq %rax, %r14
callq 0x4580
movq %r14, %rdi
callq 0x4620
movq %rax, %rdi
callq 0x100de
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/./bitset.h
// Function: Bitset::set(unsigned long)
void set(TIndexOffU i) {
		while(i >= _sz) {
			// Slow path: bitset needs to be expanded before the
			// specified bit can be set
			ASSERT_ONLY(TIndexOffU oldsz = _sz);
			expand();
			assert_gt(_sz, oldsz);
		}
		// Fast path
		assert(((_words[i / WORD_SIZE] >> (i & BITSET_MASK)) & 1) == 0);
		_cnt++;
		_words[i / WORD_SIZE] |= ((TIndexOffU)1 << (i & BITSET_MASK));
		assert(((_words[i / WORD_SIZE] >> (i & BITSET_MASK)) & 1) == 1);
	}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %rsi, %r14
movq %rdi, %rbx
movq 0x10(%rdi), %rax
cmpq %r14, %rax
ja 0x1272a
movq %rax, %r15
movq %rbx, %rdi
callq 0x1e1f8
movq 0x10(%rbx), %rax
cmpq %r15, %rax
ja 0x12669
movq 0x2492b(%rip), %r14     # 0x36fb8
leaq 0x19b11(%rip), %rsi     # 0x2c1a5
movq %r14, %rdi
callq 0x4310
movq 0x10(%rbx), %rsi
movq %rax, %rdi
callq 0x40c0
leaq 0x19b0c(%rip), %rsi     # 0x2c1bb
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movq %r15, %rsi
callq 0x40c0
leaq 0x1bcdc(%rip), %rsi     # 0x2e3a5
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
callq 0x4150
leaq 0x1af4a(%rip), %rbx     # 0x2d62a
movq %r14, %rdi
movq %rbx, %rsi
callq 0x4310
leaq 0x1b0b6(%rip), %rsi     # 0x2d7a8
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movl $0xd3, %esi
callq 0x4610
movq %rax, %rdi
callq 0x4150
leaq 0x1af72(%rip), %rdi     # 0x2d688
leaq 0x1af18(%rip), %rcx     # 0x2d635
movq %rbx, %rsi
movl $0xd3, %edx
callq 0x41c0
movq 0x18(%rbx), %rdx
movq %r14, %rax
shrq $0x6, %rax
movq (%rdx,%rax,8), %rdi
movl $0x1, %esi
movl %r14d, %ecx
shlq %cl, %rsi
btq %r14, %rdi
jb 0x12761
incq (%rbx)
orq %rsi, (%rdx,%rax,8)
movq 0x18(%rbx), %rcx
testq %rsi, (%rcx,%rax,8)
je 0x12780
popq %rbx
popq %r14
popq %r15
retq
leaq 0x1aeea(%rip), %rdi     # 0x2d652
leaq 0x1aebb(%rip), %rsi     # 0x2d62a
leaq 0x1aebf(%rip), %rcx     # 0x2d635
movl $0xd6, %edx
callq 0x41c0
leaq 0x1af03(%rip), %rdi     # 0x2d68a
leaq 0x1ae9c(%rip), %rsi     # 0x2d62a
leaq 0x1aea0(%rip), %rcx     # 0x2d635
movl $0xd9, %edx
callq 0x41c0
nop
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/./ebwt.h
// Function: Ebwt::postReadInit(EbwtParams&)
void postReadInit(EbwtParams& eh) {
		TIndexOffU sideNum     = _zOff / eh._sideBwtLen;
		TIndexOffU sideCharOff = _zOff % eh._sideBwtLen;
		TIndexOffU sideByteOff = sideNum * eh._sideSz;
		_zEbwtByteOff = sideCharOff >> 2;
		assert_lt(_zEbwtByteOff, eh._sideBwtSz);
		_zEbwtBpOff = sideCharOff & 3;
		assert_lt(_zEbwtBpOff, 4);
		if(!eh._isBt2Index && (sideNum & 1) == 0) {
			// This is an even (backward) side
			_zEbwtByteOff = eh._sideBwtSz - _zEbwtByteOff - 1;
			_zEbwtBpOff = 3 - _zEbwtBpOff;
			assert_lt(_zEbwtBpOff, 4);
		}
		_zEbwtByteOff += sideByteOff;
		assert(repOk(eh)); // Ebwt should be fully initialized now
	}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %rsi, %rbx
movq %rdi, %r14
movq 0x68(%rdi), %rax
movl 0x84(%rsi), %ecx
movl 0x8c(%rsi), %esi
xorl %edx, %edx
divq %rsi
movl %edx, %esi
shrl $0x2, %esi
movq %rsi, 0x70(%rdi)
movl 0x88(%rbx), %edi
cmpq %rdi, %rsi
jae 0x12820
imulq %rax, %rcx
andl $0x3, %edx
movq %rdx, 0x78(%r14)
testb $0x1, %al
jne 0x12800
cmpb $0x0, 0xb9(%rbx)
jne 0x12800
movl 0x88(%rbx), %eax
notq %rsi
addq %rax, %rsi
xorq $0x3, %rdx
movq %rdx, 0x78(%r14)
addq %rcx, %rsi
movq %rsi, 0x70(%r14)
movq %r14, %rdi
movq %rbx, %rsi
callq 0x1e3a8
testb %al, %al
je 0x128c7
popq %rbx
popq %r14
popq %r15
retq
movq 0x24791(%rip), %r15     # 0x36fb8
leaq 0x19ac6(%rip), %rsi     # 0x2c2f4
movq %r15, %rdi
callq 0x4310
movq 0x70(%r14), %rsi
movq %rax, %rdi
callq 0x40c0
leaq 0x19ac1(%rip), %rsi     # 0x2c30a
movq %rax, %rdi
callq 0x4310
movl 0x88(%rbx), %esi
movq %rax, %rdi
callq 0x4440
leaq 0x1bb3f(%rip), %rsi     # 0x2e3a5
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
callq 0x4150
leaq 0x198ed(%rip), %rbx     # 0x2c16a
movq %r15, %rdi
movq %rbx, %rsi
callq 0x4310
leaq 0x1af19(%rip), %rsi     # 0x2d7a8
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movl $0x418, %esi            # imm = 0x418
callq 0x4610
movq %rax, %rdi
callq 0x4150
leaq 0x1add5(%rip), %rdi     # 0x2d688
leaq 0x1ae4c(%rip), %rcx     # 0x2d706
movq %rbx, %rsi
movl $0x418, %edx            # imm = 0x418
callq 0x41c0
leaq 0x1ae5e(%rip), %rdi     # 0x2d72c
leaq 0x19895(%rip), %rsi     # 0x2c16a
leaq 0x1ae2a(%rip), %rcx     # 0x2d706
movl $0x422, %edx            # imm = 0x422
callq 0x41c0
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/./ebwt.h
// Function: Ebwt::~Ebwt()
~Ebwt() {
		// Only free buffers if we're *not* using memory-mapped files
		if(!_useMm) {
			// Delete everything that was allocated in read(false, ...)
			if(_fchr    != NULL) delete[] _fchr;
			if(_ftab    != NULL) delete[] _ftab;
			if(_eftab   != NULL) delete[] _eftab;
			if(_offs != NULL && !useShmem_)
				delete[] _offs;
			else if(_offs != NULL && useShmem_)
				FREE_SHARED(_offs);
			if(_isa     != NULL) delete[] _isa;
			if(_plen    != NULL) delete[] _plen;
			if(_rstarts != NULL) delete[] _rstarts;
			if(_ebwt != NULL && !useShmem_)
				delete[] _ebwt;
			else if(_ebwt != NULL && useShmem_)
				FREE_SHARED(_ebwt);
		}
		if (_in1 != NULL) fclose(_in1);
		if (_in2 != NULL) fclose(_in2);
#ifdef EBWT_STATS
		cout << (_fw ? "Forward index:" : "Mirror index:") << endl;
		cout << "  mapLFEx:   " << mapLFExs_ << endl;
		cout << "  mapLF:     " << mapLFs_   << endl;
		cout << "  mapLF(c):  " << mapLFcs_  << endl;
		cout << "  mapLF1(c): " << mapLF1cs_ << endl;
		cout << "  mapLF(c):  " << mapLF1s_  << endl;
#endif
	}

// Assembly:
pushq %rbx
movq %rdi, %rbx
cmpb $0x0, 0xd0(%rdi)
jne 0x1818d
movq 0xa0(%rbx), %rdi
testq %rdi, %rdi
je 0x180f6
callq 0x4420
movq 0xa8(%rbx), %rdi
testq %rdi, %rdi
je 0x18107
callq 0x4420
movq 0xb0(%rbx), %rdi
testq %rdi, %rdi
je 0x18118
callq 0x4420
movq 0xb8(%rbx), %rdi
testq %rdi, %rdi
je 0x18139
cmpb $0x0, 0xd1(%rbx)
je 0x18134
callq 0x4680
jmp 0x18139
callq 0x4420
movq 0xc0(%rbx), %rdi
testq %rdi, %rdi
je 0x1814a
callq 0x4420
movq 0x90(%rbx), %rdi
testq %rdi, %rdi
je 0x1815b
callq 0x4420
movq 0x98(%rbx), %rdi
testq %rdi, %rdi
je 0x1816c
callq 0x4420
movq 0xc8(%rbx), %rdi
testq %rdi, %rdi
je 0x1818d
cmpb $0x0, 0xd1(%rbx)
je 0x18188
callq 0x4680
jmp 0x1818d
callq 0x4420
movq 0x18(%rbx), %rdi
testq %rdi, %rdi
je 0x1819b
callq 0x4320
movq 0x20(%rbx), %rdi
testq %rdi, %rdi
je 0x181a9
callq 0x4320
leaq 0xd8(%rbx), %rdi
callq 0x21874
movq 0x48(%rbx), %rdi
leaq 0x58(%rbx), %rax
cmpq %rax, %rdi
je 0x181cd
movq (%rax), %rsi
incq %rsi
callq 0x4340
movq 0x28(%rbx), %rdi
addq $0x38, %rbx
cmpq %rbx, %rdi
je 0x181e6
movq (%rbx), %rsi
incq %rsi
popq %rbx
jmp 0x4340
popq %rbx
retq
movq %rax, %rdi
callq 0x100de
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/./ebwt.h
// Function: Ebwt::ftabHi(unsigned long*, unsigned long*, unsigned long, unsigned long, unsigned long, unsigned long)
static TIndexOffU ftabHi(TIndexOffU *ftab,
			TIndexOffU *eftab,
			TIndexOffU len,
			TIndexOffU ftabLen,
			TIndexOffU eftabLen,
			TIndexOffU i)
	{
		assert_lt(i, ftabLen);
		if(ftab[i] <= len) {
			return ftab[i];
		} else {
			TIndexOffU efIdx = ftab[i] ^ OFF_MASK;
			assert_lt(efIdx*2+1, eftabLen);
			return eftab[efIdx*2+1];
		}
	}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %r9, %r15
cmpq %rcx, %r9
jae 0x18227
movq (%rdi,%r15,8), %rax
cmpq %rdx, %rax
jbe 0x18221
movq %r8, %rbx
notq %rax
leaq 0x1(,%rax,2), %r15
cmpq %r8, %r15
jae 0x182cd
movq (%rsi,%r15,8), %rax
popq %rbx
popq %r14
popq %r15
retq
movq %rcx, %r14
movq 0x1ed87(%rip), %rbx     # 0x36fb8
leaq 0x140bc(%rip), %rsi     # 0x2c2f4
movq %rbx, %rdi
callq 0x4310
movq %rax, %rdi
movq %r15, %rsi
callq 0x40c0
leaq 0x140b8(%rip), %rsi     # 0x2c30a
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movq %r14, %rsi
callq 0x40c0
leaq 0x16139(%rip), %rsi     # 0x2e3a5
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
callq 0x4150
leaq 0x13ee7(%rip), %r14     # 0x2c16a
movq %rbx, %rdi
movq %r14, %rsi
callq 0x4310
leaq 0x15513(%rip), %rsi     # 0x2d7a8
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movl $0x3e0, %esi            # imm = 0x3E0
callq 0x4610
movq %rax, %rdi
callq 0x4150
leaq 0x153cf(%rip), %rdi     # 0x2d688
leaq 0x14dee(%rip), %rcx     # 0x2d0ae
movq %r14, %rsi
movl $0x3e0, %edx            # imm = 0x3E0
callq 0x41c0
movq 0x1ece4(%rip), %r14     # 0x36fb8
leaq 0x14019(%rip), %rsi     # 0x2c2f4
movq %r14, %rdi
callq 0x4310
movq %rax, %rdi
movq %r15, %rsi
callq 0x40c0
leaq 0x14015(%rip), %rsi     # 0x2c30a
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movq %rbx, %rsi
callq 0x40c0
leaq 0x16096(%rip), %rsi     # 0x2e3a5
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
callq 0x4150
leaq 0x13e44(%rip), %rbx     # 0x2c16a
movq %r14, %rdi
movq %rbx, %rsi
callq 0x4310
leaq 0x15470(%rip), %rsi     # 0x2d7a8
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movl $0x3e5, %esi            # imm = 0x3E5
callq 0x4610
movq %rax, %rdi
callq 0x4150
leaq 0x1532c(%rip), %rdi     # 0x2d688
leaq 0x14d4b(%rip), %rcx     # 0x2d0ae
movq %rbx, %rsi
movl $0x3e5, %edx            # imm = 0x3E5
callq 0x41c0
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/./ebwt.h
// Function: Ebwt::ftabLo(unsigned long*, unsigned long*, unsigned long, unsigned long, unsigned long, unsigned long)
static TIndexOffU ftabLo(TIndexOffU *ftab,
			TIndexOffU *eftab,
			TIndexOffU len,
			TIndexOffU ftabLen,
			TIndexOffU eftabLen,
			TIndexOffU i)
	{
		assert_lt(i, ftabLen);
		if(ftab[i] <= len) {
			return ftab[i];
		} else {
			TIndexOffU efIdx = ftab[i] ^ OFF_MASK;
			assert_lt(efIdx*2+1, eftabLen);
			return eftab[efIdx*2];
		}
	}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %r9, %r15
cmpq %rcx, %r9
jae 0x183aa
movq (%rdi,%r15,8), %rax
cmpq %rdx, %rax
jbe 0x183a4
movq %r8, %rbx
notq %rax
leaq 0x1(,%rax,2), %r15
cmpq %r8, %r15
jae 0x18450
addq %rax, %rax
movq (%rsi,%rax,8), %rax
popq %rbx
popq %r14
popq %r15
retq
movq %rcx, %r14
movq 0x1ec04(%rip), %rbx     # 0x36fb8
leaq 0x13f39(%rip), %rsi     # 0x2c2f4
movq %rbx, %rdi
callq 0x4310
movq %rax, %rdi
movq %r15, %rsi
callq 0x40c0
leaq 0x13f35(%rip), %rsi     # 0x2c30a
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movq %r14, %rsi
callq 0x40c0
leaq 0x15fb6(%rip), %rsi     # 0x2e3a5
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
callq 0x4150
leaq 0x13d64(%rip), %r14     # 0x2c16a
movq %rbx, %rdi
movq %r14, %rsi
callq 0x4310
leaq 0x15390(%rip), %rsi     # 0x2d7a8
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movl $0x402, %esi            # imm = 0x402
callq 0x4610
movq %rax, %rdi
callq 0x4150
leaq 0x1524c(%rip), %rdi     # 0x2d688
leaq 0x14cd6(%rip), %rcx     # 0x2d119
movq %r14, %rsi
movl $0x402, %edx            # imm = 0x402
callq 0x41c0
movq 0x1eb61(%rip), %r14     # 0x36fb8
leaq 0x13e96(%rip), %rsi     # 0x2c2f4
movq %r14, %rdi
callq 0x4310
movq %rax, %rdi
movq %r15, %rsi
callq 0x40c0
leaq 0x13e92(%rip), %rsi     # 0x2c30a
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movq %rbx, %rsi
callq 0x40c0
leaq 0x15f13(%rip), %rsi     # 0x2e3a5
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
callq 0x4150
leaq 0x13cc1(%rip), %rbx     # 0x2c16a
movq %r14, %rdi
movq %rbx, %rsi
callq 0x4310
leaq 0x152ed(%rip), %rsi     # 0x2d7a8
movq %rax, %rdi
callq 0x4310
movq %rax, %rdi
movl $0x407, %esi            # imm = 0x407
callq 0x4610
movq %rax, %rdi
callq 0x4150
leaq 0x151a9(%rip), %rdi     # 0x2d688
leaq 0x14c33(%rip), %rcx     # 0x2d119
movq %rbx, %rsi
movl $0x407, %edx            # imm = 0x407
callq 0x41c0
nop
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/./ebwt.h
// Function: Ebwt::repOk(EbwtParams const&) const
bool repOk(const EbwtParams& eh) const {
		assert(_eh.repOk());
		if(isInMemory()) {
			return inMemoryRepOk(eh);
		}
		return true;
	}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
addq $0x108, %rdi            # imm = 0x108
callq 0x12e8c
testb %al, %al
je 0x1e3ea
movq %r14, %rdi
callq 0xf948
testb %al, %al
je 0x1e3e0
movq %r14, %rdi
movq %rbx, %rsi
addq $0x8, %rsp
popq %rbx
popq %r14
jmp 0x1e40a
movb $0x1, %al
addq $0x8, %rsp
popq %rbx
popq %r14
retq
leaq 0xe8f9(%rip), %rdi      # 0x2ccea
leaq 0xdd72(%rip), %rsi      # 0x2c16a
leaq 0xf337(%rip), %rcx      # 0x2d736
movl $0x49f, %edx            # imm = 0x49F
callq 0x41c0
nop
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/./ref_read.h
// Function: RefRecord::RefRecord(_IO_FILE*, bool)
RefRecord(FILE *in, bool swap) {
		assert(in != NULL);
		if(!fread(&off, OFF_SIZE, 1, in)) {
			cerr << "Error reading RefRecord offset from FILE" << endl;
			throw 1;
		}
		if(swap) off = endianSwapU(off);
		if(!fread(&len, OFF_SIZE, 1, in)) {
			cerr << "Error reading RefRecord offset from FILE" << endl;
			throw 1;
		}
		if(swap) len = endianSwapU(len);
		first = fgetc(in) ? true : false;
	}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
testq %rsi, %rsi
je 0x1ef56
movl %edx, %ebp
movq %rsi, %r14
movq %rdi, %rbx
movl $0x8, %esi
movl $0x1, %edx
movq %r14, %rcx
callq 0x44e0
testq %rax, %rax
je 0x1ef1a
testb %bpl, %bpl
je 0x1eee6
movq (%rbx), %rax
bswapq %rax
movq %rax, (%rbx)
leaq 0x8(%rbx), %r15
movl $0x8, %esi
movl $0x1, %edx
movq %r15, %rdi
movq %r14, %rcx
callq 0x44e0
testq %rax, %rax
je 0x1ef1a
movq (%r15), %rax
bswapq %rax
movq %rax, (%r15)
jmp 0x1ef01
leaq 0x8(%rbx), %rdi
movl $0x8, %esi
movl $0x1, %edx
movq %r14, %rcx
callq 0x44e0
testq %rax, %rax
je 0x1ef1a
movq %r14, %rdi
callq 0x4540
testl %eax, %eax
setne 0x10(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
movq 0x180cf(%rip), %rdi     # 0x36ff0
leaq 0xeecc(%rip), %rsi      # 0x2ddf4
callq 0x4310
movq %rax, %rdi
callq 0x4150
movl $0x4, %edi
callq 0x4160
movl $0x1, (%rax)
movq 0x1800c(%rip), %rsi     # 0x36f58
movq %rax, %rdi
xorl %edx, %edx
callq 0x45f0
leaq 0xf266(%rip), %rdi      # 0x2e1c3
leaq 0xee60(%rip), %rsi      # 0x2ddc4
leaq 0xee66(%rip), %rcx      # 0x2ddd1
movl $0x40, %edx
callq 0x41c0
nop
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/./ds.h
// Function: EList<SString<char>, 128>::expandCopyExact(unsigned long)
void expandCopyExact(size_t newsz) {
		if(newsz <= sz_) return;
		T* tmp = alloc(newsz);
		assert(tmp != NULL);
		size_t cur = cur_;
		if(list_ != NULL) {
 			for(size_t i = 0; i < cur_; i++) {
				// Note: operator= is used
				tmp[i] = list_[i];
			}
			free();
		}
		list_ = tmp;
		sz_ = newsz;
		cur_ = cur;
	}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
cmpq %rsi, 0x10(%rdi)
jae 0x2040b
movq %rsi, %r14
movq %rdi, %rbx
callq 0x2032c
testq %rax, %rax
je 0x2041a
movq %rax, %r15
movq 0x18(%rbx), %r12
cmpq $0x0, 0x8(%rbx)
je 0x203ff
testq %r12, %r12
je 0x203f7
xorl %r13d, %r13d
xorl %ebp, %ebp
movq 0x8(%rbx), %rax
leaq (%r15,%r13), %rdi
movq 0x8(%rax,%r13), %rsi
movq 0x18(%rax,%r13), %rdx
movq (%r15,%r13), %rax
callq *0x10(%rax)
incq %rbp
addq $0x20, %r13
cmpq 0x18(%rbx), %rbp
jb 0x203d1
movq %rbx, %rdi
callq 0x2043a
movq %r15, 0x8(%rbx)
movq %r14, 0x10(%rbx)
movq %r12, 0x18(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
leaq 0xd960(%rip), %rdi      # 0x2dd81
leaq 0xd562(%rip), %rsi      # 0x2d98a
leaq 0xdc14(%rip), %rcx      # 0x2e043
movl $0x3c8, %edx            # imm = 0x3C8
callq 0x41c0
nop
// File: /workspace/github_cpp_makefile_star2_O3/BenLangmead[P]bowtie/./ds.h
// Function: EList<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, 128>::alloc(unsigned long)
T *alloc(size_t sz) {
		T* tmp = new T[sz];
		assert(tmp != NULL);
#ifdef USE_MEM_TALLY
		gMemTally.add(cat_, sz);
#endif
		allocCat_ = cat_;
		return tmp;
	}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %rsi, %r14
movq %rdi, %rbx
movq %rsi, %rax
shrq $0x3b, %rax
movq %rsi, %r15
shlq $0x5, %r15
xorl %edi, %edi
negq %rax
sbbq %rdi, %rdi
orq %r15, %rdi
orq $0x8, %rdi
callq 0x4030
movq %rax, %rcx
movq %r14, (%rax)
addq $0x8, %rax
testq %r14, %r14
je 0x217d1
addq $0x18, %rcx
movq %rcx, -0x10(%rcx)
movq $0x0, -0x8(%rcx)
movb $0x0, (%rcx)
addq $0x20, %rcx
addq $-0x20, %r15
jne 0x217b8
movl (%rbx), %ecx
movl %ecx, 0x4(%rbx)
popq %rbx
popq %r14
popq %r15
retq