// File: /workspace/github_cpp_makefile_star2_O1/BenLangmead[P]bowtie/bowtie_main.cpp
// Function: main
int main(int argc, const char **argv) {
	if(argc > 2 && strcmp(argv[1], "-A") == 0) {
		const char *file = argv[2];
		ifstream in;
		in.open(file);
		char buf[4096];
		int lastret = -1;
		while(in.getline(buf, 4095)) {
			EList<string> args;
			args.push_back(string(argv[0]));
			tokenize(buf, " \t", args);
			const char **myargs = (const char**)malloc(sizeof(char*)*args.size());
			for(size_t i = 0; i < args.size(); i++) {
				myargs[i] = args[i].c_str();
			}
			if(args.size() == 1) continue;
			lastret = bowtie((int)args.size(), myargs);
			free(myargs);
		}
		if(lastret == -1) {
			cerr << "Warning: No arg strings parsed from " << file << endl;
			return 0;
		}
		return lastret;
	} else {
		return bowtie(argc, argv);
	}
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x12a8, %rsp           # imm = 0x12A8
movq %rsi, %r14
movl %edi, %ebx
cmpl $0x3, %edi
jl 0x5212f
movq 0x8(%r14), %rdi
leaq 0x644e(%rip), %rsi      # 0x58574
callq 0x9670
testl %eax, %eax
je 0x5214a
movl %ebx, %edi
movq %r14, %rsi
addq $0x12a8, %rsp           # imm = 0x12A8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
jmp 0xe054
movq %r14, 0x90(%rsp)
movq 0x10(%r14), %rbx
leaq 0x98(%rsp), %r14
movq %r14, %rdi
callq 0x9550
movq %r14, %rdi
movq %rbx, 0x88(%rsp)
movq %rbx, %rsi
movl $0x8, %edx
callq 0x92a0
movl $0xffffffff, 0x4(%rsp)  # imm = 0xFFFFFFFF
leaq 0x28(%rsp), %r13
leaq 0x48(%rsp), %rbx
leaq 0x68(%rsp), %r15
movq $-0x1, %rbp
movq 0x98(%rsp), %rax
movq -0x18(%rax), %rdi
leaq 0x98(%rsp), %r14
addq %r14, %rdi
movl $0xa, %esi
callq 0x9480
movsbl %al, %ecx
movl $0xfff, %edx            # imm = 0xFFF
movq %r14, %rdi
leaq 0x2a0(%rsp), %rsi
callq 0x9a00
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
testb $0x5, 0x20(%rax,%rcx)
jne 0x523f5
movabsq $-0x100000000, %rax     # imm = 0xFFFFFFFF00000000
movq %rax, 0x68(%rsp)
xorl %eax, %eax
movq %rax, 0x70(%rsp)
movq $0x80, 0x78(%rsp)
movq %rax, 0x80(%rsp)
movq 0x90(%rsp), %rax
movq (%rax), %rsi
movq %r13, %rdi
movq %rbx, %rdx
callq 0x1b200
movq %r15, %rdi
movq %r13, %rsi
callq 0x1c634
movq 0x28(%rsp), %rdi
leaq 0x38(%rsp), %rax
cmpq %rax, %rdi
je 0x5224b
movq 0x38(%rsp), %rsi
incq %rsi
callq 0x94c0
leaq 0x58(%rsp), %rax
movq %rax, 0x48(%rsp)
leaq 0x2a0(%rsp), %r14
movq %r14, %rdi
callq 0x91b0
leaq (%rsp,%rax), %rdx
addq $0x2a0, %rdx            # imm = 0x2A0
movq %rbx, %rdi
movq %r14, %rsi
callq 0x1dde4
leaq 0x18(%rsp), %rax
movq %rax, 0x8(%rsp)
leaq 0x8(%rsp), %rdi
leaq 0x62c2(%rip), %rsi      # 0x58553
leaq 0x62bd(%rip), %rdx      # 0x58555
callq 0x1dde4
movq 0x8(%rsp), %rsi
movq 0x10(%rsp), %rcx
movq %rbx, %rdi
xorl %edx, %edx
callq 0x98a0
movq %rax, %r12
movq 0x8(%rsp), %rsi
movq 0x10(%rsp), %rcx
movq %rbx, %rdi
movq %rax, %rdx
callq 0x9770
movq %rax, %r14
andq %r12, %rax
cmpq $-0x1, %rax
je 0x5235c
movq %r14, %rcx
subq %r12, %rcx
movq %r13, %rdi
movq %rbx, %rsi
movq %r12, %rdx
callq 0x94e0
movq %r15, %rdi
movq %r13, %rsi
callq 0x1c634
movq 0x28(%rsp), %rdi
leaq 0x38(%rsp), %rax
cmpq %rax, %rdi
je 0x52314
movq 0x38(%rsp), %rsi
incq %rsi
callq 0x94c0
movq 0x8(%rsp), %rsi
movq 0x10(%rsp), %rcx
movq %rbx, %rdi
movq %r14, %rdx
callq 0x98a0
movq %rax, %r12
movq 0x8(%rsp), %rsi
movq 0x10(%rsp), %rcx
movq %rbx, %rdi
movq %rax, %rdx
callq 0x9770
movq %rax, %r14
cmpq $-0x2, 0x80(%rsp)
cmoveq %rbp, %r14
movq %r12, %rax
andq %r14, %rax
jmp 0x522cf
movq 0x8(%rsp), %rdi
leaq 0x18(%rsp), %rax
cmpq %rax, %rdi
je 0x52378
movq 0x18(%rsp), %rsi
incq %rsi
callq 0x94c0
movq 0x48(%rsp), %rdi
leaq 0x58(%rsp), %rax
cmpq %rax, %rdi
je 0x52394
movq 0x58(%rsp), %rsi
incq %rsi
callq 0x94c0
movq 0x80(%rsp), %r12
leaq (,%r12,8), %rdi
callq 0x9600
movq %rax, %r14
testq %r12, %r12
je 0x523d1
movq 0x70(%rsp), %rax
xorl %ecx, %ecx
movq (%rax), %rdx
movq %rdx, (%r14,%rcx,8)
incq %rcx
addq $0x20, %rax
cmpq %rcx, %r12
jne 0x523b8
cmpq $0x1, %r12
je 0x523e8
movl %r12d, %edi
movq %r14, %rsi
callq 0xe054
movl %eax, 0x4(%rsp)
movq %r14, %rdi
callq 0x9580
movq %r15, %rdi
callq 0x1fefe
jmp 0x5219c
movl 0x4(%rsp), %ebx
cmpl $-0x1, %ebx
jne 0x5248a
movq 0x18be7(%rip), %rbx     # 0x6aff0
leaq 0x6167(%rip), %rsi      # 0x58577
movl $0x24, %edx
movq %rbx, %rdi
callq 0x9560
movq 0x88(%rsp), %r14
testq %r14, %r14
je 0x52446
movq %r14, %rdi
callq 0x91b0
movq 0x18bb7(%rip), %rdi     # 0x6aff0
movq %r14, %rsi
movq %rax, %rdx
callq 0x9560
jmp 0x5245d
movq (%rbx), %rax
movq -0x18(%rax), %rax
leaq (%rbx,%rax), %rdi
movl 0x20(%rbx,%rax), %esi
orl $0x1, %esi
callq 0x98c0
movq (%rbx), %rax
addq -0x18(%rax), %rbx
movq %rbx, %rdi
movl $0xa, %esi
callq 0x9480
movsbl %al, %esi
movq 0x18b75(%rip), %rdi     # 0x6aff0
callq 0x9050
xorl %ebx, %ebx
movq %rax, %rdi
callq 0x92f0
leaq 0x98(%rsp), %rdi
callq 0x9110
movl %ebx, %eax
addq $0x12a8, %rsp           # imm = 0x12A8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
jmp 0x524d6
jmp 0x524d6
jmp 0x524b3
jmp 0x524b3
movq %rax, %rbx
jmp 0x52537
movq %rax, %rbx
jmp 0x5251b
movq %rax, %rbx
movq 0x28(%rsp), %rdi
leaq 0x38(%rsp), %rax
cmpq %rax, %rdi
je 0x52537
movq 0x38(%rsp), %rsi
jmp 0x5252f
movq %rax, %rbx
jmp 0x52541
movq %rax, %rbx
jmp 0x524ff
movq %rax, %rbx
movq 0x28(%rsp), %rdi
leaq 0x38(%rsp), %rax
cmpq %rax, %rdi
je 0x524ff
movq 0x38(%rsp), %rsi
incq %rsi
callq 0x94c0
movq 0x8(%rsp), %rdi
leaq 0x18(%rsp), %rax
cmpq %rax, %rdi
je 0x5251b
movq 0x18(%rsp), %rsi
incq %rsi
callq 0x94c0
movq 0x48(%rsp), %rdi
leaq 0x58(%rsp), %rax
cmpq %rax, %rdi
je 0x52537
movq 0x58(%rsp), %rsi
incq %rsi
callq 0x94c0
leaq 0x68(%rsp), %rdi
callq 0x1fefe
leaq 0x98(%rsp), %rdi
callq 0x9110
movq %rbx, %rdi
callq 0x9930