// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/evo_codingSeqs_fromGenomes.cpp
// Function: parseSeqFromGenomesOptions(int, char**)
void parseSeqFromGenomesOptions(int argc, char** argv) {
    bool die = false;
    for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
    {
        std::istringstream arg(optarg != NULL ? optarg : "");
        switch (c)
        {
            case '?': die = true; break;
            case 'g': arg >> opt::genomeFile; break;
            case 'l': arg >> opt::genomeListFile; break;
            case OPT_NEW_LABELS: arg >> opt::newLabelFile; break;
            case OPT_FOLDER: arg >> opt::outFolder; break;
            case 'h':
                std::cout << SEQFROMGENOME_USAGE_MESSAGE;
                exit(EXIT_SUCCESS);
        }
    }
    
    if (opt::genomeFile == "" && opt::genomeListFile == "") {
        std::cerr << "Either -g or -l options must be specified\n";
        die = true;
    }
    
    if (opt::genomeFile != "" && opt::genomeListFile != "") {
        std::cerr << "The -g and -l options can't both be specified\n";
        die = true;
    }
    
    if (argc - optind < 1) {
        std::cerr << "missing arguments\n";
        die = true;
    }
    else if (argc - optind > 1)
    {
        std::cerr << "too many arguments\n";
        die = true;
    }
    
    if (die) {
        std::cout << "\n" << SEQFROMGENOME_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
    opt::geneFile = argv[optind++];
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x1b8, %rsp            # imm = 0x1B8
movq %rsi, %rbx
movl %edi, %ebp
movq $0x0, 0x10(%rsp)
leaq 0x18(%rsp), %r12
leaq 0x38(%rsp), %r14
pushq $0x8
popq %r13
movl %ebp, %edi
movq %rbx, %rsi
leaq 0x67118(%rip), %rdx     # 0x98ef4
leaq 0xa8b0d(%rip), %rcx     # 0xda8f0
xorl %r8d, %r8d
callq 0x8790
movl %eax, %r15d
shll $0x18, %eax
cmpl $0xff000000, %eax       # imm = 0xFF000000
je 0x31ea1
movq 0xab18d(%rip), %rax     # 0xdcf90
movq (%rax), %rsi
testq %rsi, %rsi
leaq 0x6800f(%rip), %rax     # 0x99e1f
cmoveq %rax, %rsi
movq %r12, %rdi
leaq 0xf(%rsp), %rdx
callq 0x21904
movq %r14, %rdi
movq %r12, %rsi
movl %r13d, %edx
callq 0x87e0
movsbl %r15b, %r15d
movq %r12, %rdi
callq 0x8978
testl %r15d, %r15d
je 0x31e85
cmpl $0x1, %r15d
je 0x31e6a
cmpl $0x3f, %r15d
je 0x31e73
cmpl $0x67, %r15d
je 0x31e7c
leaq 0xabcbf(%rip), %rsi     # 0xddb18
cmpl $0x6c, %r15d
je 0x31e8c
cmpl $0x68, %r15d
jne 0x31e94
jmp 0x31f75
leaq 0xabce7(%rip), %rsi     # 0xddb58
jmp 0x31e8c
movb $0x1, %al
movq %rax, 0x10(%rsp)
jmp 0x31e94
leaq 0xabc75(%rip), %rsi     # 0xddaf8
jmp 0x31e8c
leaq 0xabcac(%rip), %rsi     # 0xddb38
movq %r14, %rdi
callq 0x8570
movq %r14, %rdi
callq 0x8220
jmp 0x31dd0
leaq 0xabc50(%rip), %rdi     # 0xddaf8
leaq 0x67f70(%rip), %rsi     # 0x99e1f
callq 0x2193f
testb %al, %al
je 0x31eec
leaq 0xabc59(%rip), %rdi     # 0xddb18
leaq 0x67f59(%rip), %rsi     # 0x99e1f
callq 0x2193f
testb %al, %al
movq 0x10(%rsp), %r14
je 0x31ef1
movq 0xab10d(%rip), %rdi     # 0xdcfe8
leaq 0x66fb8(%rip), %rsi     # 0x98e9a
callq 0x8480
movb $0x1, %r14b
jmp 0x31ef1
movq 0x10(%rsp), %r14
leaq 0xabc00(%rip), %rdi     # 0xddaf8
leaq 0x67f20(%rip), %rsi     # 0x99e1f
callq 0x2ea9b
testb %al, %al
je 0x31f35
leaq 0xabc09(%rip), %rdi     # 0xddb18
leaq 0x67f09(%rip), %rsi     # 0x99e1f
callq 0x2ea9b
testb %al, %al
je 0x31f35
movq 0xab0c2(%rip), %rdi     # 0xdcfe8
leaq 0x66f98(%rip), %rsi     # 0x98ec5
callq 0x8480
movb $0x1, %r14b
movq 0xab084(%rip), %rax     # 0xdcfc0
movslq (%rax), %rcx
subl %ecx, %ebp
jle 0x31f8f
cmpl $0x1, %ebp
jne 0x31f98
testb $0x1, %r14b
jne 0x31fab
leal 0x1(%rcx), %edx
movl %edx, (%rax)
movq (%rbx,%rcx,8), %rsi
leaq 0xabc1a(%rip), %rdi     # 0xddb78
callq 0x88f0
addq $0x1b8, %rsp            # imm = 0x1B8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0xab03c(%rip), %rdi     # 0xdcfb8
leaq 0x66f91(%rip), %rsi     # 0x98f14
callq 0x8480
xorl %edi, %edi
callq 0x8540
leaq 0x6438c(%rip), %rsi     # 0x96322
jmp 0x31f9f
leaq 0x64396(%rip), %rsi     # 0x96335
movq 0xab042(%rip), %rdi     # 0xdcfe8
callq 0x8480
movq 0xab006(%rip), %rdi     # 0xdcfb8
leaq 0x61994(%rip), %rsi     # 0x9394d
callq 0x8480
leaq 0x66f4f(%rip), %rsi     # 0x98f14
movq %rax, %rdi
callq 0x8480
pushq $0x1
popq %rdi
callq 0x8540
jmp 0x31fd7
movq %rax, %rbx
leaq 0x38(%rsp), %rdi
callq 0x8220
jmp 0x31ff8
movq %rax, %rbx
jmp 0x31ff8
movq %rax, %rbx
leaq 0x18(%rsp), %rdi
callq 0x8978
movq %rbx, %rdi
callq 0x8870