// File: /workspace/github_cpp_makefile_star2_O3/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
movl %edi, %ebp
leaq 0x92538(%rip), %rdx     # 0xcd55c
leaq 0xc47a5(%rip), %rcx     # 0xff7d0
movq $0x0, 0x8(%rsp)
movq %rsi, 0x10(%rsp)
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
je 0x3b178
leaq 0x28(%rsp), %rbx
movq $0x0, 0x8(%rsp)
leaq 0x18(%rsp), %r15
leaq 0x38(%rsp), %r12
movq 0xc6f0c(%rip), %rax     # 0x101f80
movq (%rax), %r13
testq %r13, %r13
leaq 0x9294a(%rip), %rax     # 0xcd9cb
cmoveq %rax, %r13
movq %rbx, 0x18(%rsp)
movq %r13, %rdi
callq 0x81f0
leaq (%rax,%r13), %rdx
movq %r15, %rdi
movq %r13, %rsi
callq 0x28a52
movq %r12, %rdi
movq %r15, %rsi
movl $0x8, %edx
callq 0x87b0
movq 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0x3b0c8
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
sarl $0x18, %r14d
cmpl $0x66, %r14d
jg 0x3b0ec
testl %r14d, %r14d
je 0x3b10a
cmpl $0x1, %r14d
je 0x3b11c
cmpl $0x3f, %r14d
jne 0x3b12b
movb $0x1, %al
movq %rax, 0x8(%rsp)
jmp 0x3b12b
cmpl $0x67, %r14d
je 0x3b113
leaq 0xc79ef(%rip), %rsi     # 0x102ae8
cmpl $0x6c, %r14d
je 0x3b123
cmpl $0x68, %r14d
jne 0x3b12b
jmp 0x3b279
leaq 0xc79f7(%rip), %rsi     # 0x102b08
jmp 0x3b123
leaq 0xc79ae(%rip), %rsi     # 0x102ac8
jmp 0x3b123
leaq 0xc7a05(%rip), %rsi     # 0x102b28
movq %r12, %rdi
callq 0x8560
movq %r12, %rdi
movq 0xc6e63(%rip), %rsi     # 0x101f98
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
movl %ebp, %edi
movq 0x10(%rsp), %rsi
leaq 0x92407(%rip), %rdx     # 0xcd55c
leaq 0xc4674(%rip), %rcx     # 0xff7d0
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
jne 0x3b06d
leaq 0xc7949(%rip), %rdi     # 0x102ac8
leaq 0x92845(%rip), %rsi     # 0xcd9cb
callq 0x8160
testl %eax, %eax
je 0x3b196
movq 0x8(%rsp), %rbx
jmp 0x3b1cc
leaq 0xc794b(%rip), %rdi     # 0x102ae8
leaq 0x92827(%rip), %rsi     # 0xcd9cb
callq 0x8160
testl %eax, %eax
movq 0x8(%rsp), %rbx
jne 0x3b1cc
movq 0xc6e2f(%rip), %rdi     # 0x101fe8
leaq 0x92342(%rip), %rsi     # 0xcd502
movl $0x2a, %edx
callq 0x84e0
movb $0x1, %bl
leaq 0xc78f5(%rip), %rdi     # 0x102ac8
leaq 0x927f1(%rip), %rsi     # 0xcd9cb
callq 0x8160
testl %eax, %eax
je 0x3b214
leaq 0xc78fe(%rip), %rdi     # 0x102ae8
leaq 0x927da(%rip), %rsi     # 0xcd9cb
callq 0x8160
testl %eax, %eax
je 0x3b214
movq 0xc6de7(%rip), %rdi     # 0x101fe8
leaq 0x92325(%rip), %rsi     # 0xcd52d
movl $0x2e, %edx
callq 0x84e0
movb $0x1, %bl
movq 0xc6da5(%rip), %rax     # 0x101fc0
movslq (%rax), %rcx
subl %ecx, %ebp
jle 0x3b293
cmpl $0x1, %ebp
jne 0x3b2a1
testb $0x1, %bl
jne 0x3b2b9
leal 0x1(%rcx), %edx
movl %edx, (%rax)
movq 0x10(%rsp), %rax
movq (%rax,%rcx,8), %rbx
movq 0xc790b(%rip), %r14     # 0x102b50
leaq 0xc78fc(%rip), %r15     # 0x102b48
movq %rbx, %rdi
callq 0x81f0
movq %r15, %rdi
xorl %esi, %esi
movq %r14, %rdx
movq %rbx, %rcx
movq %rax, %r8
callq 0x86c0
addq $0x1b8, %rsp            # imm = 0x1B8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0xc6d38(%rip), %rdi     # 0x101fb8
leaq 0x922f5(%rip), %rsi     # 0xcd57c
callq 0x8460
xorl %edi, %edi
callq 0x8530
leaq 0x90c48(%rip), %rsi     # 0xcbee2
movl $0x12, %edx
jmp 0x3b2ad
leaq 0x90c4d(%rip), %rsi     # 0xcbef5
movl $0x13, %edx
movq 0xc6d34(%rip), %rdi     # 0x101fe8
callq 0x84e0
movq 0xc6cf8(%rip), %rdi     # 0x101fb8
leaq 0x90176(%rip), %rsi     # 0xcb43d
callq 0x8460
leaq 0x922a9(%rip), %rsi     # 0xcd57c
movq %rax, %rdi
callq 0x8460
movl $0x1, %edi
callq 0x8530
jmp 0x3b2e7
movq %rax, %r14
movq 0xc6ca7(%rip), %rsi     # 0x101f98
leaq 0x38(%rsp), %rdi
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
jmp 0x3b329
movq %rax, %r14
jmp 0x3b329
movq %rax, %r14
movq 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0x3b329
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
movq %r14, %rdi
callq 0x8840
nop