// File: /workspace/github_cpp_makefile_star2_O1/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 0x92e1b(%rip), %rdx     # 0xd0d54
leaq 0xca990(%rip), %rcx     # 0x1088d0
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 0x3e08d
leaq 0x28(%rsp), %rbx
movq $0x0, 0x8(%rsp)
leaq 0x18(%rsp), %r15
leaq 0x38(%rsp), %r12
movq 0xccff7(%rip), %rax     # 0x10af80
movq (%rax), %r13
testq %r13, %r13
leaq 0x93ce9(%rip), %rax     # 0xd1c7f
cmoveq %rax, %r13
movq %rbx, 0x18(%rsp)
movq %r13, %rdi
callq 0x81f0
leaq (%rax,%r13), %rdx
movq %r15, %rdi
movq %r13, %rsi
callq 0x28952
movq %r12, %rdi
movq %r15, %rsi
movl $0x8, %edx
callq 0x87b0
movq 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0x3dfdd
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
sarl $0x18, %r14d
cmpl $0x66, %r14d
jg 0x3e001
testl %r14d, %r14d
je 0x3e01f
cmpl $0x1, %r14d
je 0x3e031
cmpl $0x3f, %r14d
jne 0x3e040
movb $0x1, %al
movq %rax, 0x8(%rsp)
jmp 0x3e040
cmpl $0x67, %r14d
je 0x3e028
leaq 0xcdad2(%rip), %rsi     # 0x10bae0
cmpl $0x6c, %r14d
je 0x3e038
cmpl $0x68, %r14d
jne 0x3e040
jmp 0x3e1bd
leaq 0xcdada(%rip), %rsi     # 0x10bb00
jmp 0x3e038
leaq 0xcda91(%rip), %rsi     # 0x10bac0
jmp 0x3e038
leaq 0xcdae8(%rip), %rsi     # 0x10bb20
movq %r12, %rdi
callq 0x8560
movq %r12, %rdi
movq 0xccf4e(%rip), %rsi     # 0x10af98
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
movl %ebp, %edi
movq 0x10(%rsp), %rsi
leaq 0x92cea(%rip), %rdx     # 0xd0d54
leaq 0xca85f(%rip), %rcx     # 0x1088d0
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
jne 0x3df82
leaq 0xcda2c(%rip), %rdi     # 0x10bac0
leaq 0x93be4(%rip), %rsi     # 0xd1c7f
callq 0x8160
testl %eax, %eax
je 0x3e0ab
movq 0x8(%rsp), %r14
jmp 0x3e0e2
leaq 0xcda2e(%rip), %rdi     # 0x10bae0
leaq 0x93bc6(%rip), %rsi     # 0xd1c7f
callq 0x8160
testl %eax, %eax
movq 0x8(%rsp), %r14
jne 0x3e0e2
movq 0xccf1a(%rip), %rdi     # 0x10afe8
leaq 0x92c25(%rip), %rsi     # 0xd0cfa
movl $0x2a, %edx
callq 0x84e0
movb $0x1, %r14b
leaq 0xcd9d7(%rip), %rdi     # 0x10bac0
leaq 0x93b8f(%rip), %rsi     # 0xd1c7f
callq 0x8160
testl %eax, %eax
je 0x3e12b
leaq 0xcd9e0(%rip), %rdi     # 0x10bae0
leaq 0x93b78(%rip), %rsi     # 0xd1c7f
callq 0x8160
testl %eax, %eax
je 0x3e12b
movq 0xcced1(%rip), %rdi     # 0x10afe8
leaq 0x92c07(%rip), %rsi     # 0xd0d25
movl $0x2e, %edx
callq 0x84e0
movb $0x1, %r14b
movq 0xcce8e(%rip), %rbx     # 0x10afc0
subl (%rbx), %ebp
jle 0x3e150
cmpl $0x1, %ebp
je 0x3e16b
movq 0xccea6(%rip), %rdi     # 0x10afe8
leaq 0x9007c(%rip), %rsi     # 0xce1c5
movl $0x13, %edx
jmp 0x3e163
movq 0xcce91(%rip), %rdi     # 0x10afe8
leaq 0x90054(%rip), %rsi     # 0xce1b2
movl $0x12, %edx
callq 0x84e0
movb $0x1, %r14b
testb $0x1, %r14b
jne 0x3e1d7
movslq (%rbx), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%rbx)
movq 0x10(%rsp), %rcx
movq (%rcx,%rax,8), %rbx
movq 0xcd9bf(%rip), %r14     # 0x10bb48
leaq 0xcd9b0(%rip), %r15     # 0x10bb40
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 0xccdf4(%rip), %rdi     # 0x10afb8
leaq 0x92ba9(%rip), %rsi     # 0xd0d74
callq 0x8460
xorl %edi, %edi
callq 0x8530
movq 0xccdda(%rip), %rdi     # 0x10afb8
leaq 0x8e498(%rip), %rsi     # 0xcc67d
callq 0x8460
leaq 0x92b83(%rip), %rsi     # 0xd0d74
movq %rax, %rdi
callq 0x8460
movl $0x1, %edi
callq 0x8530
jmp 0x3e205
movq %rax, %r14
movq 0xccd89(%rip), %rsi     # 0x10af98
leaq 0x38(%rsp), %rdi
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
jmp 0x3e247
movq %rax, %r14
jmp 0x3e247
movq %rax, %r14
movq 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0x3e247
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
movq %r14, %rdi
callq 0x8840
nop