// File: /workspace/github_cpp_makefile_star2_O1/millanek[P]evo/process_vcf_cbs.cpp
// Function: parseCbsOptions(int, char**)
void parseCbsOptions(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 's': arg >> opt::sampleNameFile; break;
            case 'm': arg >> opt::minScLength; break;
            case OPT_CBS: arg >> opt::undeterminedLociFile; break;
            case OPT_FEATURES: arg >> opt::featuresFile; break;
            case OPT_CHR_SIZES: arg >> opt::sizesFile; break;
            case OPT_GROUPS: arg >> opt::groupsFile; break;
            case OPT_PREPARE_GENOME: opt::bPrepareGenome = true; break;
            case 'h':
                std::cout << CBS_USAGE_MESSAGE;
                exit(EXIT_SUCCESS);
        }
    }
    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" << CBS_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
    
    // Parse the input filenames
    if (opt::bPrepareGenome)
        opt::genomeFile = argv[optind++];
    else if (!opt::undeterminedLociFile.empty()) {
        opt::vcfFile = argv[optind++];
    } else {
        std::cerr << "either the --cbs or the --prepare-genome option has to be selected" << std::endl;
        std::cout << CBS_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
    
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x1b8, %rsp            # imm = 0x1B8
movl %edi, %ebp
leaq 0x8ce8e(%rip), %rdx     # 0xd60a2
leaq 0xbfab5(%rip), %rcx     # 0x108cd0
movq $0x0, 0x8(%rsp)
movq %rsi, 0x10(%rsp)
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
jne 0x49276
movq 0xc1d78(%rip), %rbx     # 0x10afc0
subl (%rbx), %ebp
jle 0x493f2
cmpl $0x1, %ebp
movq 0x8(%rsp), %rax
je 0x4940c
movq 0xc1d83(%rip), %rdi     # 0x10afe8
leaq 0x84f59(%rip), %rsi     # 0xce1c5
movl $0x13, %edx
jmp 0x49405
leaq 0x28(%rsp), %rbx
movq $0x0, 0x8(%rsp)
leaq 0x18(%rsp), %r15
leaq 0x38(%rsp), %r12
movq 0xc1ceb(%rip), %rax     # 0x10af80
movq (%rax), %r13
testq %r13, %r13
leaq 0x889dd(%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 0x492e9
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
sarl $0x18, %r14d
cmpl $0x3e, %r14d
jg 0x4931c
cmpl $0x4, %r14d
ja 0x4936f
movl %r14d, %eax
leaq 0x8beed(%rip), %rcx     # 0xd51f0
movslq (%rcx,%rax,4), %rax
addq %rcx, %rax
leaq 0xc2dc7(%rip), %rsi     # 0x10c0d8
jmpq *%rax
movb $0x1, 0xc2e02(%rip)     # 0x10c11c
jmp 0x4936f
cmpl $0x6c, %r14d
jle 0x4933b
cmpl $0x6d, %r14d
je 0x493c1
cmpl $0x73, %r14d
jne 0x4936f
leaq 0xc2dbf(%rip), %rsi     # 0x10c0f8
jmp 0x49367
cmpl $0x3f, %r14d
jne 0x493d2
movb $0x1, %al
movq %rax, 0x8(%rsp)
jmp 0x4936f
leaq 0xc2d63(%rip), %rsi     # 0x10c0b8
jmp 0x49367
leaq 0xc2d3a(%rip), %rsi     # 0x10c098
jmp 0x49367
leaq 0xc2d11(%rip), %rsi     # 0x10c078
movq %r12, %rdi
callq 0x8560
movq %r12, %rdi
movq 0xc1c1f(%rip), %rsi     # 0x10af98
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
movl %ebp, %edi
movq 0x10(%rsp), %rsi
leaq 0x8cd09(%rip), %rdx     # 0xd60a2
leaq 0xbf930(%rip), %rcx     # 0x108cd0
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
jne 0x4928e
jmp 0x49241
movq %r12, %rdi
leaq 0xc2d4d(%rip), %rsi     # 0x10c118
callq 0x82b0
jmp 0x4936f
cmpl $0x68, %r14d
jne 0x4936f
movq 0xc1bd9(%rip), %rdi     # 0x10afb8
leaq 0x8cd13(%rip), %rsi     # 0xd60f9
callq 0x8460
xorl %edi, %edi
callq 0x8530
movq 0xc1bef(%rip), %rdi     # 0x10afe8
leaq 0x84db2(%rip), %rsi     # 0xce1b2
movl $0x12, %edx
callq 0x84e0
movb $0x1, %al
testb $0x1, %al
jne 0x49475
cmpb $0x0, 0xc2d05(%rip)     # 0x10c11c
je 0x49422
leaq 0xc2c38(%rip), %r14     # 0x10c058
jmp 0x49433
cmpq $0x0, 0xc2cb6(%rip)     # 0x10c0e0
je 0x49494
leaq 0xc2c05(%rip), %r14     # 0x10c038
movslq (%rbx), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%rbx)
movq 0x10(%rsp), %rcx
movq (%rcx,%rax,8), %rbx
movq 0x8(%r14), %r15
movq %rbx, %rdi
callq 0x81f0
movq %r14, %rdi
xorl %esi, %esi
movq %r15, %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 0xc1b3c(%rip), %rdi     # 0x10afb8
leaq 0x831fa(%rip), %rsi     # 0xcc67d
callq 0x8460
leaq 0x8cc6a(%rip), %rsi     # 0xd60f9
movq %rax, %rdi
jmp 0x494bd
movq 0xc1b4d(%rip), %rdi     # 0x10afe8
leaq 0x8cacb(%rip), %rsi     # 0xd5f6d
callq 0x8460
movq %rax, %rdi
callq 0x8200
movq 0xc1b02(%rip), %rdi     # 0x10afb8
leaq 0x8cc3c(%rip), %rsi     # 0xd60f9
callq 0x8460
movl $0x1, %edi
callq 0x8530
jmp 0x494ce
movq %rax, %r14
movq 0xc1ac0(%rip), %rsi     # 0x10af98
leaq 0x38(%rsp), %rdi
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
jmp 0x49510
movq %rax, %r14
jmp 0x49510
movq %rax, %r14
movq 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0x49510
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
movq %r14, %rdi
callq 0x8840