// File: millanek[P]evo/evo_distanceToOutgroups.cpp
// Function: parseDistOutOptions(int, char**)
void parseDistOutOptions(int argc, char** argv) {
    bool die = false; string regionArgString; std::vector<string> regionArgs;
    std::vector<string> windowSizeStep;
    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 'f': arg >> opt::fixedWindowSize; break;
            case 'n': arg >> opt::runName; break;
            case 'i': opt::allowIndels = true; break;
            case OPT_ACC_GEN_BED: arg >> opt::accesibleGenBedFile; break;
            case 'h':
                std::cout << DISTOUT_USAGE_MESSAGE;
                exit(EXIT_SUCCESS);
        }
    }
    
    if (argc - optind < 4) {
        std::cerr << "missing arguments\n";
        die = true;
    }
    else if (argc - optind > 4)
    {
        std::cerr << "too many arguments\n";
        die = true;
    }
    
    if (die) {
        std::cout << "\n" << DISTOUT_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
    
    // Parse the input filenames
    opt::vcfFile = argv[optind++];
    opt::setsFile = argv[optind++];
    opt::outgroupFile = argv[optind++];
    opt::ingroupFile = argv[optind++];
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
subq $0x250, %rsp            # imm = 0x250
movl %edi, -0x4(%rbp)
movq %rsi, -0x10(%rbp)
movb $0x0, -0x11(%rbp)
leaq -0x38(%rbp), %rdi
callq 0xa820
leaq -0x50(%rbp), %rdi
callq 0x48da0
leaq -0x68(%rbp), %rdi
callq 0x48da0
movl -0x4(%rbp), %edi
movq -0x10(%rbp), %rsi
movq 0x840d9(%rip), %rdx     # 0x199a68
leaq 0x82faa(%rip), %rcx     # 0x198940
xorl %eax, %eax
movl %eax, %r8d
callq 0xaa40
movb %al, -0x69(%rbp)
movsbl %al, %eax
cmpl $-0x1, %eax
je 0x115ba4
movq 0x835da(%rip), %rax     # 0x198f90
cmpq $0x0, (%rax)
je 0x1159cf
movq 0x835cd(%rip), %rax     # 0x198f90
movq (%rax), %rax
movq %rax, -0x230(%rbp)
jmp 0x1159df
leaq 0x20509(%rip), %rax     # 0x135edf
movq %rax, -0x230(%rbp)
jmp 0x1159df
movq -0x230(%rbp), %rax
movq %rax, -0x240(%rbp)
leaq -0x211(%rbp), %rdi
movq %rdi, -0x238(%rbp)
callq 0xab60
movq -0x240(%rbp), %rsi
movq -0x238(%rbp), %rdx
leaq -0x210(%rbp), %rdi
callq 0x2d6c0
jmp 0x115a1c
leaq -0x1f0(%rbp), %rdi
leaq -0x210(%rbp), %rsi
movl $0x8, %edx
callq 0xaaa0
jmp 0x115a36
leaq -0x210(%rbp), %rdi
callq 0xac88
leaq -0x211(%rbp), %rdi
callq 0xa640
movsbl -0x69(%rbp), %eax
movl %eax, -0x244(%rbp)
testl %eax, %eax
je 0x115b60
jmp 0x115a62
movl -0x244(%rbp), %eax
subl $0x3f, %eax
je 0x115afd
jmp 0x115a73
movl -0x244(%rbp), %eax
subl $0x66, %eax
je 0x115b06
jmp 0x115a84
movl -0x244(%rbp), %eax
subl $0x68, %eax
je 0x115b77
jmp 0x115a95
movl -0x244(%rbp), %eax
subl $0x69, %eax
je 0x115b57
jmp 0x115aa6
movl -0x244(%rbp), %eax
subl $0x6e, %eax
je 0x115b40
jmp 0x115b93
movq %rax, %rcx
movl %edx, %eax
movq %rcx, -0x220(%rbp)
movl %eax, -0x224(%rbp)
jmp 0x115aec
movq %rax, %rcx
movl %edx, %eax
movq %rcx, -0x220(%rbp)
movl %eax, -0x224(%rbp)
leaq -0x210(%rbp), %rdi
callq 0xac88
leaq -0x211(%rbp), %rdi
callq 0xa640
jmp 0x115d10
movb $0x1, -0x11(%rbp)
jmp 0x115b93
leaq 0x83f53(%rip), %rsi     # 0x199a60
leaq -0x1f0(%rbp), %rdi
callq 0xa370
jmp 0x115b1b
jmp 0x115b93
movq %rax, %rcx
movl %edx, %eax
movq %rcx, -0x220(%rbp)
movl %eax, -0x224(%rbp)
leaq -0x1f0(%rbp), %rdi
callq 0xa290
jmp 0x115d10
leaq 0x85b69(%rip), %rsi     # 0x19b6b0
leaq -0x1f0(%rbp), %rdi
callq 0xa750
jmp 0x115b55
jmp 0x115b93
movb $0x1, 0x85b92(%rip)     # 0x19b6f0
jmp 0x115b93
leaq 0x85b69(%rip), %rsi     # 0x19b6d0
leaq -0x1f0(%rbp), %rdi
callq 0xa750
jmp 0x115b75
jmp 0x115b93
movq 0x83ef2(%rip), %rsi     # 0x199a70
movq 0x83433(%rip), %rdi     # 0x198fb8
callq 0xa5c0
jmp 0x115b8c
xorl %edi, %edi
callq 0xa700
leaq -0x1f0(%rbp), %rdi
callq 0xa290
jmp 0x115981
movl -0x4(%rbp), %eax
movq 0x83412(%rip), %rcx     # 0x198fc0
subl (%rcx), %eax
cmpl $0x4, %eax
jge 0x115be7
movq 0x83434(%rip), %rdi     # 0x198ff0
leaq 0x1c867(%rip), %rsi     # 0x13242a
callq 0xa5c0
jmp 0x115bca
movb $0x1, -0x11(%rbp)
jmp 0x115c13
movq %rax, %rcx
movl %edx, %eax
movq %rcx, -0x220(%rbp)
movl %eax, -0x224(%rbp)
jmp 0x115d10
movl -0x4(%rbp), %eax
movq 0x833cf(%rip), %rcx     # 0x198fc0
subl (%rcx), %eax
cmpl $0x4, %eax
jle 0x115c11
movq 0x833f1(%rip), %rdi     # 0x198ff0
leaq 0x1c837(%rip), %rsi     # 0x13243d
callq 0xa5c0
jmp 0x115c0d
movb $0x1, -0x11(%rbp)
jmp 0x115c13
testb $0x1, -0x11(%rbp)
je 0x115c54
movq 0x83398(%rip), %rdi     # 0x198fb8
leaq 0x19c66(%rip), %rsi     # 0x12f88d
callq 0xa5c0
movq %rax, -0x250(%rbp)
jmp 0x115c35
movq -0x250(%rbp), %rdi
movq 0x83e2d(%rip), %rsi     # 0x199a70
callq 0xa5c0
jmp 0x115c4a
movl $0x1, %edi
callq 0xa700
movq -0x10(%rbp), %rax
movq 0x83361(%rip), %rdx     # 0x198fc0
movslq (%rdx), %rcx
movl %ecx, %esi
incl %esi
movl %esi, (%rdx)
movq (%rax,%rcx,8), %rsi
leaq 0x859bd(%rip), %rdi     # 0x19b630
callq 0xa810
jmp 0x115c7a
movq -0x10(%rbp), %rax
movq 0x8333b(%rip), %rdx     # 0x198fc0
movslq (%rdx), %rcx
movl %ecx, %esi
incl %esi
movl %esi, (%rdx)
movq (%rax,%rcx,8), %rsi
leaq 0x859b7(%rip), %rdi     # 0x19b650
callq 0xa810
jmp 0x115ca0
movq -0x10(%rbp), %rax
movq 0x83315(%rip), %rdx     # 0x198fc0
movslq (%rdx), %rcx
movl %ecx, %esi
incl %esi
movl %esi, (%rdx)
movq (%rax,%rcx,8), %rsi
leaq 0x859b1(%rip), %rdi     # 0x19b670
callq 0xa810
jmp 0x115cc6
movq -0x10(%rbp), %rax
movq 0x832ef(%rip), %rdx     # 0x198fc0
movslq (%rdx), %rcx
movl %ecx, %esi
incl %esi
movl %esi, (%rdx)
movq (%rax,%rcx,8), %rsi
leaq 0x859ab(%rip), %rdi     # 0x19b690
callq 0xa810
jmp 0x115cec
leaq -0x68(%rbp), %rdi
callq 0x3dfa0
leaq -0x50(%rbp), %rdi
callq 0x3dfa0
leaq -0x38(%rbp), %rdi
callq 0xac88
addq $0x250, %rsp            # imm = 0x250
popq %rbp
retq
leaq -0x68(%rbp), %rdi
callq 0x3dfa0
leaq -0x50(%rbp), %rdi
callq 0x3dfa0
leaq -0x38(%rbp), %rdi
callq 0xac88
movq -0x220(%rbp), %rdi
callq 0xab50
nopw (%rax,%rax)