// File: /workspace/github_cpp_makefile_star2_O1/millanek[P]evo/evo_findDiscordantPairsFromSAM.cpp
// Function: parseDiscordPairsFromSAMOptions(int, char**)
void parseDiscordPairsFromSAMOptions(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 'n': arg >> opt::runName; break;
            case 'b': arg >> opt::minBQ; break;
            case 'm': arg >> opt::minMQ; break;
            case 'd': arg >> opt::minDist; break;
            case OPT_HAPCUT: opt::hapcutFormat = true; break;
            case 'h':
                std::cout << DISCORDPAIRS_USAGE_MESSAGE;
                exit(EXIT_SUCCESS);
        }
    }
    
    if (argc - optind < 2) {
        std::cerr << "missing arguments\n";
        die = true;
    }
    else if (argc - optind > 2)
    {
        std::cerr << "too many arguments\n";
        die = true;
    }
    
    if (die) {
        std::cout << "\n" << DISCORDPAIRS_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
    
    // Parse the input filenames
    opt::hetsFile = argv[optind++];
    opt::samFile = argv[optind++];
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x1b8, %rsp            # imm = 0x1B8
movl %edi, %ebp
leaq 0x2148a(%rip), %rdx     # 0xea363
leaq 0x41d60(%rip), %rcx     # 0x10ac40
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 0xc8f30
movq 0x420b3(%rip), %rbx     # 0x10afc0
subl (%rbx), %ebp
cmpl $0x2, %ebp
jge 0xc908c
movq 0x420c9(%rip), %rdi     # 0x10afe8
leaq 0x528c(%rip), %rsi      # 0xce1b2
movl $0x12, %edx
jmp 0xc90a6
leaq 0x28(%rsp), %rbx
movq $0x0, 0x8(%rsp)
leaq 0x18(%rsp), %r15
leaq 0x38(%rsp), %r12
movq 0x42031(%rip), %rax     # 0x10af80
movq (%rax), %r13
testq %r13, %r13
leaq 0x8d23(%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 0xc8fa3
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
sarl $0x18, %r14d
cmpl $0x63, %r14d
jle 0xc8fd0
cmpl $0x6c, %r14d
jle 0xc8fea
cmpl $0x6d, %r14d
je 0xc8ff9
cmpl $0x6e, %r14d
jne 0xc901a
movq %r12, %rdi
leaq 0x44437(%rip), %rsi     # 0x10d400
callq 0x8560
jmp 0xc901a
testl %r14d, %r14d
je 0xc900a
cmpl $0x3f, %r14d
je 0xc9013
leaq 0x4261a(%rip), %rsi     # 0x10b5fc
cmpl $0x62, %r14d
je 0xc9000
jmp 0xc901a
cmpl $0x64, %r14d
jne 0xc906c
leaq 0x42609(%rip), %rsi     # 0x10b600
jmp 0xc9000
leaq 0x42604(%rip), %rsi     # 0x10b604
movq %r12, %rdi
callq 0x82b0
jmp 0xc901a
movb $0x1, 0x4440f(%rip)     # 0x10d420
jmp 0xc901a
movb $0x1, %al
movq %rax, 0x8(%rsp)
movq %r12, %rdi
movq 0x41f74(%rip), %rsi     # 0x10af98
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
movl %ebp, %edi
movq 0x10(%rsp), %rsi
leaq 0x2131f(%rip), %rdx     # 0xea363
leaq 0x41bf5(%rip), %rcx     # 0x10ac40
xorl %r8d, %r8d
callq 0x8770
movl %eax, %r14d
shll $0x18, %r14d
cmpl $0xff000000, %r14d      # imm = 0xFF000000
jne 0xc8f48
jmp 0xc8f06
cmpl $0x68, %r14d
jne 0xc901a
movq 0x41f3f(%rip), %rdi     # 0x10afb8
leaq 0x212f8(%rip), %rsi     # 0xea378
callq 0x8460
xorl %edi, %edi
callq 0x8530
movq 0x8(%rsp), %rax
je 0xc90ad
movq 0x41f4e(%rip), %rdi     # 0x10afe8
leaq 0x5124(%rip), %rsi      # 0xce1c5
movl $0x13, %edx
callq 0x84e0
movb $0x1, %al
testb $0x1, %al
jne 0xc9138
movslq (%rbx), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%rbx)
movq 0x10(%rsp), %r13
movq (%r13,%rax,8), %r14
movq 0x442fa(%rip), %r15     # 0x10d3c8
leaq 0x442eb(%rip), %r12     # 0x10d3c0
movq %r14, %rdi
callq 0x81f0
movq %r12, %rdi
xorl %esi, %esi
movq %r15, %rdx
movq %r14, %rcx
movq %rax, %r8
callq 0x86c0
movslq (%rbx), %rax
leal 0x1(%rax), %ecx
movl %ecx, (%rbx)
movq (%r13,%rax,8), %rbx
movq 0x442e4(%rip), %r14     # 0x10d3e8
leaq 0x442d5(%rip), %r15     # 0x10d3e0
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 0x41e79(%rip), %rdi     # 0x10afb8
leaq 0x3537(%rip), %rsi      # 0xcc67d
callq 0x8460
leaq 0x21226(%rip), %rsi     # 0xea378
movq %rax, %rdi
callq 0x8460
movl $0x1, %edi
callq 0x8530
jmp 0xc9166
movq %rax, %r14
movq 0x41e28(%rip), %rsi     # 0x10af98
leaq 0x38(%rsp), %rdi
callq 0x8620
leaq 0xb0(%rsp), %rdi
callq 0x8190
jmp 0xc91a8
movq %rax, %r14
jmp 0xc91a8
movq %rax, %r14
movq 0x18(%rsp), %rdi
cmpq %rbx, %rdi
je 0xc91a8
movq 0x28(%rsp), %rsi
incq %rsi
callq 0x8480
movq %r14, %rdi
callq 0x8840