// File: /workspace/github_cpp_makefile_star2_O3/soccin[P]BIC-RNAseq/tools/MergeFusion/main.cpp
// Function: parseOption(int, char**)
void parseOption(int argc, char* argv[])
{
    if(argc == 1)
        printUsage();
    int next_option;
    int option_index = 0;
    do
    {
        next_option = getopt_long(argc, const_cast<char**>(argv), "C:D:F:H:S:M:o:s:g:", long_options, &option_index);
        switch(next_option)
        {
            case 'C':
                input_files.push_back(make_pair(optarg, CHIMERASCAN));
                break;
            case 'D':
                input_files.push_back(make_pair(optarg, DEFUSE));
                break;
            case 'F':
                input_files.push_back(make_pair(optarg, FUSIONCATCHER));
                break;
            case 'H':
                input_files.push_back(make_pair(optarg, FUSIONHUNTER));
                break;
            case 'S':
                input_files.push_back(make_pair(optarg, STAR));
                break;
            case 'M':
                input_files.push_back(make_pair(optarg, MAPSPLICE));
                break;
            case 'o':
                output_file = optarg;
                break;
            case 's':
                sorting_criteria = optarg;
                if(sorting_criteria != "CALLER" && sorting_criteria != "GENOMIC" && sorting_criteria != "GENE" && sorting_criteria != "BREAKPOINT_COVERAGE")
                    printUsage("[ERROR]: invalid value for --sort");
                break;
            /*case 'c':
                if(strcmp(optarg, "0")  == 0)
                    normalize_chrom = false;
                else if(strcmp(optarg, "1")  == 0)
                    normalize_chrom = true;
                else
                    printUsage("[ERROR]: invalid value for --normalize_chrom");
                break;*/
            case 'g':
                hugo_data_file = optarg;
                normalize_gene = true;
                break;
            case -1:
                break; //parsed all options
            default:
                printUsage(string("[ERROR]: Argument error: ") + argv[optind - 1]);
        }
    } while(next_option != -1);
    if(input_files.size() == 0)
        printUsage("[ERROR]: Please specify at least one input file");
    if(output_file.empty())
        printUsage("[ERROR]: Please specify output file");
    #ifdef _DEBUG
    cout << "[DEBUG]: Parsing options complete." << endl;
    #endif
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0xd8, %rsp
cmpl $0x1, %edi
je 0x3e78
movq %rsi, %rbx
movl %edi, %r14d
leaq -0x5c(%rbp), %r13
movl $0x0, (%r13)
leaq -0x48(%rbp), %r12
leaq -0x58(%rbp), %r15
movl %edi, -0x60(%rbp)
movl %r14d, %edi
movq %rbx, %rsi
leaq 0x8943(%rip), %rdx      # 0xc409
leaq 0xd733(%rip), %rcx      # 0x11200
movq %r13, %r8
callq 0x3310
cmpl $0x52, %eax
jg 0x3b27
leal -0x43(%rax), %ecx
cmpl $0xa, %ecx
ja 0x3d91
leaq 0x8517(%rip), %rdx      # 0xc004
movslq (%rdx,%rcx,4), %rax
addq %rdx, %rax
jmpq *%rax
movq 0xd4b3(%rip), %rax      # 0x10fb0
movq (%rax), %rsi
movq %r15, %rdi
leaq -0x29(%rbp), %rdx
callq 0x412a
movl $0x0, -0x38(%rbp)
leaq 0xd896(%rip), %rdi      # 0x113b0
movq %r15, %rsi
callq 0x4312
jmp 0x3d36
cmpl $0x6e, %eax
jg 0x3b82
cmpl $0x53, %eax
je 0x3d0a
cmpl $0x67, %eax
jne 0x3dca
movq 0xd46b(%rip), %rax      # 0x10fb0
movq (%rax), %r12
movq 0xd8c9(%rip), %r13      # 0x11418
movq %r12, %rdi
callq 0x3100
leaq 0xd8b2(%rip), %rdi      # 0x11410
xorl %esi, %esi
movq %r13, %rdx
leaq -0x5c(%rbp), %r13
movq %r12, %rcx
leaq -0x48(%rbp), %r12
movq %rax, %r8
callq 0x32c0
movb $0x1, 0xd88b(%rip)      # 0x11408
jmp 0x3ab9
cmpl $0x6f, %eax
je 0x3d54
cmpl $0x73, %eax
jne 0x3dca
movq 0xd415(%rip), %rax      # 0x10fb0
movq (%rax), %r12
movq 0xd84b(%rip), %r13      # 0x113f0
movq %r12, %rdi
callq 0x3100
movq %rbx, %r14
movq %r15, %rbx
leaq 0xd82e(%rip), %r15      # 0x113e8
movq %r15, %rdi
xorl %esi, %esi
movq %r13, %rdx
leaq -0x5c(%rbp), %r13
movq %r12, %rcx
leaq -0x48(%rbp), %r12
movq %rax, %r8
callq 0x32c0
movq %r15, %rdi
movq %rbx, %r15
movq %r14, %rbx
movl -0x60(%rbp), %r14d
leaq 0x8833(%rip), %rsi      # 0xc41c
callq 0x30b0
testl %eax, %eax
je 0x3ab9
leaq 0xd7eb(%rip), %rdi      # 0x113e8
leaq 0x843e(%rip), %rsi      # 0xc042
callq 0x30b0
testl %eax, %eax
je 0x3ab9
leaq 0xd7d0(%rip), %rdi      # 0x113e8
leaq 0x8804(%rip), %rsi      # 0xc423
callq 0x30b0
testl %eax, %eax
je 0x3ab9
leaq 0xd7b5(%rip), %rdi      # 0x113e8
leaq 0x87ee(%rip), %rsi      # 0xc428
callq 0x30b0
testl %eax, %eax
je 0x3ab9
jmp 0x3e1c
movq 0xd35d(%rip), %rax      # 0x10fb0
movq (%rax), %rsi
movq %r15, %rdi
leaq -0x29(%rbp), %rdx
callq 0x412a
movl $0x3, -0x38(%rbp)
leaq 0xd740(%rip), %rdi      # 0x113b0
movq %r15, %rsi
callq 0x4312
jmp 0x3d36
movq 0xd32c(%rip), %rax      # 0x10fb0
movq (%rax), %rsi
movq %r15, %rdi
leaq -0x29(%rbp), %rdx
callq 0x412a
movl $0x2, -0x38(%rbp)
leaq 0xd70f(%rip), %rdi      # 0x113b0
movq %r15, %rsi
callq 0x4312
jmp 0x3d36
movq 0xd2fb(%rip), %rax      # 0x10fb0
movq (%rax), %rsi
movq %r15, %rdi
leaq -0x29(%rbp), %rdx
callq 0x412a
movl $0x1, -0x38(%rbp)
leaq 0xd6de(%rip), %rdi      # 0x113b0
movq %r15, %rsi
callq 0x4312
jmp 0x3d36
movq 0xd2cd(%rip), %rax      # 0x10fb0
movq (%rax), %rsi
movq %r15, %rdi
leaq -0x29(%rbp), %rdx
callq 0x412a
movl $0x4, -0x38(%rbp)
leaq 0xd6b0(%rip), %rdi      # 0x113b0
movq %r15, %rsi
callq 0x4312
jmp 0x3d36
movq 0xd29f(%rip), %rax      # 0x10fb0
movq (%rax), %rsi
movq %r15, %rdi
leaq -0x29(%rbp), %rdx
callq 0x412a
movl $0x5, -0x38(%rbp)
leaq 0xd682(%rip), %rdi      # 0x113b0
movq %r15, %rsi
callq 0x4312
movq -0x58(%rbp), %rdi
cmpq %r12, %rdi
je 0x3ab9
movq -0x48(%rbp), %rsi
incq %rsi
callq 0x3200
jmp 0x3ab9
movq 0xd255(%rip), %rax      # 0x10fb0
movq (%rax), %r12
movq 0xd66b(%rip), %r13      # 0x113d0
movq %r12, %rdi
callq 0x3100
leaq 0xd654(%rip), %rdi      # 0x113c8
xorl %esi, %esi
movq %r13, %rdx
leaq -0x5c(%rbp), %r13
movq %r12, %rcx
leaq -0x48(%rbp), %r12
movq %rax, %r8
callq 0x32c0
jmp 0x3ab9
cmpl $-0x1, %eax
jne 0x3dca
movq 0xd61b(%rip), %rax      # 0x113b8
cmpq 0xd60c(%rip), %rax      # 0x113b0
je 0x3ea4
cmpq $0x0, 0xd61e(%rip)      # 0x113d0
je 0x3ed5
addq $0xd8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
leaq -0x58(%rbp), %rdi
movq %r12, (%rdi)
leaq 0x8686(%rip), %rsi      # 0xc45e
leaq 0x8698(%rip), %rdx      # 0xc477
callq 0x4274
movq 0xd1e5(%rip), %rax      # 0x10fd0
movslq (%rax), %rax
movq -0x8(%rbx,%rax,8), %rsi
leaq -0x58(%rbp), %rdi
callq 0x33a0
leaq -0x70(%rbp), %r14
movq %r14, -0x10(%r14)
movq (%rax), %rdx
movq %rax, %rcx
addq $0x10, %rcx
cmpq %rcx, %rdx
jne 0x3e4d
movups (%rcx), %xmm0
movups %xmm0, (%r14)
jmp 0x3e58
leaq -0xd0(%rbp), %r14
movq %r14, -0x10(%r14)
leaq 0x860e(%rip), %rsi      # 0xc43c
leaq 0x8628(%rip), %rdx      # 0xc45d
leaq -0xe0(%rbp), %rdi
callq 0x4274
leaq -0xe0(%rbp), %rdi
callq 0x371c
movq %rdx, -0x80(%rbp)
movq (%rcx), %rdx
movq %rdx, -0x70(%rbp)
movq 0x8(%rax), %rdx
leaq -0x80(%rbp), %rdi
movq %rdx, 0x8(%rdi)
movq %rcx, (%rax)
movq $0x0, 0x8(%rax)
movb $0x0, 0x10(%rax)
callq 0x371c
leaq -0xf0(%rbp), %r14
movq %r14, -0x10(%r14)
leaq 0x87cc(%rip), %rdx      # 0xc656
leaq -0x100(%rbp), %rbx
movq %rbx, %rdi
movq %rdx, %rsi
callq 0x4274
movq %rbx, %rdi
callq 0x371c
leaq -0xb0(%rbp), %r14
movq %r14, -0x10(%r14)
leaq 0x85c2(%rip), %rsi      # 0xc478
leaq 0x85ea(%rip), %rdx      # 0xc4a7
leaq -0xc0(%rbp), %rdi
callq 0x4274
leaq -0xc0(%rbp), %rdi
callq 0x371c
leaq -0x90(%rbp), %r14
movq %r14, -0x10(%r14)
leaq 0x85c1(%rip), %rsi      # 0xc4a8
leaq 0x85dd(%rip), %rdx      # 0xc4cb
leaq -0xa0(%rbp), %rdi
callq 0x4274
leaq -0xa0(%rbp), %rdi
callq 0x371c
movq %rax, %rbx
movq -0xa0(%rbp), %rdi
cmpq %r14, %rdi
je 0x3fca
movq -0x90(%rbp), %rsi
jmp 0x3fc2
jmp 0x3fa3
movq %rax, %rbx
movq -0xc0(%rbp), %rdi
cmpq %r14, %rdi
je 0x3fca
movq -0xb0(%rbp), %rsi
jmp 0x3fc2
jmp 0x3fa3
movq %rax, %rbx
movq -0x100(%rbp), %rdi
cmpq %r14, %rdi
je 0x3fca
movq -0xf0(%rbp), %rsi
jmp 0x3fc2
movq %rax, %rbx
movq -0xe0(%rbp), %rdi
cmpq %r14, %rdi
je 0x3fca
movq -0xd0(%rbp), %rsi
jmp 0x3fc2
jmp 0x3fa3
movq %rax, %rbx
movq -0x80(%rbp), %rdi
cmpq %r14, %rdi
je 0x3f94
movq -0x70(%rbp), %rsi
incq %rsi
callq 0x3200
jmp 0x3f94
movq %rax, %rbx
movq -0x58(%rbp), %rdi
leaq -0x48(%rbp), %rax
cmpq %rax, %rdi
jne 0x3fbe
jmp 0x3fca
movq %rax, %rbx
jmp 0x3fca
jmp 0x3fb2
jmp 0x3fb2
jmp 0x3fb2
jmp 0x3fb2
jmp 0x3fb2
movq %rax, %rbx
movq -0x58(%rbp), %rdi
cmpq %r12, %rdi
je 0x3fca
movq -0x48(%rbp), %rsi
incq %rsi
callq 0x3200
movq %rbx, %rdi
callq 0x3340