// File: /workspace/github_cpp_makefile_star2_O1/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 $0xe8, %rsp
movq %rsi, -0x68(%rbp)
cmpl $0x1, %edi
je 0x3e32
movl %edi, %r14d
leaq -0x5c(%rbp), %r12
movl $0x0, (%r12)
leaq -0x48(%rbp), %r15
movl %r14d, %edi
movq -0x68(%rbp), %rsi
leaq 0x8948(%rip), %rdx      # 0xc409
leaq 0xd738(%rip), %rcx      # 0x11200
movq %r12, %r8
callq 0x3310
movl %eax, %r13d
cmpl $0x52, %eax
jg 0x3b2a
leal -0x43(%r13), %eax
cmpl $0xa, %eax
ja 0x3dcf
leaq 0x8518(%rip), %rcx      # 0xc004
movslq (%rcx,%rax,4), %rax
addq %rcx, %rax
jmpq *%rax
movq 0xd4b4(%rip), %rax      # 0x10fb0
movq (%rax), %rsi
leaq -0x58(%rbp), %rbx
movq %rbx, %rdi
leaq -0x29(%rbp), %rdx
callq 0x4150
movl $0x0, -0x38(%rbp)
leaq 0xd893(%rip), %rdi      # 0x113b0
movq %rbx, %rsi
callq 0x432c
jmp 0x3d42
cmpl $0x6e, %r13d
jg 0x3b88
cmpl $0x53, %r13d
je 0x3d12
cmpl $0x67, %r13d
jne 0x3dd5
movq 0xd465(%rip), %rax      # 0x10fb0
movq (%rax), %r15
movq 0xd8c3(%rip), %r12      # 0x11418
movq %r15, %rdi
callq 0x3100
leaq 0xd8ac(%rip), %rdi      # 0x11410
xorl %esi, %esi
movq %r12, %rdx
leaq -0x5c(%rbp), %r12
movq %r15, %rcx
leaq -0x48(%rbp), %r15
movq %rax, %r8
callq 0x32c0
movb $0x1, 0xd885(%rip)      # 0x11408
jmp 0x3d91
cmpl $0x6f, %r13d
je 0x3d59
cmpl $0x73, %r13d
jne 0x3dd5
movq 0xd40d(%rip), %rax      # 0x10fb0
movq (%rax), %r15
movq 0xd843(%rip), %r12      # 0x113f0
movq %r15, %rdi
callq 0x3100
leaq 0xd82c(%rip), %rbx      # 0x113e8
movq %rbx, %rdi
xorl %esi, %esi
movq %r12, %rdx
leaq -0x5c(%rbp), %r12
movq %r15, %rcx
leaq -0x48(%rbp), %r15
movq %rax, %r8
callq 0x32c0
movq %rbx, %rdi
leaq 0x883b(%rip), %rsi      # 0xc41c
callq 0x30b0
testl %eax, %eax
je 0x3d91
leaq 0xd7f3(%rip), %rdi      # 0x113e8
leaq 0x8446(%rip), %rsi      # 0xc042
callq 0x30b0
testl %eax, %eax
je 0x3d91
leaq 0xd7d8(%rip), %rdi      # 0x113e8
leaq 0x880c(%rip), %rsi      # 0xc423
callq 0x30b0
testl %eax, %eax
je 0x3d91
leaq 0xd7bd(%rip), %rdi      # 0x113e8
leaq 0x87f6(%rip), %rsi      # 0xc428
callq 0x30b0
testl %eax, %eax
je 0x3d91
jmp 0x3ec0
movq 0xd365(%rip), %rax      # 0x10fb0
movq (%rax), %rsi
leaq -0x58(%rbp), %rbx
movq %rbx, %rdi
leaq -0x29(%rbp), %rdx
callq 0x4150
movl $0x3, -0x38(%rbp)
leaq 0xd744(%rip), %rdi      # 0x113b0
movq %rbx, %rsi
callq 0x432c
jmp 0x3d42
movq 0xd330(%rip), %rax      # 0x10fb0
movq (%rax), %rsi
leaq -0x58(%rbp), %rbx
movq %rbx, %rdi
leaq -0x29(%rbp), %rdx
callq 0x4150
movl $0x2, -0x38(%rbp)
leaq 0xd70f(%rip), %rdi      # 0x113b0
movq %rbx, %rsi
callq 0x432c
jmp 0x3d42
movq 0xd2fb(%rip), %rax      # 0x10fb0
movq (%rax), %rsi
leaq -0x58(%rbp), %rbx
movq %rbx, %rdi
leaq -0x29(%rbp), %rdx
callq 0x4150
movl $0x1, -0x38(%rbp)
leaq 0xd6da(%rip), %rdi      # 0x113b0
movq %rbx, %rsi
callq 0x432c
jmp 0x3d42
movq 0xd2c9(%rip), %rax      # 0x10fb0
movq (%rax), %rsi
leaq -0x58(%rbp), %rbx
movq %rbx, %rdi
leaq -0x29(%rbp), %rdx
callq 0x4150
movl $0x4, -0x38(%rbp)
leaq 0xd6a8(%rip), %rdi      # 0x113b0
movq %rbx, %rsi
callq 0x432c
jmp 0x3d42
movq 0xd297(%rip), %rax      # 0x10fb0
movq (%rax), %rsi
leaq -0x58(%rbp), %rbx
movq %rbx, %rdi
leaq -0x29(%rbp), %rdx
callq 0x4150
movl $0x5, -0x38(%rbp)
leaq 0xd676(%rip), %rdi      # 0x113b0
movq %rbx, %rsi
callq 0x432c
movq -0x58(%rbp), %rdi
cmpq %r15, %rdi
je 0x3d91
movq -0x48(%rbp), %rsi
incq %rsi
callq 0x3200
jmp 0x3d91
movq 0xd250(%rip), %rax      # 0x10fb0
movq (%rax), %r15
movq 0xd666(%rip), %r12      # 0x113d0
movq %r15, %rdi
callq 0x3100
leaq 0xd64f(%rip), %rdi      # 0x113c8
xorl %esi, %esi
movq %r12, %rdx
leaq -0x5c(%rbp), %r12
movq %r15, %rcx
leaq -0x48(%rbp), %r15
movq %rax, %r8
callq 0x32c0
cmpl $-0x1, %r13d
jne 0x3ab3
movq 0xd616(%rip), %rax      # 0x113b8
cmpq 0xd607(%rip), %rax      # 0x113b0
je 0x3e5e
cmpq $0x0, 0xd619(%rip)      # 0x113d0
je 0x3e8f
addq $0xe8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
cmpl $-0x1, %r13d
je 0x3d9b
leaq -0x58(%rbp), %rdi
movq %r15, (%rdi)
leaq 0x867b(%rip), %rsi      # 0xc45e
leaq 0x868d(%rip), %rdx      # 0xc477
callq 0x4292
movq 0xd1da(%rip), %rax      # 0x10fd0
movslq (%rax), %rax
movq -0x68(%rbp), %rcx
movq -0x8(%rcx,%rax,8), %rsi
leaq -0x58(%rbp), %rdi
callq 0x33a0
leaq -0x78(%rbp), %r14
movq %r14, -0x10(%r14)
movq (%rax), %rdx
movq %rax, %rcx
addq $0x10, %rcx
cmpq %rcx, %rdx
jne 0x3ef1
movups (%rcx), %xmm0
movups %xmm0, (%r14)
jmp 0x3eff
leaq -0xf8(%rbp), %r14
movq %r14, -0x10(%r14)
leaq 0x8812(%rip), %rdx      # 0xc656
leaq -0x108(%rbp), %rbx
movq %rbx, %rdi
movq %rdx, %rsi
callq 0x4292
movq %rbx, %rdi
callq 0x371c
leaq -0xb8(%rbp), %r14
movq %r14, -0x10(%r14)
leaq 0x8608(%rip), %rsi      # 0xc478
leaq 0x8630(%rip), %rdx      # 0xc4a7
leaq -0xc8(%rbp), %rdi
callq 0x4292
leaq -0xc8(%rbp), %rdi
callq 0x371c
leaq -0x98(%rbp), %r14
movq %r14, -0x10(%r14)
leaq 0x8607(%rip), %rsi      # 0xc4a8
leaq 0x8623(%rip), %rdx      # 0xc4cb
leaq -0xa8(%rbp), %rdi
callq 0x4292
leaq -0xa8(%rbp), %rdi
callq 0x371c
leaq -0xd8(%rbp), %r14
movq %r14, -0x10(%r14)
leaq 0x856a(%rip), %rsi      # 0xc43c
leaq 0x8584(%rip), %rdx      # 0xc45d
leaq -0xe8(%rbp), %rdi
callq 0x4292
leaq -0xe8(%rbp), %rdi
callq 0x371c
movq %rdx, -0x88(%rbp)
movq (%rcx), %rdx
movq %rdx, -0x78(%rbp)
movq 0x8(%rax), %rdx
leaq -0x88(%rbp), %rdi
movq %rdx, 0x8(%rdi)
movq %rcx, (%rax)
movq $0x0, 0x8(%rax)
movb $0x0, 0x10(%rax)
callq 0x371c
movq %rax, %rbx
movq -0xe8(%rbp), %rdi
cmpq %r14, %rdi
je 0x3fef
movq -0xd8(%rbp), %rsi
jmp 0x3fe7
jmp 0x3fc8
movq %rax, %rbx
movq -0xa8(%rbp), %rdi
cmpq %r14, %rdi
je 0x3fef
movq -0x98(%rbp), %rsi
jmp 0x3fe7
jmp 0x3fc8
movq %rax, %rbx
movq -0xc8(%rbp), %rdi
cmpq %r14, %rdi
je 0x3fef
movq -0xb8(%rbp), %rsi
jmp 0x3fe7
jmp 0x3fc8
movq %rax, %rbx
movq -0x88(%rbp), %rdi
cmpq %r14, %rdi
je 0x3fa1
movq -0x78(%rbp), %rsi
incq %rsi
callq 0x3200
jmp 0x3fa1
movq %rax, %rbx
movq -0x58(%rbp), %rdi
leaq -0x48(%rbp), %rax
cmpq %rax, %rdi
jne 0x3fe3
jmp 0x3fef
movq %rax, %rbx
movq -0x108(%rbp), %rdi
cmpq %r14, %rdi
je 0x3fef
movq -0xf8(%rbp), %rsi
jmp 0x3fe7
movq %rax, %rbx
jmp 0x3fef
jmp 0x3fd7
jmp 0x3fd7
jmp 0x3fd7
jmp 0x3fd7
jmp 0x3fd7
movq %rax, %rbx
movq -0x58(%rbp), %rdi
cmpq %r15, %rdi
je 0x3fef
movq -0x48(%rbp), %rsi
incq %rsi
callq 0x3200
movq %rbx, %rdi
callq 0x3340