// File: /workspace/github_cpp_makefile_star2_O2/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
cmpl $0x1, %edi
je 0x2acc
movq %rsi, %rbx
movl %edi, %r14d
leaq -0x3c(%rbp), %rax
andl $0x0, (%rax)
leaq 0xba27(%rip), %r13      # 0xe1e0
leaq -0x68(%rbp), %r15
leaq 0x6840(%rip), %r12      # 0x9004
movl %r14d, %edi
movq %rbx, %rsi
leaq 0x6c38(%rip), %rdx      # 0x9409
movq %r13, %rcx
leaq -0x3c(%rbp), %r8
callq 0x22d0
leal -0x43(%rax), %ecx
cmpl $0xa, %ecx
ja 0x2820
movslq (%r12,%rcx,4), %rax
addq %r12, %rax
jmpq *%rax
movq 0xb7c3(%rip), %rax      # 0xdfb8
movq (%rax), %rax
movq %rax, -0x38(%rbp)
andl $0x0, -0x30(%rbp)
movq %r15, %rdi
leaq -0x38(%rbp), %rsi
callq 0x2d26
leaq 0xbb7d(%rip), %rdi      # 0xe390
movq %r15, %rsi
callq 0x2ea0
jmp 0x2a24
cmpl $0x53, %eax
je 0x29f4
cmpl $0x67, %eax
je 0x29d2
cmpl $0x6f, %eax
je 0x29b7
cmpl $0x73, %eax
jne 0x2a31
movq 0xb76d(%rip), %rax      # 0xdfb8
movq (%rax), %rsi
movl %r14d, %r15d
movq %rbx, %r14
movq %r12, %rbx
movq %r13, %r12
leaq 0xbb67(%rip), %r13      # 0xe3c8
movq %r13, %rdi
callq 0x2360
movq %r13, %rdi
movq %r12, %r13
movq %rbx, %r12
movq %r14, %rbx
movl %r15d, %r14d
leaq -0x68(%rbp), %r15
leaq 0x6b99(%rip), %rsi      # 0x941c
callq 0x2d53
testb %al, %al
je 0x27c4
leaq 0xbb31(%rip), %rdi      # 0xe3c8
leaq 0x67a4(%rip), %rsi      # 0x9042
callq 0x2d53
testb %al, %al
je 0x27c4
leaq 0xbb16(%rip), %rdi      # 0xe3c8
leaq 0x6b6a(%rip), %rsi      # 0x9423
callq 0x2d53
testb %al, %al
je 0x27c4
leaq 0xbafb(%rip), %rdi      # 0xe3c8
leaq 0x6b54(%rip), %rsi      # 0x9428
callq 0x2d53
testb %al, %al
je 0x27c4
jmp 0x2aa9
movq 0xb6cb(%rip), %rax      # 0xdfb8
movq (%rax), %rax
movq %rax, -0x38(%rbp)
movl $0x3, -0x30(%rbp)
movq %r15, %rdi
leaq -0x38(%rbp), %rsi
callq 0x2d26
leaq 0xba82(%rip), %rdi      # 0xe390
movq %r15, %rsi
callq 0x2ea0
jmp 0x2a24
movq 0xb696(%rip), %rax      # 0xdfb8
movq (%rax), %rax
movq %rax, -0x38(%rbp)
movl $0x4, -0x30(%rbp)
movq %r15, %rdi
leaq -0x38(%rbp), %rsi
callq 0x2d26
leaq 0xba4d(%rip), %rdi      # 0xe390
movq %r15, %rsi
callq 0x2ea0
jmp 0x2a24
movq 0xb661(%rip), %rax      # 0xdfb8
movq (%rax), %rax
movq %rax, -0x38(%rbp)
movl $0x2, -0x30(%rbp)
movq %r15, %rdi
leaq -0x38(%rbp), %rsi
callq 0x2d26
leaq 0xba18(%rip), %rdi      # 0xe390
movq %r15, %rsi
callq 0x2ea0
jmp 0x2a24
movq 0xb62c(%rip), %rax      # 0xdfb8
movq (%rax), %rax
movq %rax, -0x38(%rbp)
movl $0x1, -0x30(%rbp)
movq %r15, %rdi
leaq -0x38(%rbp), %rsi
callq 0x2d26
leaq 0xb9e3(%rip), %rdi      # 0xe390
movq %r15, %rsi
callq 0x2ea0
jmp 0x2a24
movq 0xb5fa(%rip), %rax      # 0xdfb8
movq (%rax), %rsi
leaq 0xb9e0(%rip), %rdi      # 0xe3a8
callq 0x2360
jmp 0x27c4
movq 0xb5df(%rip), %rax      # 0xdfb8
movq (%rax), %rsi
leaq 0xba0d(%rip), %rdi      # 0xe3f0
callq 0x2360
movb $0x1, 0xb9f9(%rip)      # 0xe3e8
jmp 0x27c4
movq 0xb5bd(%rip), %rax      # 0xdfb8
movq (%rax), %rax
movq %rax, -0x38(%rbp)
movl $0x5, -0x30(%rbp)
movq %r15, %rdi
leaq -0x38(%rbp), %rsi
callq 0x2d26
leaq 0xb974(%rip), %rdi      # 0xe390
movq %r15, %rsi
callq 0x2ea0
movq %r15, %rdi
callq 0x2388
jmp 0x27c4
cmpl $-0x1, %eax
jne 0x2a6a
movq 0xb95b(%rip), %rax      # 0xe398
cmpq 0xb94c(%rip), %rax      # 0xe390
je 0x2aef
cmpq $0x0, 0xb95e(%rip)      # 0xe3b0
je 0x2b12
addq $0xe8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
leaq 0x69ed(%rip), %rsi      # 0x945e
leaq -0x68(%rbp), %rdi
leaq -0x38(%rbp), %rdx
callq 0x2cbe
movq 0xb54b(%rip), %rax      # 0xdfd0
movslq (%rax), %rax
movq -0x8(%rbx,%rax,8), %rdx
leaq -0xc8(%rbp), %rdi
leaq -0x68(%rbp), %rsi
callq 0x2d60
leaq -0xc8(%rbp), %rdi
callq 0x263c
leaq 0x698c(%rip), %rsi      # 0x943c
leaq -0xe8(%rbp), %rdi
leaq -0x68(%rbp), %rdx
callq 0x2cbe
leaq -0xe8(%rbp), %rdi
callq 0x263c
leaq 0x6b83(%rip), %rsi      # 0x9656
leaq -0x108(%rbp), %rdi
leaq -0x68(%rbp), %rdx
callq 0x2cbe
leaq -0x108(%rbp), %rdi
callq 0x263c
leaq 0x6982(%rip), %rsi      # 0x9478
leaq -0xa8(%rbp), %rdi
leaq -0x68(%rbp), %rdx
callq 0x2cbe
leaq -0xa8(%rbp), %rdi
callq 0x263c
leaq 0x698f(%rip), %rsi      # 0x94a8
leaq -0x88(%rbp), %rdi
leaq -0x68(%rbp), %rdx
callq 0x2cbe
leaq -0x88(%rbp), %rdi
callq 0x263c
movq %rax, %rbx
leaq -0x88(%rbp), %rdi
jmp 0x2b96
jmp 0x2b80
movq %rax, %rbx
leaq -0xa8(%rbp), %rdi
jmp 0x2b96
jmp 0x2b80
movq %rax, %rbx
leaq -0x108(%rbp), %rdi
jmp 0x2b96
jmp 0x2b80
movq %rax, %rbx
leaq -0xe8(%rbp), %rdi
jmp 0x2b96
jmp 0x2b80
movq %rax, %rbx
leaq -0xc8(%rbp), %rdi
callq 0x2388
jmp 0x2b92
jmp 0x2b8f
movq %rax, %rbx
jmp 0x2b9b
jmp 0x2b8f
jmp 0x2b8f
jmp 0x2b8f
jmp 0x2b8f
jmp 0x2b8f
movq %rax, %rbx
leaq -0x68(%rbp), %rdi
callq 0x2388
movq %rbx, %rdi
callq 0x2300