// File: /workspace/github_cpp_makefile_star2_O3/tonymugen[P]sampleSNPs/varfiles.cpp
// Function: sampFiles::TpedFileI::_numLines()
uint64_t TpedFileI::_numLines(){
    uint64_t N = 0;

    /*
     * I am using the line-end counting method. It is > 2-fold faster than reading lines with getline().
     */
    if (_varFile.is_open()) {
        _varFile.close();
    }
    try {
        _varFile.open(_fileName.c_str(), ios::in);
		if (!_varFile.is_open()) {
			cerr << "ERROR: failed to open .tped file " << _fileName << " for input" << endl;
			exit(2);
		}

    } catch (system_error &error) {
        cerr << "ERROR: cannot open .tped file " << _fileName << " for input: " << error.code().message() << flush;
        perror(" ");
        exit(1);

    }

    const size_t bufSize = BUF_SIZE;
    char *buf;
    try {
        buf = new char[bufSize];
    } catch (bad_alloc& error) {
        cerr << "ERROR: failed to allocate buffer in TpedFile::_numLines(): " << error.what() << endl;
        exit(4);
    }

    while (_varFile) {
        _varFile.read(buf, bufSize);
        for (size_t i = 0; i < _varFile.gcount(); i++) {
            if (buf[i] == '\n') {
                N++;
            }
        }
    }
    _varFile.close();
    delete [] buf;

    return N;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %rdi, %rbx
leaq 0x8(%rdi), %r14
leaq 0x88(%rdi), %r15
movq %r15, %rdi
callq 0x40a0
testb %al, %al
je 0x12f1f
movq %r14, %rdi
callq 0x4060
movq 0x218(%rbx), %rsi
movq %r14, %rdi
movl $0x8, %edx
callq 0x4270
movq %r15, %rdi
callq 0x40a0
testb %al, %al
je 0x12fc5
movl $0xa00000, %edi         # imm = 0xA00000
callq 0x4030
movq %rax, %r15
movq 0x8(%rbx), %rax
movq -0x18(%rax), %rax
testb $0x5, 0x28(%rbx,%rax)
je 0x12f64
xorl %r12d, %r12d
jmp 0x12fa6
xorl %r12d, %r12d
movl $0xa00000, %edx         # imm = 0xA00000
movq %r14, %rdi
movq %r15, %rsi
callq 0x4350
movq 0x10(%rbx), %rax
testq %rax, %rax
je 0x12f97
xorl %ecx, %ecx
xorl %edx, %edx
cmpb $0xa, (%r15,%rcx)
sete %dl
addq %rdx, %r12
incq %rcx
cmpq %rcx, %rax
jne 0x12f82
movq 0x8(%rbx), %rax
movq -0x18(%rax), %rax
testb $0x5, 0x28(%rbx,%rax)
je 0x12f67
movq %r14, %rdi
callq 0x4060
movq %r15, %rdi
callq 0x4380
movq %r12, %rax
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
movq 0xd024(%rip), %rdi      # 0x1fff0
leaq 0x5d66(%rip), %rsi      # 0x18d39
movl $0x21, %edx
callq 0x42f0
movq 0x218(%rbx), %rsi
movq 0x220(%rbx), %rdx
movq 0xcffe(%rip), %rdi      # 0x1fff0
callq 0x42f0
movq %rax, %r14
leaq 0x556b(%rip), %rsi      # 0x1856c
movl $0xa, %edx
movq %rax, %rdi
callq 0x42f0
movq %r14, %rdi
callq 0x4130
movl $0x2, %edi
callq 0x4320
movq %rax, %r14
cmpl $0x2, %edx
jne 0x13147
movq %r14, %rdi
callq 0x4110
movq %rax, %rbx
movq 0xcfb2(%rip), %rdi      # 0x1fff0
leaq 0x5c41(%rip), %rsi      # 0x18c86
movl $0x3b, %edx
callq 0x42f0
movq (%rbx), %rax
movq %rbx, %rdi
callq *0x10(%rax)
movq 0xcf91(%rip), %rdi      # 0x1fff0
movq %rax, %rsi
callq 0x42a0
movq %rax, %rdi
callq 0x4130
movl $0x4, %edi
callq 0x4320
movq %rax, %r14
callq 0x4480
jmp 0x13147
movq %rax, %r14
cmpl $0x1, %edx
jne 0x13147
movq %r14, %rdi
callq 0x4110
movq %rax, %r14
movq 0xcf4c(%rip), %rdi      # 0x1fff0
leaq 0x5cb0(%rip), %rsi      # 0x18d5b
movl $0x1e, %edx
callq 0x42f0
movq 0x218(%rbx), %rsi
movq 0x220(%rbx), %rdx
movq 0xcf26(%rip), %rdi      # 0x1fff0
callq 0x42f0
movq %rax, %rbx
leaq 0x5924(%rip), %rsi      # 0x189fd
movl $0xc, %edx
movq %rax, %rdi
callq 0x42f0
movq 0x18(%r14), %rsi
movl 0x10(%r14), %edx
movq (%rsi), %rax
leaq 0x8(%rsp), %rdi
callq *0x20(%rax)
movq 0x8(%rsp), %rsi
movq 0x10(%rsp), %rdx
movq %rbx, %rdi
callq 0x42f0
movq %rax, %rdi
callq 0x41b0
leaq 0x8(%rsp), %rdi
callq 0x4981
movq %rax, %r14
leaq 0x18(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x13142
movq 0x18(%rsp), %rsi
incq %rsi
callq 0x42d0
jmp 0x13142
jmp 0x1313f
movq %rax, %r14
callq 0x4480
movq %r14, %rdi
callq 0x44e0
movq %rax, %rdi
callq 0x76d8
nop