// File: /workspace/github_cpp_makefile_star2_O1/tonymugen[P]sampleSNPs/varfiles.cpp
// Function: sampFiles::HmpFileI::_numLines()
uint64_t HmpFileI::_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 HMP file " << _fileName << " for input" << endl;
			exit(2);
		}

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

    }
    // skip header line if present.
    string trash;
    if (_head) {
        getline(_varFile, trash);
    }

    const size_t bufSize = BUF_SIZE;
    char *buf;
    try {
        buf = new char[bufSize];
    } catch (bad_alloc& error) {
        cerr << "ERROR: failed to allocate buffer in HmpFileI::_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 %r13
pushq %r12
pushq %rbx
subq $0x20, %rsp
movq %rdi, %rbx
leaq 0x8(%rdi), %r14
leaq 0x88(%rdi), %r15
movq %r15, %rdi
callq 0x40a0
testb %al, %al
je 0x15c21
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 0x15d20
leaq 0x10(%rsp), %r13
movq %r13, -0x10(%r13)
movq $0x0, -0x8(%r13)
movb $0x0, (%r13)
cmpb $0x1, 0x238(%rbx)
jne 0x15c86
movq (%r14), %rax
movq -0x18(%rax), %rdi
addq %r14, %rdi
movl $0xa, %esi
callq 0x4290
movsbl %al, %edx
movq %rsp, %rsi
movq %r14, %rdi
callq 0x4500
movl $0xa00000, %edi         # imm = 0xA00000
callq 0x4030
movq %rax, %r12
movq 0x8(%rbx), %rax
movq -0x18(%rax), %rax
testb $0x5, 0x28(%rbx,%rax)
je 0x15ca7
xorl %r15d, %r15d
jmp 0x15ce9
xorl %r15d, %r15d
movl $0xa00000, %edx         # imm = 0xA00000
movq %r14, %rdi
movq %r12, %rsi
callq 0x4350
movq 0x10(%rbx), %rax
testq %rax, %rax
je 0x15cda
xorl %ecx, %ecx
xorl %edx, %edx
cmpb $0xa, (%r12,%rcx)
sete %dl
addq %rdx, %r15
incq %rcx
cmpq %rcx, %rax
jne 0x15cc5
movq 0x8(%rbx), %rax
movq -0x18(%rax), %rax
testb $0x5, 0x28(%rbx,%rax)
je 0x15caa
movq %r14, %rdi
callq 0x4060
movq %r12, %rdi
callq 0x4380
movq (%rsp), %rdi
cmpq %r13, %rdi
je 0x15d0f
movq 0x10(%rsp), %rsi
incq %rsi
callq 0x42d0
movq %r15, %rax
addq $0x20, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
movq 0xa2c9(%rip), %rdi      # 0x1fff0
leaq 0x3140(%rip), %rsi      # 0x18e6e
movl $0x1f, %edx
callq 0x42f0
movq 0x218(%rbx), %rsi
movq 0x220(%rbx), %rdx
movq 0xa2a3(%rip), %rdi      # 0x1fff0
callq 0x42f0
movq %rax, %r14
leaq 0x2810(%rip), %rsi      # 0x1856c
movl $0xa, %edx
movq %rax, %rdi
callq 0x42f0
movq %r14, %rdi
callq 0x4130
movl $0x2, %edi
callq 0x4320
jmp 0x15eb1
movq %rax, %r14
cmpl $0x2, %edx
jne 0x15eb4
movq %r14, %rdi
callq 0x4110
movq %rax, %rbx
movq 0xa252(%rip), %rdi      # 0x1fff0
leaq 0x3106(%rip), %rsi      # 0x18eab
movl $0x3b, %edx
callq 0x42f0
movq (%rbx), %rax
movq %rbx, %rdi
callq *0x10(%rax)
movq 0xa231(%rip), %rdi      # 0x1fff0
movq %rax, %rsi
callq 0x42a0
movq %rax, %rdi
callq 0x4130
movl $0x4, %edi
callq 0x4320
movq %rax, %r14
callq 0x4480
jmp 0x15eb4
jmp 0x15eb1
movq %rax, %r14
cmpl $0x1, %edx
jne 0x15eca
movq %r14, %rdi
callq 0x4110
movq %rax, %r14
movq 0xa1e7(%rip), %rdi      # 0x1fff0
leaq 0x307e(%rip), %rsi      # 0x18e8e
movl $0x1c, %edx
callq 0x42f0
movq 0x218(%rbx), %rsi
movq 0x220(%rbx), %rdx
movq 0xa1c1(%rip), %rdi      # 0x1fff0
callq 0x42f0
movq %rax, %rbx
leaq 0x2bbf(%rip), %rsi      # 0x189fd
movl $0xc, %edx
movq %rax, %rdi
callq 0x42f0
movq 0x18(%r14), %rsi
movl 0x10(%r14), %edx
movq (%rsi), %rax
movq %rsp, %rdi
callq *0x20(%rax)
movq (%rsp), %rsi
movq 0x8(%rsp), %rdx
movq %rbx, %rdi
callq 0x42f0
movq %rax, %rdi
callq 0x41b0
movq %rsp, %rdi
callq 0x4b6f
movq %rax, %r14
leaq 0x10(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x15ea2
movq 0x10(%rsp), %rsi
incq %rsi
callq 0x42d0
jmp 0x15ea2
jmp 0x15e9f
movq %rax, %r14
callq 0x4480
jmp 0x15eca
movq %rax, %rdi
callq 0x7714
movq %rax, %r14
movq (%rsp), %rdi
cmpq %r13, %rdi
je 0x15eca
movq 0x10(%rsp), %rsi
incq %rsi
callq 0x42d0
movq %r14, %rdi
callq 0x44e0