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

	/*
	 * I am using the line-end counting method. It is > 2-fold faster than reading lines with getline().
	 */
	if (_famFile.is_open()) {
        _famFile.close();
    }
    string famName = _fileStub + ".fam";
    try {
        _famFile.open(famName.c_str(), ios::in);
		if (!_famFile.is_open()) {
			cerr << "ERROR: failed to open .fam file " << famName << " for input" << endl;
			exit(2);
		}
    } catch (system_error &error) {
        cerr << "ERROR: cannot open .fam file " << famName << " 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 BedFile::_famLines(): " << error.what() << endl;
		exit(4);
	}

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

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x40, %rsp
movq %rdi, %r14
leaq 0x248(%rdi), %rbx
leaq 0x2c8(%rdi), %r15
movq %r15, %rdi
callq 0x40a0
testb %al, %al
je 0x913a
movq %rbx, %rdi
callq 0x4060
leaq 0x10(%rsp), %r13
movq %r13, -0x10(%r13)
movq 0x668(%r14), %rsi
movq 0x670(%r14), %rdx
addq %rsi, %rdx
movq %rsp, %r12
movq %r12, %rdi
callq 0x76e4
leaq 0xf62f(%rip), %rsi      # 0x18795
movq %r12, %rdi
callq 0x4530
movq (%rsp), %rsi
movq %rbx, %rdi
movl $0x8, %edx
callq 0x4270
movq %r15, %rdi
callq 0x40a0
testb %al, %al
je 0x923a
movl $0xa00000, %edi         # imm = 0xA00000
callq 0x4030
movq %rax, %r12
movq 0x248(%r14), %rax
movq -0x18(%rax), %rax
testb $0x5, 0x268(%r14,%rax)
je 0x91b7
xorl %r15d, %r15d
jmp 0x9203
xorl %r15d, %r15d
movl $0xa00000, %edx         # imm = 0xA00000
movq %rbx, %rdi
movq %r12, %rsi
callq 0x4350
movq 0x250(%r14), %rax
testq %rax, %rax
je 0x91ed
xorl %ecx, %ecx
xorl %edx, %edx
cmpb $0xa, (%r12,%rcx)
sete %dl
addq %rdx, %r15
incq %rcx
cmpq %rcx, %rax
jne 0x91d8
movq 0x248(%r14), %rax
movq -0x18(%rax), %rax
testb $0x5, 0x268(%r14,%rax)
je 0x91ba
movq %r12, %rdi
callq 0x4380
movq %rbx, %rdi
callq 0x4060
movq (%rsp), %rdi
cmpq %r13, %rdi
je 0x9229
movq 0x10(%rsp), %rsi
incq %rsi
callq 0x42d0
movq %r15, %rax
addq $0x40, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
movq 0x16daf(%rip), %rdi     # 0x1fff0
leaq 0xf552(%rip), %rsi      # 0x1879a
movl $0x20, %edx
callq 0x42f0
movq (%rsp), %rsi
movq 0x8(%rsp), %rdx
movq 0x16d8e(%rip), %rdi     # 0x1fff0
callq 0x42f0
movq %rax, %rbx
leaq 0xf2fb(%rip), %rsi      # 0x1856c
movl $0xa, %edx
movq %rax, %rdi
callq 0x42f0
movq %rbx, %rdi
callq 0x4130
movl $0x2, %edi
callq 0x4320
jmp 0x93c5
movq %rax, %rbx
cmpl $0x2, %edx
jne 0x93c8
movq %rbx, %rdi
callq 0x4110
movq %rax, %rbx
movq 0x16d3d(%rip), %rdi     # 0x1fff0
leaq 0xf51f(%rip), %rsi      # 0x187d9
movl $0x3a, %edx
callq 0x42f0
movq (%rbx), %rax
movq %rbx, %rdi
callq *0x10(%rax)
movq 0x16d1c(%rip), %rdi     # 0x1fff0
movq %rax, %rsi
callq 0x42a0
movq %rax, %rdi
callq 0x4130
movl $0x4, %edi
callq 0x4320
movq %rax, %rbx
callq 0x4480
jmp 0x93c8
jmp 0x93c5
movq %rax, %rbx
cmpl $0x1, %edx
jne 0x93c8
movq %rbx, %rdi
callq 0x4110
movq %rax, %rbx
movq 0x16cd2(%rip), %rdi     # 0x1fff0
leaq 0xf496(%rip), %rsi      # 0x187bb
movl $0x1d, %edx
callq 0x42f0
movq (%rsp), %rsi
movq 0x8(%rsp), %rdx
movq 0x16cb1(%rip), %rdi     # 0x1fff0
callq 0x42f0
movq %rax, %r14
leaq 0xf6af(%rip), %rsi      # 0x189fd
movl $0xc, %edx
movq %rax, %rdi
callq 0x42f0
movq 0x18(%rbx), %rsi
movl 0x10(%rbx), %edx
movq (%rsi), %rax
leaq 0x20(%rsp), %rdi
callq *0x20(%rax)
movq 0x20(%rsp), %rsi
movq 0x28(%rsp), %rdx
movq %r14, %rdi
callq 0x42f0
movq %rax, %rdi
callq 0x41b0
leaq 0x20(%rsp), %rdi
callq 0x4641
movq %rax, %rbx
leaq 0x30(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x93b6
movq 0x30(%rsp), %rsi
incq %rsi
callq 0x42d0
jmp 0x93b6
jmp 0x93b3
movq %rax, %rbx
callq 0x4480
jmp 0x93c8
movq %rax, %rdi
callq 0x76d8
movq %rax, %rbx
movq (%rsp), %rdi
cmpq %r13, %rdi
je 0x93de
movq 0x10(%rsp), %rsi
incq %rsi
callq 0x42d0
movq %rbx, %rdi
callq 0x44e0