// File: /workspace/github_cpp_makefile_star2_O2/auton1[P]viterbi/bcf_entry.cpp
// Function: bcf_entry::parse_basic_entry(bool, bool, bool)
void bcf_entry::parse_basic_entry(bool parse_ALT, bool parse_FILTER, bool parse_INFO)
{
	if (line.empty())
	{
		if (parse_ALT)
			set_ALT("");
		return;
	}

	if (!basic_parsed)
	{
		uint32_t n_allele_info, n_fmt_sample;
		uint32_t chrom, pos, rlen;
		uint32_t shared, indiv;
		float qual;

		line_pos = 0;

		get_number(shared, &line_pos, line);
		get_number(indiv, &line_pos, line);
		L_shared = shared;
		L_indiv = indiv;

		get_number(chrom, &line_pos, line);
		get_number(pos, &line_pos, line);
		get_number(rlen, &line_pos, line);

		qual = *reinterpret_cast<const float*>(&line[line_pos]);
		line_pos += sizeof(qual);

		get_number(n_allele_info, &line_pos, line);
		get_number(n_fmt_sample, &line_pos, line);

		N_format = n_fmt_sample >> 24;
		CHROM = entry_header.CONTIG_map[chrom].ID;
		POS = pos + 1;
		ID = get_typed_string( &line_pos, line );
		REF = get_typed_string( &line_pos, line );
		QUAL = qual;

		N_allele = n_allele_info >> 16;
		N_info = n_allele_info & (uint32_t)65535;

		ALT_pos = line_pos;
		for (unsigned int ui=1; ui<N_allele; ui++)
			skip_section(&line_pos, line);

		FILTER_pos = line_pos;
		skip_section(&line_pos, line);

		INFO_pos = line_pos;
		std::transform(REF.begin(), REF.end(), REF.begin(), ::toupper);

		basic_parsed = true;
	}
	if (parse_ALT && !parsed_ALT)
		set_ALT(N_allele);
	if (parse_FILTER && !parsed_FILTER)
		set_FILTER();
	if (parse_INFO && !parsed_INFO)
		set_INFO();
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x58, %rsp
movl %esi, %r15d
movq %rdi, %rbx
movq 0x3c0(%rdi), %rax
cmpq 0x3c8(%rdi), %rax
je 0x141a4
movl %ecx, %ebp
movl %edx, %r14d
cmpb $0x0, 0x3d8(%rbx)
jne 0x1423f
movl %r14d, 0xc(%rsp)
movl %ebp, 0x10(%rsp)
leaq 0x3c0(%rbx), %r12
leaq 0x6cc(%rbx), %r13
andl $0x0, 0x6cc(%rbx)
leaq 0x28(%rsp), %rbp
movq %rbx, %rdi
movq %rbp, %rsi
movq %r13, %rdx
movq %r12, %rcx
callq 0x1b918
leaq 0x24(%rsp), %r14
movq %rbx, %rdi
movq %r14, %rsi
movq %r13, %rdx
movq %r12, %rcx
callq 0x1b918
movl (%rbp), %eax
movl %eax, 0x6c4(%rbx)
movl (%r14), %eax
movl %eax, 0x6c8(%rbx)
leaq 0x30(%rsp), %rbp
movq %rbx, %rdi
movq %rbp, %rsi
movq %r13, %rdx
movq %r12, %rcx
callq 0x1b918
leaq 0x14(%rsp), %rsi
movq %rbx, %rdi
movq %r13, %rdx
movq %r12, %rcx
callq 0x1b918
leaq 0x2c(%rsp), %rsi
movq %rbx, %rdi
movq %r13, %rdx
movq %r12, %rcx
callq 0x1b918
movl 0x6cc(%rbx), %eax
movq 0x3c0(%rbx), %rcx
leal 0x4(%rax), %edx
cvtss2sd (%rcx,%rax), %xmm0
movsd %xmm0, 0x18(%rsp)
movl %edx, 0x6cc(%rbx)
leaq 0x8(%rsp), %rsi
movq %rbx, %rdi
movq %r13, %rdx
movq %r12, %rcx
callq 0x1b918
leaq 0x34(%rsp), %r14
movq %rbx, %rdi
movq %r14, %rsi
movq %r13, %rdx
movq %r12, %rcx
callq 0x1b918
movzbl 0x3(%r14), %eax
movl %eax, 0x6bc(%rbx)
leaq 0x100(%rbx), %rdi
movl (%rbp), %eax
leaq 0x38(%rsp), %rsi
movl %eax, (%rsi)
callq 0x162fe
leaq 0x20(%rax), %rsi
leaq 0x3e0(%rbx), %rdi
callq 0x5210
leaq 0x14(%rsp), %rax
movl (%rax), %eax
incl %eax
movl %eax, 0x400(%rbx)
leaq 0x38(%rsp), %r14
movq %r14, %rdi
movq %rbx, %rsi
movq %r13, %rdx
movq %r12, %rcx
callq 0x1b356
leaq 0x408(%rbx), %rdi
movq %r14, %rsi
callq 0x5580
movq %r14, %rdi
callq 0x5908
leaq 0x38(%rsp), %r14
movq %r14, %rdi
movq %rbx, %rsi
movq %r13, %rdx
movq %r12, %rcx
callq 0x1b356
leaq 0x428(%rbx), %rdi
movq %r14, %rsi
callq 0x5580
movq %r14, %rdi
callq 0x5908
movsd 0x18(%rsp), %xmm0
movsd %xmm0, 0x460(%rbx)
leaq 0x8(%rsp), %rax
movl (%rax), %eax
movzwl %ax, %ecx
shrl $0x10, %eax
movl %eax, 0x6c0(%rbx)
movl %ecx, 0x6b8(%rbx)
movl 0x6cc(%rbx), %ecx
movl %ecx, 0x6f0(%rbx)
pushq $0x1
popq %rbp
cmpl %eax, %ebp
jae 0x141e0
movq %rbx, %rdi
movq %r13, %rsi
movq %r12, %rdx
callq 0x1b7c6
incl %ebp
movl 0x6c0(%rbx), %eax
jmp 0x14188
testb %r15b, %r15b
je 0x14287
leaq 0x1ac83(%rip), %rsi     # 0x2ee37
leaq 0x38(%rsp), %r14
leaq 0x8(%rsp), %rdx
movq %r14, %rdi
callq 0x5160
movq %rbx, %rdi
movq %r14, %rsi
callq 0x2005a
leaq 0x38(%rsp), %rdi
callq 0x5908
jmp 0x14287
movl 0x6cc(%rbx), %eax
movl %eax, 0x6ec(%rbx)
movq %rbx, %rdi
movq %r13, %rsi
movq %r12, %rdx
callq 0x1b7c6
movl 0x6cc(%rbx), %eax
movl %eax, 0x6e8(%rbx)
movq 0x428(%rbx), %r14
movq 0x430(%rbx), %r12
xorl %r13d, %r13d
movl 0x10(%rsp), %ebp
cmpq %r13, %r12
je 0x14233
movsbl (%r14,%r13), %edi
callq 0x5880
movb %al, (%r14,%r13)
incq %r13
jmp 0x1421b
movb $0x1, 0x3d8(%rbx)
movl 0xc(%rsp), %r14d
testb %r15b, %r15b
je 0x1425b
cmpb $0x0, 0x3da(%rbx)
jne 0x1425b
movl 0x6c0(%rbx), %esi
movq %rbx, %rdi
callq 0x1ff34
testb %r14b, %r14b
je 0x14271
cmpb $0x0, 0x3db(%rbx)
jne 0x14271
movq %rbx, %rdi
callq 0x21418
testb %bpl, %bpl
je 0x14287
cmpb $0x0, 0x3dc(%rbx)
jne 0x14287
movq %rbx, %rdi
callq 0x20118
addq $0x58, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %rbx
leaq 0x38(%rsp), %rdi
callq 0x5908
movq %rbx, %rdi
callq 0x5800
nop