// File: /workspace/github_cpp_makefile_star2_O1/auton1[P]viterbi/bcf_file.cpp
// Function: bcf_file::bcf_file(parameters const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>&, int)
bcf_file::bcf_file(const parameters &p, string &vcf_filename, int idx)
{
	filename = vcf_filename;

	big_endian = is_big_endian();
	is_BGZF = false; stream = p.stream_in;
	N_entries = 0; N_kept_entries = 0;
	meta_data = header();

	if (stream)
	{
		is_BGZF = true;
		open_gz();
	}
	else
		open();

	check_bcf();
	read_header();

	include_indv = vector<bool>(meta_data.N_indv,true);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x1f8, %rsp            # imm = 0x1F8
movq %rdx, %r13
movq %rsi, %r14
movq %rdi, %rbx
leaq 0x3b4bf(%rip), %rax     # 0x49b00
movq %rax, (%rdi)
leaq 0x8(%rdi), %rax
movq %rax, 0x10(%rsp)
leaq 0x18(%rdi), %r15
movq %r15, 0x8(%rdi)
movq $0x0, 0x10(%rdi)
movb $0x0, 0x18(%rdi)
leaq 0x38(%rdi), %rbp
movq %rbp, %rdi
callq 0x54e0
leaq 0x250(%rbx), %r12
movq %r12, %rdi
callq 0x1385c
xorl %eax, %eax
movq %rax, 0x430(%rbx)
movl %eax, 0x438(%rbx)
movq %rax, 0x440(%rbx)
movl %eax, 0x448(%rbx)
movq %rax, 0x450(%rbx)
leaq 0x3b3e2(%rip), %rax     # 0x49a88
movq %rax, (%rbx)
movq 0x10(%rsp), %rdi
movq %r13, %rsi
callq 0x51f0
movw $0x0, 0x460(%rbx)
movb (%r14), %al
movb %al, 0x462(%rbx)
movq $0x0, 0x458(%rbx)
leaq 0x18(%rsp), %rdi
callq 0x1385c
leaq 0x28(%rsp), %rsi
movb -0x8(%rsi), %al
movb %al, 0x8(%r12)
movq -0x10(%rsi), %rax
movq %rax, (%r12)
leaq 0x260(%rbx), %rdi
callq 0xf346
leaq 0x278(%rbx), %rdi
leaq 0x40(%rsp), %rsi
callq 0xf346
leaq 0x290(%rbx), %rdi
leaq 0x58(%rsp), %rsi
callq 0xf48e
leaq 0x78(%rsp), %rsi
movl -0x8(%rsi), %eax
movl %eax, 0x2a8(%rbx)
leaq 0x2b0(%rbx), %rdi
callq 0xfed0
leaq 0x2e0(%rbx), %rdi
leaq 0xa8(%rsp), %rsi
callq 0xfed0
leaq 0x310(%rbx), %rdi
leaq 0xd8(%rsp), %rsi
callq 0xfed0
leaq 0x340(%rbx), %rdi
leaq 0x108(%rsp), %rsi
callq 0xfed0
leaq 0x370(%rbx), %rdi
leaq 0x138(%rsp), %rsi
callq 0x10214
leaq 0x3a0(%rbx), %rdi
leaq 0x168(%rsp), %rsi
callq 0x10214
leaq 0x3d0(%rbx), %rdi
leaq 0x198(%rsp), %rsi
callq 0x10214
leaq 0x400(%rbx), %rdi
leaq 0x1c8(%rsp), %rsi
callq 0x10214
leaq 0x18(%rsp), %rdi
callq 0xf232
cmpb $0x1, 0x462(%rbx)
jne 0xe7e9
movb $0x1, 0x460(%rbx)
movq (%rbx), %rax
addq $0x8, %rax
jmp 0xe7ec
movq (%rbx), %rax
movq %rbx, %rdi
callq *(%rax)
movq %rbx, %rdi
callq 0xe8be
movq %rbx, %rdi
callq 0xe96e
movl 0x2a8(%rbx), %esi
leaq 0xf(%rsp), %rdx
movb $0x1, (%rdx)
leaq 0x18(%rsp), %rdi
leaq 0xe(%rsp), %rcx
callq 0xf2b2
addq $0x430, %rbx            # imm = 0x430
movq %rbx, %rdi
callq 0xc7b2
movq 0x38(%rsp), %rax
movq %rax, 0x20(%rbx)
movups 0x18(%rsp), %xmm0
movups 0x28(%rsp), %xmm1
movups %xmm1, 0x10(%rbx)
movups %xmm0, (%rbx)
xorl %eax, %eax
movl %eax, 0x20(%rsp)
movq $0x0, 0x28(%rsp)
movl %eax, 0x30(%rsp)
addq $0x1f8, %rsp            # imm = 0x1F8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %rdi
callq 0xc7a6
jmp 0xe89c
jmp 0xe89c
movq %rax, %r14
movq %rbp, %rdi
callq 0x58a0
jmp 0xe888
movq %rax, %r14
movq 0x10(%rsp), %rax
movq (%rax), %rdi
cmpq %r15, %rdi
je 0xe8b6
callq 0x5410
jmp 0xe8b6
movq %rax, %r14
jmp 0xe8ae
movq %rax, %r14
leaq 0x18(%rsp), %rdi
callq 0xf232
movq %rbx, %rdi
callq 0x11498
movq %r14, %rdi
callq 0x57d0