// File: /workspace/github_cpp_makefile_star2_O3/auton1[P]viterbi/vcf_file.cpp
// Function: vcf_file::vcf_file(parameters const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>&, int)
vcf_file::vcf_file(const parameters &p, string &vcf_filename, int idx)
{
	filename = vcf_filename;
	compressed = p.vcf_compressed[idx];
	stream = p.stream_in;

	gzMAX_LINE_LEN = 0;
	N_entries = 0; N_kept_entries = 0;
	meta_data = header();

	if (stream && compressed)
		open_gz();
	else if (stream)
	{
		char first = cin.peek();
		if (first == 0x1f)
			LOG.error("File starts with gzip magic string. Shouldn't you be using --gzvcf?\n");

		file_in = &std::cin;
	}
	else
		open();

	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 $0x218, %rsp            # imm = 0x218
movl %ecx, 0xc(%rsp)
movq %rdx, %r13
movq %rsi, %r14
movq %rdi, %rbx
leaq 0x383af(%rip), %rax     # 0x48b00
movq %rax, (%rdi)
leaq 0x8(%rdi), %rax
movq %rax, 0x10(%rsp)
leaq 0x18(%rdi), %rbp
movq %rbp, 0x8(%rdi)
movq $0x0, 0x10(%rdi)
movb $0x0, 0x18(%rdi)
leaq 0x38(%rdi), %r12
movq %r12, %rdi
callq 0x54e0
leaq 0x250(%rbx), %r15
movq %r15, %rdi
callq 0x13830
xorl %eax, %eax
movq %rax, 0x430(%rbx)
movl %eax, 0x438(%rbx)
movq %rax, 0x440(%rbx)
movl %eax, 0x448(%rbx)
movq %rax, 0x450(%rbx)
leaq 0x3839a(%rip), %rax     # 0x48b50
movq %rax, (%rbx)
movq 0x10(%rsp), %rdi
movq %r13, %rsi
callq 0x51f0
movslq 0xc(%rsp), %rax
leal 0x3f(%rax), %ecx
testl %eax, %eax
cmovnsl %eax, %ecx
sarl $0x6, %ecx
movslq %ecx, %rcx
shlq $0x3, %rcx
addq 0x498(%r14), %rcx
movabsq $-0x8000000000000000, %rdx # imm = 0x8000000000000000
leaq 0x3f(%rdx), %rsi
andq %rax, %rsi
xorl %edi, %edi
cmpq %rdx, %rsi
setbe %dil
movq -0x8(%rcx,%rdi,8), %rcx
btq %rax, %rcx
setb 0x28(%rbx)
movb (%r14), %al
movb %al, 0x468(%rbx)
movl $0x0, 0x240(%rbx)
movq $0x0, 0x458(%rbx)
leaq 0x38(%rsp), %rdi
callq 0x13830
leaq 0x48(%rsp), %rsi
movb -0x8(%rsi), %al
movb %al, 0x8(%r15)
movq -0x10(%rsi), %rax
movq %rax, (%r15)
leaq 0x260(%rbx), %rdi
callq 0xf35e
leaq 0x278(%rbx), %rdi
leaq 0x60(%rsp), %rsi
callq 0xf35e
leaq 0x290(%rbx), %rdi
leaq 0x78(%rsp), %rsi
callq 0xf4ce
leaq 0x98(%rsp), %rsi
movl -0x8(%rsi), %eax
movl %eax, 0x2a8(%rbx)
leaq 0x2b0(%rbx), %rdi
callq 0xff16
leaq 0x2e0(%rbx), %rdi
leaq 0xc8(%rsp), %rsi
callq 0xff16
leaq 0x310(%rbx), %rdi
leaq 0xf8(%rsp), %rsi
callq 0xff16
leaq 0x340(%rbx), %rdi
leaq 0x128(%rsp), %rsi
callq 0xff16
leaq 0x370(%rbx), %rdi
leaq 0x158(%rsp), %rsi
callq 0x10258
leaq 0x3a0(%rbx), %rdi
leaq 0x188(%rsp), %rsi
callq 0x10258
leaq 0x3d0(%rbx), %rdi
leaq 0x1b8(%rsp), %rsi
callq 0x10258
leaq 0x400(%rbx), %rdi
leaq 0x1e8(%rsp), %rsi
callq 0x10258
leaq 0x38(%rsp), %rdi
callq 0xf24a
cmpb $0x1, 0x468(%rbx)
jne 0x1093f
cmpb $0x1, 0x28(%rbx)
jne 0x1094c
movq (%rbx), %rax
addq $0x8, %rax
jmp 0x10942
movq (%rbx), %rax
movq %rbx, %rdi
callq *(%rax)
jmp 0x109db
movq 0x38685(%rip), %r14     # 0x48fd8
movq %r14, %rdi
callq 0x5140
cmpb $0x1f, %al
jne 0x109d7
leaq 0x28(%rsp), %r13
movq %r13, -0x10(%r13)
leaq 0x38(%rsp), %rsi
movq $0x44, (%rsi)
leaq 0x18(%rsp), %rdi
xorl %edx, %edx
callq 0x57f0
movq %rax, %r15
leaq 0x18(%rsp), %r12
movq %rax, (%r12)
movq 0x38(%rsp), %rbp
movq %rbp, 0x10(%r12)
leaq 0x27c8d(%rip), %rsi     # 0x3862a
movl $0x44, %edx
movq %rax, %rdi
callq 0x5380
movq %rbp, 0x8(%r12)
movb $0x0, (%r15,%rbp)
leaq 0x38aed(%rip), %rdi     # 0x494a8
movq %r12, %rsi
movl $0x1, %edx
callq 0x36ec8
movq 0x18(%rsp), %rdi
cmpq %r13, %rdi
je 0x109d7
callq 0x5410
movq %r14, 0x30(%rbx)
movq %rbx, %rdi
callq 0x10aa6
movl 0x2a8(%rbx), %esi
leaq 0xb(%rsp), %rdx
movb $0x1, (%rdx)
leaq 0x38(%rsp), %rdi
leaq 0xa(%rsp), %rcx
callq 0xf2ca
addq $0x430, %rbx            # imm = 0x430
movq %rbx, %rdi
callq 0xc7a2
movq 0x58(%rsp), %rax
movq %rax, 0x20(%rbx)
movups 0x38(%rsp), %xmm0
movups 0x48(%rsp), %xmm1
movups %xmm1, 0x10(%rbx)
movups %xmm0, (%rbx)
addq $0x218, %rsp            # imm = 0x218
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %r14
movq 0x18(%rsp), %rdi
cmpq %r13, %rdi
je 0x10a95
callq 0x5410
jmp 0x10a95
jmp 0x10a83
jmp 0x10a83
movq %rax, %rdi
callq 0xc796
jmp 0x10a83
jmp 0x10a83
movq %rax, %r14
movq %r12, %rdi
callq 0x58a0
jmp 0x10a6f
movq %rax, %r14
movq 0x10(%rsp), %rax
movq (%rax), %rdi
cmpq %rbp, %rdi
je 0x10a9d
callq 0x5410
jmp 0x10a9d
movq %rax, %r14
jmp 0x10a95
movq %rax, %r14
leaq 0x38(%rsp), %rdi
callq 0xf24a
movq %rbx, %rdi
callq 0x114e4
movq %r14, %rdi
callq 0x57d0
nop