// File: auton1[P]viterbi/bcf_entry.cpp
// Function: bcf_entry::read_all_entries(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>&)
void bcf_entry::read_all_entries(string &out)
{
	if (fully_parsed == false)
		parse_full_entry(true);

	if (parsed_FORMAT == false)
		set_FORMAT();

	ostringstream outstream, tmpstream;
	string tmpstr;
	outstream.str("");
	tmpstream.str("");
	bool format_miss, indv_miss;

	for(unsigned int ui=0; ui<N_indv; ui++)
	{
		if(include_indv[ui] == false)
			continue;
		outstream << "\t";
		indv_miss = true;

		for(unsigned int uj=0; uj<N_format; uj++)
		{
			if (uj != 0)
				tmpstream << ":";

			if ( ((int)uj == GT_idx) && (include_genotype[ui] == false) )
			{
				tmpstr = ".";
				for (int uk=1; uk<ploidy[ui]; uk++)
					tmpstr = tmpstr + "/.";
				format_miss = false;
			}
			else if ((int)uj == GT_idx)
			{
				read_indv_generic_entry(ui, uj, tmpstr);
				format_miss = false;
			}
			else
			{
				read_indv_generic_entry(ui, uj, tmpstr);
				format_miss = (tmpstr == ".");
			}
			indv_miss = indv_miss && format_miss;
			tmpstream << tmpstr;

			if (!format_miss)
			{
				tmpstr = tmpstream.str();
				outstream << tmpstr;
				tmpstream.str("");
			}
		}
		tmpstream.str("");
	}
	out = outstream.str();
	outstream.str("");
}

// Assembly:
subq $0x508, %rsp            # imm = 0x508
movq %rdi, 0x500(%rsp)
movq %rsi, 0x4f8(%rsp)
movq 0x500(%rsp), %rax
movq %rax, 0x70(%rsp)
movb 0x3d9(%rax), %al
andb $0x1, %al
movzbl %al, %eax
cmpl $0x0, %eax
jne 0x37754
movq 0x70(%rsp), %rdi
movq (%rdi), %rax
movl $0x1, %esi
callq *0x18(%rax)
movq 0x70(%rsp), %rax
movb 0x3dd(%rax), %al
andb $0x1, %al
movzbl %al, %eax
cmpl $0x0, %eax
jne 0x37773
movq 0x70(%rsp), %rdi
callq 0x56ee0
leaq 0x380(%rsp), %rdi
callq 0x67a0
leaq 0x208(%rsp), %rdi
callq 0x67a0
jmp 0x3778f
leaq 0x1d8(%rsp), %rdi
callq 0x67e0
leaq 0x1b7(%rsp), %rdi
movq %rdi, 0x68(%rsp)
callq 0x69f0
movq 0x68(%rsp), %rdx
leaq 0x3e56f(%rip), %rsi     # 0x75d29
leaq 0x1b8(%rsp), %rdi
callq 0x67c0
jmp 0x377c9
leaq 0x380(%rsp), %rdi
leaq 0x1b8(%rsp), %rsi
callq 0x61f0
jmp 0x377e0
leaq 0x1b8(%rsp), %rdi
callq 0x6b50
leaq 0x1b7(%rsp), %rdi
callq 0x65f0
leaq 0x18f(%rsp), %rdi
movq %rdi, 0x60(%rsp)
callq 0x69f0
movq 0x60(%rsp), %rdx
leaq 0x3e511(%rip), %rsi     # 0x75d29
leaq 0x190(%rsp), %rdi
callq 0x67c0
jmp 0x37827
leaq 0x208(%rsp), %rdi
leaq 0x190(%rsp), %rsi
callq 0x61f0
jmp 0x3783e
leaq 0x190(%rsp), %rdi
callq 0x6b50
leaq 0x18f(%rsp), %rdi
callq 0x65f0
movl $0x0, 0x188(%rsp)
movq 0x70(%rsp), %rcx
movl 0x188(%rsp), %eax
cmpl 0x8(%rcx), %eax
jae 0x37dfe
movq 0x70(%rsp), %rdi
addq $0x1f0, %rdi            # imm = 0x1F0
movl 0x188(%rsp), %eax
movl %eax, %esi
callq 0x102b0
movq %rdx, 0x50(%rsp)
movq %rax, 0x58(%rsp)
jmp 0x3789e
movq 0x50(%rsp), %rax
movq 0x58(%rsp), %rcx
movq %rcx, 0x178(%rsp)
movq %rax, 0x180(%rsp)
leaq 0x178(%rsp), %rdi
callq 0x10310
andb $0x1, %al
movzbl %al, %eax
cmpl $0x0, %eax
jne 0x3799c
jmp 0x37d9f
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x200(%rsp)
movl %eax, 0x1fc(%rsp)
jmp 0x37f19
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x200(%rsp)
movl %eax, 0x1fc(%rsp)
jmp 0x37928
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x200(%rsp)
movl %eax, 0x1fc(%rsp)
leaq 0x1b8(%rsp), %rdi
callq 0x6b50
leaq 0x1b7(%rsp), %rdi
callq 0x65f0
jmp 0x37eff
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x200(%rsp)
movl %eax, 0x1fc(%rsp)
jmp 0x37971
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x200(%rsp)
movl %eax, 0x1fc(%rsp)
leaq 0x190(%rsp), %rdi
callq 0x6b50
leaq 0x18f(%rsp), %rdi
callq 0x65f0
jmp 0x37eff
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x200(%rsp)
movl %eax, 0x1fc(%rsp)
jmp 0x37eff
leaq 0x3e385(%rip), %rsi     # 0x75d28
leaq 0x380(%rsp), %rdi
callq 0x6540
jmp 0x379b2
movb $0x1, 0x18d(%rsp)
movl $0x0, 0x174(%rsp)
movq 0x70(%rsp), %rcx
movl 0x174(%rsp), %eax
cmpl 0x6bc(%rcx), %eax
jae 0x37d41
cmpl $0x0, 0x174(%rsp)
je 0x379ff
leaq 0x3e4f1(%rip), %rsi     # 0x75edf
leaq 0x208(%rsp), %rdi
callq 0x6540
jmp 0x379fd
jmp 0x379ff
movq 0x70(%rsp), %rdx
movl 0x174(%rsp), %ecx
xorl %eax, %eax
cmpl 0x630(%rdx), %ecx
movb %al, 0x4f(%rsp)
jne 0x37a75
movq 0x70(%rsp), %rdi
addq $0x218, %rdi            # imm = 0x218
movl 0x188(%rsp), %eax
movl %eax, %esi
callq 0x102b0
movq %rdx, 0x38(%rsp)
movq %rax, 0x40(%rsp)
jmp 0x37a3f
movq 0x38(%rsp), %rax
movq 0x40(%rsp), %rcx
movq %rcx, 0x160(%rsp)
movq %rax, 0x168(%rsp)
leaq 0x160(%rsp), %rdi
callq 0x10310
andb $0x1, %al
movzbl %al, %eax
cmpl $0x0, %eax
sete %al
movb %al, 0x4f(%rsp)
movb 0x4f(%rsp), %al
testb $0x1, %al
jne 0x37a82
jmp 0x37b36
leaq 0x3d655(%rip), %rsi     # 0x750de
leaq 0x1d8(%rsp), %rdi
callq 0x67b0
jmp 0x37a98
movl $0x1, 0x15c(%rsp)
movq 0x70(%rsp), %rdi
movl 0x15c(%rsp), %eax
movl %eax, 0x34(%rsp)
addq $0x4e8, %rdi            # imm = 0x4E8
movl 0x188(%rsp), %eax
movl %eax, %esi
callq 0xecf0
movq %rax, %rcx
movl 0x34(%rsp), %eax
cmpl (%rcx), %eax
jge 0x37b29
leaq 0x3d603(%rip), %rdx     # 0x750dd
leaq 0x138(%rsp), %rdi
leaq 0x1d8(%rsp), %rsi
callq 0x2a270
jmp 0x37af1
leaq 0x1d8(%rsp), %rdi
leaq 0x138(%rsp), %rsi
callq 0x66c0
leaq 0x138(%rsp), %rdi
callq 0x6b50
movl 0x15c(%rsp), %eax
addl $0x1, %eax
movl %eax, 0x15c(%rsp)
jmp 0x37aa3
movb $0x0, 0x18e(%rsp)
jmp 0x37bdf
movq 0x70(%rsp), %rcx
movl 0x174(%rsp), %eax
cmpl 0x630(%rcx), %eax
jne 0x37b85
movq 0x70(%rsp), %rdi
movl 0x188(%rsp), %esi
movl 0x174(%rsp), %eax
movl %eax, 0x134(%rsp)
leaq 0x134(%rsp), %rdx
leaq 0x1d8(%rsp), %rcx
callq 0x366a0
jmp 0x37b7b
movb $0x0, 0x18e(%rsp)
jmp 0x37bdd
movq 0x70(%rsp), %rdi
movl 0x188(%rsp), %esi
movl 0x174(%rsp), %eax
movl %eax, 0x130(%rsp)
leaq 0x130(%rsp), %rdx
leaq 0x1d8(%rsp), %rcx
callq 0x366a0
jmp 0x37bb6
leaq 0x3d521(%rip), %rsi     # 0x750de
leaq 0x1d8(%rsp), %rdi
callq 0xea20
movb %al, 0x33(%rsp)
jmp 0x37bd0
movb 0x33(%rsp), %al
andb $0x1, %al
movb %al, 0x18e(%rsp)
jmp 0x37bdf
xorl %eax, %eax
testb $0x1, 0x18d(%rsp)
movb %al, 0x32(%rsp)
je 0x37bfa
movb 0x18e(%rsp), %al
movb %al, 0x32(%rsp)
movb 0x32(%rsp), %al
andb $0x1, %al
movb %al, 0x18d(%rsp)
leaq 0x208(%rsp), %rdi
leaq 0x1d8(%rsp), %rsi
callq 0x64a0
jmp 0x37c1e
testb $0x1, 0x18e(%rsp)
jne 0x37d29
leaq 0x110(%rsp), %rdi
leaq 0x208(%rsp), %rsi
callq 0x6570
jmp 0x37c43
leaq 0x1d8(%rsp), %rdi
movq %rdi, 0x28(%rsp)
leaq 0x110(%rsp), %rsi
movq %rsi, 0x20(%rsp)
callq 0x66c0
movq 0x20(%rsp), %rdi
callq 0x6b50
movq 0x28(%rsp), %rsi
leaq 0x380(%rsp), %rdi
callq 0x64a0
jmp 0x37c80
leaq 0xef(%rsp), %rdi
movq %rdi, 0x18(%rsp)
callq 0x69f0
movq 0x18(%rsp), %rdx
leaq 0x3e08b(%rip), %rsi     # 0x75d29
leaq 0xf0(%rsp), %rdi
callq 0x67c0
jmp 0x37cad
leaq 0x208(%rsp), %rdi
leaq 0xf0(%rsp), %rsi
callq 0x61f0
jmp 0x37cc4
leaq 0xf0(%rsp), %rdi
callq 0x6b50
leaq 0xef(%rsp), %rdi
callq 0x65f0
jmp 0x37d29
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x200(%rsp)
movl %eax, 0x1fc(%rsp)
jmp 0x37d17
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x200(%rsp)
movl %eax, 0x1fc(%rsp)
leaq 0xf0(%rsp), %rdi
callq 0x6b50
leaq 0xef(%rsp), %rdi
callq 0x65f0
jmp 0x37eff
jmp 0x37d2b
movl 0x174(%rsp), %eax
addl $0x1, %eax
movl %eax, 0x174(%rsp)
jmp 0x379c5
leaq 0xc7(%rsp), %rdi
movq %rdi, 0x10(%rsp)
callq 0x69f0
movq 0x10(%rsp), %rdx
leaq 0x3dfca(%rip), %rsi     # 0x75d29
leaq 0xc8(%rsp), %rdi
callq 0x67c0
jmp 0x37d6e
leaq 0x208(%rsp), %rdi
leaq 0xc8(%rsp), %rsi
callq 0x61f0
jmp 0x37d85
leaq 0xc8(%rsp), %rdi
callq 0x6b50
leaq 0xc7(%rsp), %rdi
callq 0x65f0
movl 0x188(%rsp), %eax
addl $0x1, %eax
movl %eax, 0x188(%rsp)
jmp 0x37863
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x200(%rsp)
movl %eax, 0x1fc(%rsp)
jmp 0x37dec
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x200(%rsp)
movl %eax, 0x1fc(%rsp)
leaq 0xc8(%rsp), %rdi
callq 0x6b50
leaq 0xc7(%rsp), %rdi
callq 0x65f0
jmp 0x37eff
leaq 0xa0(%rsp), %rdi
leaq 0x380(%rsp), %rsi
callq 0x6570
jmp 0x37e15
movq 0x4f8(%rsp), %rdi
leaq 0xa0(%rsp), %rsi
movq %rsi, (%rsp)
callq 0x66c0
movq (%rsp), %rdi
callq 0x6b50
leaq 0x7f(%rsp), %rdi
movq %rdi, 0x8(%rsp)
callq 0x69f0
movq 0x8(%rsp), %rdx
leaq 0x3ded7(%rip), %rsi     # 0x75d29
leaq 0x80(%rsp), %rdi
callq 0x67c0
jmp 0x37e61
leaq 0x380(%rsp), %rdi
leaq 0x80(%rsp), %rsi
callq 0x61f0
jmp 0x37e78
leaq 0x80(%rsp), %rdi
callq 0x6b50
leaq 0x7f(%rsp), %rdi
callq 0x65f0
leaq 0x1d8(%rsp), %rdi
callq 0x6b50
leaq 0x208(%rsp), %rdi
callq 0x6b30
leaq 0x380(%rsp), %rdi
callq 0x6b30
addq $0x508, %rsp            # imm = 0x508
retq
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x200(%rsp)
movl %eax, 0x1fc(%rsp)
jmp 0x37ef5
movq %rax, %rcx
movl %edx, %eax
movq %rcx, 0x200(%rsp)
movl %eax, 0x1fc(%rsp)
leaq 0x80(%rsp), %rdi
callq 0x6b50
leaq 0x7f(%rsp), %rdi
callq 0x65f0
leaq 0x1d8(%rsp), %rdi
callq 0x6b50
leaq 0x208(%rsp), %rdi
callq 0x6b30
leaq 0x380(%rsp), %rdi
callq 0x6b30
movq 0x200(%rsp), %rdi
callq 0x69e0
nopw %cs:(%rax,%rax)