// File: /workspace/github_cpp_makefile_star2_O3/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:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x348, %rsp            # imm = 0x348
movq %rsi, %rbx
movq %rdi, %r14
cmpb $0x0, 0x3d9(%rdi)
jne 0x1a28e
movq (%r14), %rax
movq %r14, %rdi
movl $0x1, %esi
callq *0x18(%rax)
cmpb $0x0, 0x3dd(%r14)
jne 0x1a2a0
movq %r14, %rdi
callq 0x27570
leaq 0x1d0(%rsp), %rdi
callq 0x55d0
leaq 0x58(%rsp), %rdi
callq 0x55d0
leaq 0x30(%rsp), %rax
movq %rax, -0x10(%rax)
movq $0x0, -0x8(%rax)
movb $0x0, (%rax)
leaq 0x10(%rsp), %rax
movq %rax, -0x10(%rax)
leaq 0x1fbfc(%rip), %rdx     # 0x39ed7
movq %rsp, %rdi
movq %rdx, %rsi
callq 0xc85e
leaq 0x1d8(%rsp), %rdi
movq %rsp, %rsi
callq 0x5640
movq (%rsp), %rdi
leaq 0x10(%rsp), %rax
cmpq %rax, %rdi
je 0x1a309
callq 0x5410
movq %rsp, %rdi
leaq 0x10(%rsp), %rax
movq %rax, (%rdi)
leaq 0x1fbbc(%rip), %rdx     # 0x39ed7
movq %rdx, %rsi
callq 0xc85e
movq %rbx, 0x40(%rsp)
leaq 0x60(%rsp), %rdi
movq %rsp, %rsi
callq 0x5640
movq (%rsp), %rdi
leaq 0x10(%rsp), %rax
cmpq %rax, %rdi
je 0x1a348
callq 0x5410
movl 0x8(%r14), %eax
testl %eax, %eax
je 0x1a5bd
xorl %r13d, %r13d
movq %rsp, %rbp
leaq 0x20(%rsp), %r15
movq 0x1f0(%r14), %rdx
movl $0x1, %esi
movl %r13d, %ecx
shlq %cl, %rsi
movq %rsi, 0x50(%rsp)
movq %r13, %rcx
shrq $0x6, %rcx
movq %rcx, 0x48(%rsp)
movq (%rdx,%rcx,8), %rcx
btq %r13, %rcx
jae 0x1a5af
movl $0x1, %edx
leaq 0x1d0(%rsp), %rdi
leaq 0x1fb32(%rip), %rsi     # 0x39ed6
callq 0x54f0
cmpl $0x0, 0x6bc(%r14)
je 0x1a570
xorl %r12d, %r12d
testl %r12d, %r12d
je 0x1a3d5
movl $0x1, %edx
leaq 0x58(%rsp), %rdi
leaq 0x1fcbd(%rip), %rsi     # 0x3a08d
callq 0x54f0
cmpl 0x630(%r14), %r12d
jne 0x1a40f
movq 0x218(%r14), %rax
movq 0x50(%rsp), %rcx
movq 0x48(%rsp), %rdx
testq %rcx, (%rax,%rdx,8)
movq %r15, %rcx
je 0x1a440
movl %r12d, (%rsp)
movq %r14, %rdi
movl %r13d, %esi
movq %rbp, %rdx
callq 0x19804
jmp 0x1a4c9
movl %r12d, (%rsp)
movq %r14, %rdi
movl %r13d, %esi
movq %rbp, %rdx
movq %r15, %rbx
movq %r15, %rcx
callq 0x19804
movq %rbx, %rdi
leaq 0x1edbc(%rip), %rsi     # 0x391ed
callq 0x50e0
testl %eax, %eax
sete %bl
jmp 0x1a4cb
movq 0x28(%rsp), %rdx
movl $0x1, %r8d
movq %rcx, %rdi
xorl %esi, %esi
leaq 0x1ed96(%rip), %rcx     # 0x391ed
callq 0x5690
movq 0x4e8(%r14), %rax
cmpl $0x2, (%rax,%r13,4)
jl 0x1a4c9
movl $0x1, %ebx
leaq 0x10(%rsp), %rax
movq %rax, (%rsp)
movq 0x20(%rsp), %rsi
movq 0x28(%rsp), %rdx
addq %rsi, %rdx
movq %rbp, %rdi
callq 0xc7c8
movq %rbp, %rdi
leaq 0x1ed55(%rip), %rsi     # 0x391ec
callq 0x5870
movq %r15, %rdi
movq %rbp, %rsi
callq 0x5550
movq (%rsp), %rdi
leaq 0x10(%rsp), %rax
cmpq %rax, %rdi
je 0x1a4ba
callq 0x5410
incl %ebx
movq 0x4e8(%r14), %rax
cmpl (%rax,%r13,4), %ebx
jl 0x1a46f
xorl %ebx, %ebx
movq 0x20(%rsp), %rsi
movq 0x28(%rsp), %rdx
leaq 0x58(%rsp), %rdi
callq 0x54f0
testb %bl, %bl
jne 0x1a560
movq %rbp, %rdi
leaq 0x60(%rsp), %rsi
callq 0x56c0
movq %r15, %rdi
movq %rbp, %rsi
callq 0x5550
movq (%rsp), %rdi
leaq 0x10(%rsp), %rax
cmpq %rax, %rdi
je 0x1a50e
callq 0x5410
movq 0x20(%rsp), %rsi
movq 0x28(%rsp), %rdx
leaq 0x1d0(%rsp), %rdi
callq 0x54f0
leaq 0x10(%rsp), %rax
movq %rax, (%rsp)
movq %rbp, %rdi
leaq 0x1f99f(%rip), %rdx     # 0x39ed7
movq %rdx, %rsi
callq 0xc85e
leaq 0x60(%rsp), %rdi
movq %rbp, %rsi
callq 0x5640
movq (%rsp), %rdi
leaq 0x10(%rsp), %rax
cmpq %rax, %rdi
je 0x1a560
callq 0x5410
incl %r12d
cmpl 0x6bc(%r14), %r12d
jb 0x1a3ba
leaq 0x10(%rsp), %rax
movq %rax, (%rsp)
movq %rbp, %rdi
leaq 0x1f954(%rip), %rdx     # 0x39ed7
movq %rdx, %rsi
callq 0xc85e
leaq 0x60(%rsp), %rdi
movq %rbp, %rsi
callq 0x5640
movq (%rsp), %rdi
leaq 0x10(%rsp), %rax
cmpq %rax, %rdi
je 0x1a5ab
callq 0x5410
movl 0x8(%r14), %eax
incq %r13
movl %eax, %ecx
cmpq %rcx, %r13
jb 0x1a35f
movq %rsp, %rdi
leaq 0x1d8(%rsp), %r14
movq %r14, %rsi
callq 0x56c0
movq %rsp, %rbx
movq 0x40(%rsp), %rdi
movq %rbx, %rsi
callq 0x5550
movq (%rbx), %rdi
leaq 0x10(%rsp), %rax
cmpq %rax, %rdi
je 0x1a5f2
callq 0x5410
movq %rsp, %rdi
leaq 0x10(%rsp), %rax
movq %rax, (%rdi)
leaq 0x1f8d3(%rip), %rdx     # 0x39ed7
movq %rdx, %rsi
callq 0xc85e
movq %rsp, %rsi
movq %r14, %rdi
callq 0x5640
movq (%rsp), %rdi
leaq 0x10(%rsp), %rax
cmpq %rax, %rdi
je 0x1a62a
callq 0x5410
movq 0x20(%rsp), %rdi
leaq 0x30(%rsp), %rax
cmpq %rax, %rdi
je 0x1a63e
callq 0x5410
movq 0x2e97b(%rip), %rbx     # 0x48fc0
leaq 0x58(%rsp), %rdi
movq %rbx, %rsi
callq 0x51e0
leaq 0xc8(%rsp), %rdi
callq 0x5100
leaq 0x1d0(%rsp), %rdi
movq %rbx, %rsi
callq 0x51e0
leaq 0x240(%rsp), %rdi
callq 0x5100
addq $0x348, %rsp            # imm = 0x348
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
jmp 0x1a6b3
jmp 0x1a6cb
jmp 0x1a6cb
jmp 0x1a6b3
jmp 0x1a6cb
jmp 0x1a6b3
jmp 0x1a6cb
movq %rax, %rbx
jmp 0x1a700
jmp 0x1a6b3
jmp 0x1a6cb
jmp 0x1a6cb
jmp 0x1a6cb
jmp 0x1a6cb
jmp 0x1a6cb
jmp 0x1a6b3
jmp 0x1a6cb
jmp 0x1a6cb
movq %rax, %rbx
movq (%rsp), %rdi
leaq 0x10(%rsp), %rax
cmpq %rax, %rdi
je 0x1a6ce
callq 0x5410
jmp 0x1a6ce
movq %rax, %rbx
movq 0x20(%rsp), %rdi
leaq 0x30(%rsp), %rax
cmpq %rax, %rdi
je 0x1a6e2
callq 0x5410
movq 0x2e8d7(%rip), %rsi     # 0x48fc0
leaq 0x58(%rsp), %rdi
callq 0x51e0
leaq 0xc8(%rsp), %rdi
callq 0x5100
movq 0x2e8b9(%rip), %rsi     # 0x48fc0
leaq 0x1d0(%rsp), %rdi
callq 0x51e0
leaq 0x240(%rsp), %rdi
callq 0x5100
movq %rbx, %rdi
callq 0x57d0
nop