// File: /workspace/github_cpp_makefile_star2_O3/auton1[P]viterbi/bcf_entry.cpp
// Function: bcf_entry::parse_genotype_entry(unsigned int, bool, bool, bool, bool)
void bcf_entry::parse_genotype_entry(unsigned int indv, bool GT, bool GQ, bool DP, bool FT)
{
	if (fully_parsed == false)
		parse_full_entry(true);

	if (parsed_FORMAT == false)
		set_FORMAT();

	unsigned int l_pos, indv_size, type, size, ui;
	vector<int> ids;

	if ( GT && !parsed_GT[indv] && GT_idx != -1 )
		ids.push_back(GT_idx);
	if (GQ && !parsed_GQ[indv] && GQ_idx != -1)
		ids.push_back(GQ_idx);
	if (DP && !parsed_DP[indv] && DP_idx != -1)
		ids.push_back(DP_idx);
	if (FT && !parsed_FT[indv] && FT_idx != -1)
		ids.push_back(FT_idx);

	for(unsigned int i=0; i<ids.size(); i++)
	{
		ui = ids[i];
		type = FORMAT_types[ui];
		size = FORMAT_sizes[ui];
		indv_size = FORMAT_skip[ui];
		l_pos = FORMAT_positions[ui] + indv*indv_size;

		if ((int)ui == GT_idx)
			set_indv_GENOTYPE_and_PHASE(indv, l_pos, size);
		else if ((int)ui == GQ_idx)
		{
			if (size>1)
				LOG.error("Error: Only expect single value for QUALITY.\n");

			float tmp;
			if (type==5)
				tmp = *reinterpret_cast<const float*>(&line[l_pos]);
			else if (type==1)
			{
				int8_t tmp2 = *reinterpret_cast<const int8_t*>(&line[l_pos]);
				tmp = (float)tmp2;
			}
			else if (type==2)
			{
				int16_t tmp2 = *reinterpret_cast<const int16_t*>(&line[l_pos]);
				tmp = (float)tmp2;
			}
			else if (type==3)
			{
				int32_t tmp2 = *reinterpret_cast<const int32_t*>(&line[l_pos]);
				tmp = (float)tmp2;
			}
			else
				LOG.error("Error: Invalid type for QUALITY.\n");

			set_indv_GQUALITY(indv, tmp);
		}
		else if ((int)ui == DP_idx)
		{
			if (size>1)
				LOG.error("Error: Only expect single value for DEPTH.\n");

			int tmp = -1;

			if (type==1)
			{
				if ( !check_missing(l_pos, 1, line) )
					tmp = *reinterpret_cast<const int8_t*>(&line[l_pos]);
			}
			else if (type==2)
			{
				if ( !check_missing(l_pos, 2, line) )
					tmp = *reinterpret_cast<const int16_t*>(&line[l_pos]);
			}
			else if (type==3)
			{
				if ( !check_missing(l_pos, 3, line) )
					tmp = *reinterpret_cast<const int32_t*>(&line[l_pos]);
			}
			else if (type==5)
			{
				float tmp2 = -1;
				if ( !check_missing(l_pos, 5, line) )
					tmp2 = *reinterpret_cast<const float*>(&line[l_pos]);
				tmp = (int)tmp2;
			}
			else
				LOG.error("Error: Invalid type for DEPTH.\n");

			set_indv_DEPTH(indv, tmp);
		}
		else if ((int)ui == FT_idx)
		{
			if (type == 7)
			{
				vector<char> tmp;
				tmp.resize( size*sizeof(char) );
				memcpy(&tmp[0], &line[l_pos], size*sizeof(char));
				set_indv_GFILTER(indv, tmp);
			}
			else
				LOG.one_off_warning("Warning: FT values must be encoded in string format.\n");
		}
	}
	// Set missing return values if requested a value, but couldn't find it
	if (GT && (parsed_GT[indv] == false))
	{
		set_indv_GENOTYPE_and_PHASE(indv, make_pair(-1,-1), '/');
	}
	if (GQ && (parsed_GQ[indv] == false))
	{
		set_indv_GQUALITY(indv, -1);
	}
	if (DP && (parsed_DP[indv] == false))
	{
		set_indv_DEPTH(indv, -1);
	}
	if (FT && (parsed_FT[indv] == false))
	{
		set_indv_GFILTER(indv, "");
	}
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x108, %rsp            # imm = 0x108
movl %r9d, %ebp
movl %r8d, %r15d
movl %ecx, %r12d
movl %edx, 0x28(%rsp)
movl %esi, %ebx
movq %rdi, %r14
cmpb $0x0, 0x3d9(%rdi)
jne 0x18f94
movq (%r14), %rax
movq %r14, %rdi
movl $0x1, %esi
callq *0x18(%rax)
cmpb $0x0, 0x3dd(%r14)
jne 0x18fa6
movq %r14, %rdi
callq 0x27570
xorps %xmm0, %xmm0
movaps %xmm0, 0x10(%rsp)
movq $0x0, 0x20(%rsp)
cmpb $0x0, 0x28(%rsp)
je 0x18ff1
movq 0x560(%r14), %rax
movl %ebx, %ecx
shrl $0x6, %ecx
movq (%rax,%rcx,8), %rax
btq %rbx, %rax
jb 0x18ff1
cmpl $-0x1, 0x630(%r14)
je 0x18ff1
leaq 0x630(%r14), %rdx
leaq 0x10(%rsp), %rdi
xorl %esi, %esi
callq 0xca58
testb %r12b, %r12b
je 0x19010
movq 0x588(%r14), %rax
movl %ebx, %ecx
shrl $0x6, %ecx
movq (%rax,%rcx,8), %rax
btq %rbx, %rax
jae 0x195dc
testb %r15b, %r15b
je 0x1902f
movq 0x5b0(%r14), %rax
movl %ebx, %ecx
shrl $0x6, %ecx
movq (%rax,%rcx,8), %rax
btq %rbx, %rax
jae 0x19608
testb %bpl, %bpl
je 0x1904e
movq 0x5d8(%r14), %rax
movl %ebx, %ecx
shrl $0x6, %ecx
movq (%rax,%rcx,8), %rax
btq %rbx, %rax
jae 0x19634
movl %r12d, 0x60(%rsp)
movl %r15d, 0x64(%rsp)
movl %ebp, 0x5c(%rsp)
movq 0x10(%rsp), %rax
cmpq %rax, 0x18(%rsp)
je 0x194c6
leaq 0x3c0(%r14), %rbp
movl $0x1, %r15d
xorl %ecx, %ecx
movl (%rax,%rcx,4), %eax
movq 0x658(%r14), %rcx
movq 0x670(%r14), %rdx
movl (%rcx,%rax,4), %r13d
movl (%rdx,%rax,4), %esi
movl %esi, 0x2c(%rsp)
movq 0x640(%r14), %rcx
movq 0x688(%r14), %rdx
movl (%rdx,%rax,4), %edx
imull %ebx, %edx
addl (%rcx,%rax,4), %edx
movl %edx, 0xc(%rsp)
cmpl 0x630(%r14), %eax
jne 0x190d4
movq %r14, %rdi
movl %ebx, %esi
leaq 0xc(%rsp), %rdx
leaq 0x2c(%rsp), %rcx
callq 0x27b9e
jmp 0x194a6
cmpl 0x634(%r14), %eax
jne 0x19170
cmpl $0x2, %esi
jb 0x19142
leaq 0xf8(%rsp), %rax
movq %rax, 0xe8(%rsp)
leaq 0xe8(%rsp), %r12
movq %r12, %rdi
leaq 0x1ff40(%rip), %rsi     # 0x39048
leaq 0x1ff66(%rip), %rdx     # 0x39075
callq 0xc85e
leaq 0x3038d(%rip), %rdi     # 0x494a8
movq %r12, %rsi
movl $0x1, %edx
callq 0x36ec8
movq 0xe8(%rsp), %rdi
leaq 0xf8(%rsp), %rax
cmpq %rax, %rdi
je 0x19142
callq 0x5410
decl %r13d
cmpl $0x4, %r13d
ja 0x192ee
leaq 0x1feaa(%rip), %rcx     # 0x39000
movslq (%rcx,%r13,4), %rax
addq %rcx, %rax
jmpq *%rax
movl 0xc(%rsp), %eax
movq (%rbp), %rcx
movsbl (%rcx,%rax), %eax
jmp 0x192bb
cmpl 0x638(%r14), %eax
jne 0x1922f
cmpl $0x2, %esi
jb 0x191de
leaq 0xb8(%rsp), %rax
movq %rax, 0xa8(%rsp)
leaq 0xa8(%rsp), %r12
movq %r12, %rdi
leaq 0x1fef4(%rip), %rsi     # 0x39098
leaq 0x1ff18(%rip), %rdx     # 0x390c3
callq 0xc85e
leaq 0x302f1(%rip), %rdi     # 0x494a8
movq %r12, %rsi
movl $0x1, %edx
callq 0x36ec8
movq 0xa8(%rsp), %rdi
leaq 0xb8(%rsp), %rax
cmpq %rax, %rdi
je 0x191de
callq 0x5410
decl %r13d
cmpl $0x4, %r13d
ja 0x19437
leaq 0x1fdfa(%rip), %rcx     # 0x38fec
movslq (%rcx,%r13,4), %rax
addq %rcx, %rax
jmpq *%rax
movl 0xc(%rsp), %esi
movq %r14, %rdi
movl $0x1, %edx
movq %rbp, %rcx
callq 0x21712
movl $0xffffffff, %r13d      # imm = 0xFFFFFFFF
testb %al, %al
jne 0x19499
movl 0xc(%rsp), %eax
movq (%rbp), %rcx
movsbl (%rcx,%rax), %r13d
jmp 0x19499
cmpl 0x63c(%r14), %eax
jne 0x194a6
cmpl $0x7, %r13d
jne 0x19351
xorps %xmm0, %xmm0
movaps %xmm0, 0x30(%rsp)
movq $0x0, 0x40(%rsp)
leaq 0x30(%rsp), %r12
movq %r12, %rdi
callq 0xf332
movq 0x30(%rsp), %rdi
movl 0xc(%rsp), %esi
addq 0x3c0(%r14), %rsi
movl 0x2c(%rsp), %edx
callq 0x5380
movq %r14, %rdi
movl %ebx, %esi
movq %r12, %rdx
callq 0x282ca
movq 0x30(%rsp), %rdi
testq %rdi, %rdi
jne 0x19398
jmp 0x194a6
movl 0xc(%rsp), %eax
movq (%rbp), %rcx
xorps %xmm0, %xmm0
cvtsi2ssl (%rcx,%rax), %xmm0
jmp 0x192d1
movl 0xc(%rsp), %eax
movq (%rbp), %rcx
movswl (%rcx,%rax), %eax
xorps %xmm0, %xmm0
cvtsi2ss %eax, %xmm0
jmp 0x192d1
movl 0xc(%rsp), %eax
movq (%rbp), %rcx
movss (%rcx,%rax), %xmm0
movss %xmm0, 0x30(%rsp)
leaq 0x30(%rsp), %r12
movq %r14, %rdi
movl %ebx, %esi
movq %r12, %rdx
callq 0x2820e
jmp 0x194a6
leaq 0xd8(%rsp), %rax
movq %rax, 0xc8(%rsp)
leaq 0xc8(%rsp), %r12
movq %r12, %rdi
leaq 0x1fd66(%rip), %rsi     # 0x39076
leaq 0x1fd80(%rip), %rdx     # 0x39097
callq 0xc85e
leaq 0x30185(%rip), %rdi     # 0x494a8
movq %r12, %rsi
movl $0x1, %edx
callq 0x36ec8
leaq 0x30(%rsp), %r12
movq 0xc8(%rsp), %rdi
leaq 0xd8(%rsp), %rax
cmpq %rax, %rdi
je 0x192dc
callq 0x5410
jmp 0x192dc
leaq 0x78(%rsp), %rax
movq %rax, 0x68(%rsp)
leaq 0x68(%rsp), %r12
movq %r12, %rdi
leaq 0x1fd7a(%rip), %rsi     # 0x390e4
leaq 0x1fda8(%rip), %rdx     # 0x39119
callq 0xc85e
leaq 0x3012b(%rip), %rdi     # 0x494a8
movq %r12, %rsi
callq 0x371c0
movq 0x68(%rsp), %rdi
leaq 0x78(%rsp), %rax
cmpq %rax, %rdi
je 0x194a6
callq 0x5410
jmp 0x194a6
movl 0xc(%rsp), %esi
movq %r14, %rdi
movl $0x3, %edx
movq %rbp, %rcx
callq 0x21712
movl $0xffffffff, %r13d      # imm = 0xFFFFFFFF
testb %al, %al
jne 0x19499
movl 0xc(%rsp), %eax
movq (%rbp), %rcx
movl (%rcx,%rax), %r13d
jmp 0x19499
movl 0xc(%rsp), %esi
movq %r14, %rdi
movl $0x2, %edx
movq %rbp, %rcx
callq 0x21712
movl $0xffffffff, %r13d      # imm = 0xFFFFFFFF
testb %al, %al
jne 0x19499
movl 0xc(%rsp), %eax
movq (%rbp), %rcx
movswl (%rcx,%rax), %r13d
jmp 0x19499
movl 0xc(%rsp), %esi
movq %r14, %rdi
movl $0x5, %edx
movq %rbp, %rcx
callq 0x21712
movl $0xffffffff, %r13d      # imm = 0xFFFFFFFF
testb %al, %al
jne 0x19499
movl 0xc(%rsp), %eax
movq (%rbp), %rcx
cvttss2si (%rcx,%rax), %r13d
jmp 0x19499
leaq 0x98(%rsp), %rax
movq %rax, 0x88(%rsp)
leaq 0x88(%rsp), %r12
movq %r12, %rdi
leaq 0x1fc6b(%rip), %rsi     # 0x390c4
leaq 0x1fc83(%rip), %rdx     # 0x390e3
callq 0xc85e
leaq 0x3003c(%rip), %rdi     # 0x494a8
movq %r12, %rsi
movl $0x1, %edx
callq 0x36ec8
movq 0x88(%rsp), %rdi
movl $0xffffffff, %r13d      # imm = 0xFFFFFFFF
leaq 0x98(%rsp), %rax
cmpq %rax, %rdi
je 0x19499
callq 0x5410
movq %r14, %rdi
movl %ebx, %esi
movl %r13d, %edx
callq 0x244ee
movl %r15d, %ecx
movq 0x10(%rsp), %rax
movq 0x18(%rsp), %rdx
subq %rax, %rdx
sarq $0x2, %rdx
incl %r15d
cmpq %rcx, %rdx
ja 0x1907b
cmpb $0x0, 0x28(%rsp)
movl 0x64(%rsp), %r15d
movl 0x60(%rsp), %ebp
je 0x19507
movq 0x560(%r14), %rax
movl %ebx, %ecx
shrl $0x6, %ecx
movq (%rax,%rcx,8), %rax
btq %rbx, %rax
jb 0x19507
leaq 0x30(%rsp), %rdx
movq $-0x1, (%rdx)
movq %r14, %rdi
movl %ebx, %esi
movl $0x2f, %ecx
callq 0x28024
testb %bpl, %bpl
movl 0x5c(%rsp), %ebp
je 0x1953b
movq 0x588(%r14), %rax
movl %ebx, %ecx
shrl $0x6, %ecx
movq (%rax,%rcx,8), %rax
btq %rbx, %rax
jb 0x1953b
leaq 0x30(%rsp), %rdx
movl $0xbf800000, (%rdx)     # imm = 0xBF800000
movq %r14, %rdi
movl %ebx, %esi
callq 0x2820e
testb %r15b, %r15b
je 0x19565
movq 0x5b0(%r14), %rax
movl %ebx, %ecx
shrl $0x6, %ecx
movq (%rax,%rcx,8), %rax
btq %rbx, %rax
jb 0x19565
movq %r14, %rdi
movl %ebx, %esi
movl $0xffffffff, %edx       # imm = 0xFFFFFFFF
callq 0x244ee
testb %bpl, %bpl
je 0x195bb
movq 0x5d8(%r14), %rax
movl %ebx, %ecx
shrl $0x6, %ecx
movq (%rax,%rcx,8), %rax
btq %rbx, %rax
jb 0x195bb
leaq 0x40(%rsp), %r15
movq %r15, -0x10(%r15)
leaq 0x20947(%rip), %rdx     # 0x39ed7
leaq 0x30(%rsp), %rdi
movq %rdx, %rsi
callq 0xc85e
leaq 0x30(%rsp), %rdx
movq %r14, %rdi
movl %ebx, %esi
callq 0x28572
movq 0x30(%rsp), %rdi
cmpq %r15, %rdi
je 0x195bb
callq 0x5410
movq 0x10(%rsp), %rdi
testq %rdi, %rdi
je 0x195ca
callq 0x5410
addq $0x108, %rsp            # imm = 0x108
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movl 0x634(%r14), %eax
cmpl $-0x1, %eax
je 0x19010
movq 0x18(%rsp), %rsi
cmpq 0x20(%rsp), %rsi
je 0x19660
movl %eax, (%rsi)
addq $0x4, %rsi
movq %rsi, 0x18(%rsp)
jmp 0x19010
movl 0x638(%r14), %eax
cmpl $-0x1, %eax
je 0x1902f
movq 0x18(%rsp), %rsi
cmpq 0x20(%rsp), %rsi
je 0x19676
movl %eax, (%rsi)
addq $0x4, %rsi
movq %rsi, 0x18(%rsp)
jmp 0x1902f
movl 0x63c(%r14), %eax
cmpl $-0x1, %eax
je 0x1904e
movq 0x18(%rsp), %rsi
cmpq 0x20(%rsp), %rsi
je 0x1968c
movl %eax, (%rsi)
addq $0x4, %rsi
movq %rsi, 0x18(%rsp)
jmp 0x1904e
leaq 0x634(%r14), %rdx
leaq 0x10(%rsp), %rdi
callq 0xca58
jmp 0x19010
leaq 0x638(%r14), %rdx
leaq 0x10(%rsp), %rdi
callq 0xca58
jmp 0x1902f
leaq 0x63c(%r14), %rdx
leaq 0x10(%rsp), %rdi
callq 0xca58
jmp 0x1904e
movq %rax, %rbx
movq 0x30(%rsp), %rdi
cmpq %r15, %rdi
jne 0x1974b
jmp 0x1975b
jmp 0x19758
jmp 0x19758
jmp 0x19758
jmp 0x19758
movq %rax, %rbx
movq 0x88(%rsp), %rdi
leaq 0x98(%rsp), %rax
jmp 0x19746
jmp 0x19758
jmp 0x19758
movq %rax, %rbx
movq 0x68(%rsp), %rdi
leaq 0x78(%rsp), %rax
jmp 0x19746
jmp 0x19758
movq %rax, %rbx
movq 0xc8(%rsp), %rdi
leaq 0xd8(%rsp), %rax
jmp 0x19746
jmp 0x19758
movq %rax, %rbx
movq 0xa8(%rsp), %rdi
leaq 0xb8(%rsp), %rax
jmp 0x19746
jmp 0x19758
movq %rax, %rbx
movq 0x30(%rsp), %rdi
testq %rdi, %rdi
jne 0x1974b
jmp 0x1975b
movq %rax, %rbx
movq 0xe8(%rsp), %rdi
leaq 0xf8(%rsp), %rax
cmpq %rax, %rdi
je 0x1975b
callq 0x5410
jmp 0x1975b
jmp 0x19758
jmp 0x19758
jmp 0x19758
movq %rax, %rbx
movq 0x10(%rsp), %rdi
testq %rdi, %rdi
je 0x1976a
callq 0x5410
movq %rbx, %rdi
callq 0x57d0