// File: /workspace/github_cpp_makefile_star2_O3/auton1[P]viterbi/header.cpp
// Function: header::add_CONTIG_descriptor(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, int)
void header::add_CONTIG_descriptor(const string &in, int index)
{
	size_t found_end=in.find_last_of(">");
	string details = in.substr(0, found_end);

	vector<string> tokens;
	tokenize(details, ',', tokens);
	Field_description I;
	I.Field = "contig";
	bool id_found = false;
	vector<string> entry;

	for (unsigned int ui=0; ui<tokens.size(); ui++)
	{
		tokenize(tokens[ui], '=', entry);
		if (entry[0] == "ID")
		{
			I.ID = entry[1];
			id_found = true;
		}
		else if (entry[0] == "length") I.Length = entry[1];
		else if (entry[0] == "assembly") I.Assembly = entry[1];
		else
		{
			if (I.Other != "")
				I.Other += ",";
			I.Other += tokens[ui];
		}
	}
	if (id_found == false)
		LOG.warning("CONTIG declaration found without ID: "+ in + "\n");

	parsed_lines.push_back(I);
	CONTIG_map[index] = I;
	CONTIG_reverse_map[I.ID] = index;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x208, %rsp            # imm = 0x208
movq %rsi, %r14
movq %rdi, %r12
movl %edx, 0xc(%rsp)
leaq 0x22be0(%rip), %rsi     # 0x38bb8
movl $0x1, %ecx
movq %r14, %rdi
movq $-0x1, %rdx
callq 0x5890
leaq 0x98(%rsp), %rbx
movq %rbx, %rdi
movq %r14, %rsi
xorl %edx, %edx
movq %rax, %rcx
callq 0x5480
xorps %xmm0, %xmm0
leaq 0x30(%rsp), %rdx
movaps %xmm0, (%rdx)
movq $0x0, 0x10(%rdx)
movq %rbx, %rdi
movl $0x2c, %esi
callq 0x16a0a
leaq 0xb8(%rsp), %rdi
callq 0x174bc
leaq 0xb8(%rsp), %rdi
movq 0x8(%rdi), %rdx
leaq 0x22e61(%rip), %rcx     # 0x38ea5
movl $0x6, %r8d
xorl %esi, %esi
callq 0x5690
xorps %xmm0, %xmm0
movaps %xmm0, 0x10(%rsp)
movq $0x0, 0x20(%rsp)
movq 0x30(%rsp), %rdi
cmpq %rdi, 0x38(%rsp)
je 0x1619f
movq %r14, 0x48(%rsp)
movq %r12, 0x50(%rsp)
movl $0x1, %r12d
xorl %r15d, %r15d
leaq 0x10(%rsp), %r13
leaq 0x229e9(%rip), %rbp     # 0x38a7a
leaq 0x22e14(%rip), %rbx     # 0x38eac
xorl %r14d, %r14d
shlq $0x5, %r15
addq %r15, %rdi
movl $0x3d, %esi
movq %r13, %rdx
callq 0x16a0a
movq 0x10(%rsp), %rdi
movq %rbp, %rsi
callq 0x50e0
movq 0x10(%rsp), %rsi
testl %eax, %eax
je 0x16135
movq %rsi, %rdi
movq %rbx, %rsi
callq 0x50e0
movq 0x10(%rsp), %rsi
testl %eax, %eax
je 0x1614b
movq %rsi, %rdi
leaq 0x22dd0(%rip), %rsi     # 0x38eb3
callq 0x50e0
testl %eax, %eax
je 0x16155
leaq 0x1e8(%rsp), %rdi
leaq 0x23ddc(%rip), %rsi     # 0x39ed7
callq 0x50e0
testl %eax, %eax
je 0x16118
leaq 0x1e8(%rsp), %rdi
leaq 0x22b79(%rip), %rsi     # 0x38c8c
callq 0x5870
movq 0x30(%rsp), %rax
movq (%rax,%r15), %rsi
movq 0x8(%rax,%r15), %rdx
leaq 0x1e8(%rsp), %rdi
callq 0x50f0
jmp 0x1616b
addq $0x20, %rsi
movb $0x1, %r14b
leaq 0xd8(%rsp), %rdi
callq 0x51f0
jmp 0x1616b
leaq 0x168(%rsp), %rdi
jmp 0x16162
movq 0x10(%rsp), %rsi
leaq 0x188(%rsp), %rdi
addq $0x20, %rsi
callq 0x51f0
movl %r12d, %r15d
movq 0x30(%rsp), %rdi
movq 0x38(%rsp), %rax
subq %rdi, %rax
sarq $0x5, %rax
incl %r12d
cmpq %r15, %rax
ja 0x1609b
testb $0x1, %r14b
movq 0x50(%rsp), %r12
movq 0x48(%rsp), %r14
jne 0x1623f
leaq 0x22d16(%rip), %rsi     # 0x38ebc
leaq 0x78(%rsp), %rdi
movq %r14, %rdx
callq 0xb777
leaq 0x21f9c(%rip), %rsi     # 0x38156
leaq 0x78(%rsp), %rdi
callq 0x5870
leaq 0x68(%rsp), %r14
movq %r14, -0x10(%r14)
movq (%rax), %rdx
movq %rax, %rcx
addq $0x10, %rcx
cmpq %rcx, %rdx
je 0x161eb
movq %rdx, 0x58(%rsp)
movq (%rcx), %rdx
movq %rdx, 0x68(%rsp)
jmp 0x161f2
movups (%rcx), %xmm0
movups %xmm0, (%r14)
movq 0x8(%rax), %rdx
leaq 0x58(%rsp), %rsi
movq %rdx, 0x8(%rsi)
movq %rcx, (%rax)
movq $0x0, 0x8(%rax)
movb $0x0, 0x10(%rax)
leaq 0x33293(%rip), %rdi     # 0x494a8
callq 0x37146
movq 0x58(%rsp), %rdi
cmpq %r14, %rdi
je 0x16229
callq 0x5410
leaq 0x88(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x1623f
callq 0x5410
leaq 0x40(%r12), %rdi
leaq 0xb8(%rsp), %rsi
callq 0x17752
leaq 0xf0(%r12), %rdi
leaq 0xc(%rsp), %rsi
callq 0x17782
movq %rax, %rbx
leaq 0xb8(%rsp), %r15
movq %rax, %rdi
movq %r15, %rsi
callq 0x51f0
leaq 0x20(%rbx), %rdi
leaq 0xd8(%rsp), %r14
movq %r14, %rsi
callq 0x51f0
leaq 0x100(%rsp), %rsi
movq -0x8(%rsi), %rax
movq %rax, 0x40(%rbx)
leaq 0x48(%rbx), %rdi
callq 0x51f0
leaq 0x68(%rbx), %rdi
leaq 0x120(%rsp), %rsi
callq 0x51f0
movl 0x140(%rsp), %eax
movl %eax, 0x88(%rbx)
movl $0x90, %esi
leaq (%rbx,%rsi), %rdi
addq %r15, %rsi
callq 0x51f0
movl $0xb0, %esi
leaq (%rbx,%rsi), %rdi
addq %r15, %rsi
callq 0x51f0
movl $0xd0, %esi
leaq (%rbx,%rsi), %rdi
addq %r15, %rsi
callq 0x51f0
movl $0xf0, %esi
leaq (%rbx,%rsi), %rdi
addq %r15, %rsi
callq 0x51f0
movl $0x110, %esi            # imm = 0x110
leaq (%rbx,%rsi), %rdi
addq %r15, %rsi
callq 0x51f0
movl $0x130, %eax            # imm = 0x130
addq %rax, %rbx
addq %rax, %r15
movq %rbx, %rdi
movq %r15, %rsi
callq 0x51f0
movl 0xc(%rsp), %ebx
addq $0x120, %r12            # imm = 0x120
movq %r12, %rdi
movq %r14, %rsi
callq 0x177e8
movl %ebx, (%rax)
leaq 0x10(%rsp), %rdi
callq 0xc4da
leaq 0xb8(%rsp), %rdi
callq 0xfb7c
leaq 0x30(%rsp), %rdi
callq 0xc4da
leaq 0xa8(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x1637e
callq 0x5410
addq $0x208, %rsp            # imm = 0x208
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %rbx
movq 0x58(%rsp), %rdi
cmpq %r14, %rdi
je 0x163a7
callq 0x5410
jmp 0x163a7
movq %rax, %rbx
leaq 0x88(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x163d2
callq 0x5410
jmp 0x163d2
jmp 0x163cf
movq %rax, %rbx
jmp 0x163dc
jmp 0x163c8
movq %rax, %rbx
jmp 0x163e9
jmp 0x163cf
movq %rax, %rbx
leaq 0x10(%rsp), %rdi
callq 0xc4da
leaq 0xb8(%rsp), %rdi
callq 0xfb7c
leaq 0x30(%rsp), %rdi
callq 0xc4da
leaq 0xa8(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x16409
callq 0x5410
movq %rbx, %rdi
callq 0x57d0
nop