// File: /workspace/github_cpp_makefile_star2_O2/auton1[P]viterbi/variant_file.cpp
// Function: variant_file::get_contigs(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>>>&)
void variant_file::get_contigs(const string &contigs_file, vector<string> &contig_vector)
{
	if (contigs_file == "")
		LOG.error("Contig declarations in header are necessary for BCF conversion. Use --contigs <filename> to add contigs to the header.");

	ifstream contigs(contigs_file.c_str());
	if (!contigs.is_open())
		LOG.error("Could not open contigs file: " + contigs_file);

	string line;
	int contig_lines = 0;
	contig_vector.resize(0);

	while (getline(contigs, line))
	{
		if (line.find("##contig=")==string::npos)
			LOG.error("Contigs file must contain only contig header lines.");

		contig_vector.push_back(line);
		contig_lines++;
	}

	contigs.close();
	LOG.printLOG("Including "+header::int2str(contig_lines)+" header lines from the contig file.\n");
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x2e8, %rsp            # imm = 0x2E8
movq %rdx, %rbx
movq %rsi, %r14
leaq 0x2046f(%rip), %rsi     # 0x2ee37
movq %r14, %rdi
callq 0x96f3
testb %al, %al
je 0xea14
leaq 0x1ecd1(%rip), %rsi     # 0x2d6ac
leaq 0xa0(%rsp), %rdi
leaq 0xe0(%rsp), %rdx
callq 0x5160
leaq 0x32ad9(%rip), %rdi     # 0x414d0
leaq 0xa0(%rsp), %rsi
pushq $0x1
popq %rdx
callq 0x2bf18
leaq 0xa0(%rsp), %rdi
callq 0x5908
movq (%r14), %rsi
leaq 0xe0(%rsp), %rdi
pushq $0x8
popq %rdx
callq 0x5860
leaq 0x158(%rsp), %rdi
callq 0x50d0
testb %al, %al
jne 0xea73
leaq 0x1ece4(%rip), %rsi     # 0x2d723
leaq 0x80(%rsp), %rdi
movq %r14, %rdx
callq 0x967d
leaq 0x32a7a(%rip), %rdi     # 0x414d0
leaq 0x80(%rsp), %rsi
pushq $0x1
popq %rdx
callq 0x2bf18
leaq 0x80(%rsp), %rdi
callq 0x5908
leaq 0x70(%rsp), %rax
movq %rax, -0x10(%rax)
andq $0x0, -0x8(%rax)
movb $0x0, (%rax)
xorl %r14d, %r14d
movq %rbx, %rdi
xorl %esi, %esi
callq 0xfd72
leaq 0xe0(%rsp), %r15
leaq 0x60(%rsp), %r12
leaq 0x1ec9c(%rip), %r13     # 0x2d741
leaq 0xc0(%rsp), %rbp
movq %r15, %rdi
movq %r12, %rsi
callq 0x5090
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
testb $0x5, 0x20(%rax,%rcx)
jne 0xeb15
movq %r12, %rdi
movq %r13, %rsi
xorl %edx, %edx
callq 0x58e0
cmpq $-0x1, %rax
jne 0xeb05
movq %rbp, %rdi
leaq 0x1ec68(%rip), %rsi     # 0x2d74b
movq %rsp, %rdx
callq 0x5160
leaq 0x329de(%rip), %rdi     # 0x414d0
movq %rbp, %rsi
pushq $0x1
popq %rdx
callq 0x2bf18
movq %rbp, %rdi
callq 0x5908
movq %rbx, %rdi
movq %r12, %rsi
callq 0xfda2
incl %r14d
jmp 0xeaad
leaq 0xe0(%rsp), %rdi
callq 0x50a0
leaq 0x20(%rsp), %rdi
pushq $-0x1
popq %rdx
movl %r14d, %esi
callq 0x12c9c
leaq 0x1ec46(%rip), %rsi     # 0x2d77f
movq %rsp, %rdi
leaq 0x20(%rsp), %rdx
callq 0x98d5
leaq 0x1ec3d(%rip), %rdx     # 0x2d78a
leaq 0x40(%rsp), %rdi
movq %rsp, %rsi
callq 0x98b6
leaq 0x3296f(%rip), %rdi     # 0x414d0
leaq 0x40(%rsp), %rsi
callq 0x2beca
leaq 0x40(%rsp), %rdi
callq 0x5908
movq %rsp, %rdi
callq 0x5908
leaq 0x20(%rsp), %rdi
callq 0x5908
leaq 0x60(%rsp), %rdi
callq 0x5908
leaq 0xe0(%rsp), %rdi
callq 0x58f8
addq $0x2e8, %rsp            # imm = 0x2E8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %rbx
leaq 0x80(%rsp), %rdi
jmp 0xec1f
movq %rax, %rbx
jmp 0xec24
movq %rax, %rbx
leaq 0xa0(%rsp), %rdi
callq 0x5908
jmp 0xec31
movq %rax, %rbx
jmp 0xec31
movq %rax, %rbx
leaq 0x40(%rsp), %rdi
callq 0x5908
jmp 0xebeb
movq %rax, %rbx
movq %rsp, %rdi
callq 0x5908
jmp 0xebf8
movq %rax, %rbx
leaq 0x20(%rsp), %rdi
jmp 0xec10
jmp 0xec17
jmp 0xec17
jmp 0xec17
movq %rax, %rbx
leaq 0xc0(%rsp), %rdi
callq 0x5908
jmp 0xec1a
movq %rax, %rbx
leaq 0x60(%rsp), %rdi
callq 0x5908
leaq 0xe0(%rsp), %rdi
callq 0x58f8
movq %rbx, %rdi
callq 0x5800
nop