// File: /workspace/github_cpp_makefile_star2_O2/ncbi[P]amr/gff.cpp
// Function: GFF_sp::Annot::Annot(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&)
Annot::Annot (const string &fName)
{
	if (fName. empty ())
		throw runtime_error ("Empty BED file name");
	
  LineInput f (fName /*, 100 * 1024, 1*/);
  while (f. nextLine ())
  {
    trim (f. line);
    if (   f. line. empty () 
        || f. line [0] == '#'
       )
      continue;

    replace (f. line, ' ', '_');  // to use '\t' as delimiter

   	const string errorS ("File " + fName + ", " + f. lineStr () + ": ");

    string contig, prot;
    size_t start, stop;
    double score;
    char strand = ' ';
    static Istringstream iss;
    iss. reset (f. line);
    iss >> contig >> start >> stop >> prot >> score >> strand;

    if (strand == ' ')
    	throw runtime_error (errorS + "at least 5 fields are expected in each line");

	  for (const char c : contig)
	  	if (! printable (c))
	  		throw runtime_error (errorS + "Non-printable character in the sequence identifier: " + to_string (c));

    if (start >= stop)
    	throw runtime_error (errorS + "start should be less than stop");

    if (   strand != '+'
        && strand != '-'
       )
    	throw runtime_error (errorS + "strand should be '+' or '-'");
           
	  trim (prot, '_');
	  ASSERT (! prot. empty ());
    prot2loci [prot] << Locus ((size_t) f. lineNum, contig, start, stop, strand == '+', false/*partial*/, 0, noString, noString);
  }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x4f8, %rsp            # imm = 0x4F8
leaq 0x356d8(%rip), %rax     # 0x83b50
movq %rax, (%rdi)
leaq 0x10(%rdi), %rax
andl $0x0, 0x10(%rdi)
andq $0x0, 0x18(%rdi)
movq %rax, 0x20(%rdi)
movq %rax, 0x28(%rdi)
andq $0x0, 0x30(%rdi)
leaq 0x40(%rdi), %rax
andl $0x0, 0x40(%rdi)
andq $0x0, 0x48(%rdi)
movq %rax, 0x50(%rdi)
movq %rax, 0x58(%rdi)
andq $0x0, 0x60(%rdi)
movq %rdi, 0x60(%rsp)
leaq 0x8(%rdi), %rax
movq %rax, 0x28(%rsp)
xorl %eax, %eax
cmpq %rax, 0x8(%rsi)
je 0x4eab9
movq %rsi, %rbx
leaq 0x250(%rsp), %rdi
xorl %edx, %edx
callq 0x1d20a
leaq 0x4b8(%rsp), %r14
leaq 0x250(%rsp), %r15
pushq $0x5f
popq %r12
leaq 0x40(%rsp), %r13
leaq 0xd8(%rsp), %rbp
movq %rbx, 0x68(%rsp)
movq %r15, %rdi
callq 0x219d4
testb %al, %al
je 0x4e82c
movq %r14, %rdi
callq 0x3c32f
cmpq $0x0, 0x4c0(%rsp)
je 0x4e501
movq 0x4b8(%rsp), %rax
cmpb $0x23, (%rax)
je 0x4e501
movq %r14, %rdi
pushq $0x20
popq %rsi
movl %r12d, %edx
callq 0x236cf
movq %r13, %rdi
leaq 0x10cf4(%rip), %rsi     # 0x5f23d
movq %rbx, %rdx
callq 0x1b8b7
leaq 0x8(%rsp), %rdi
movq %r13, %rsi
leaq 0xacbe(%rip), %rdx      # 0x5921e
callq 0x1b92d
leaq 0x78(%rsp), %rbx
movq %rbx, %rdi
movq %r15, %rsi
pushq $0x1
popq %rdx
callq 0x4ff74
movq %rbp, %rdi
leaq 0x8(%rsp), %rsi
movq %rbx, %rdx
callq 0x1ca3c
leaq 0x98(%rsp), %rdi
movq %rbp, %rsi
leaq 0xd376(%rip), %rdx      # 0x5b910
callq 0x1b92d
movq %rbp, %rdi
callq 0xbb68
movq %rbx, %rdi
callq 0xbb68
leaq 0x8(%rsp), %rdi
callq 0xbb68
movq %r13, %rdi
callq 0xbb68
leaq 0x18(%rsp), %rax
movq %rax, 0x8(%rsp)
andq $0x0, 0x10(%rsp)
xorl %ecx, %ecx
movb %cl, 0x18(%rsp)
leaq 0x50(%rsp), %rax
movq %rax, 0x40(%rsp)
andq $0x0, 0x48(%rsp)
movb %cl, 0x50(%rsp)
movb $0x20, 0x5(%rsp)
movb 0x36792(%rip), %al      # 0x84d88
testb %al, %al
je 0x4e7d4
leaq 0x36603(%rip), %rbx     # 0x84c08
movq %rbx, %rdi
movq %r14, %rsi
callq 0x1d2f2
movq %rbx, %rdi
leaq 0x8(%rsp), %rsi
callq 0xb730
movq %rax, %rdi
leaq 0x38(%rsp), %rsi
callq 0xb360
movq %rax, %rdi
leaq 0x30(%rsp), %rsi
callq 0xb360
movq %rax, %rdi
movq %r13, %rsi
callq 0xb730
movq %rax, %rdi
leaq 0x188(%rsp), %rsi
callq 0xb3f0
movq %rax, %rdi
leaq 0x5(%rsp), %rsi
callq 0xb770
movzbl 0x5(%rsp), %eax
cmpl $0x20, %eax
je 0x4e920
movq 0x8(%rsp), %rcx
movq 0x10(%rsp), %rdx
xorl %esi, %esi
cmpq %rsi, %rdx
je 0x4e695
movsbl (%rcx,%rsi), %r14d
leal -0x20(%r14), %edi
incq %rsi
cmpb $0x5f, %dil
jb 0x4e679
jmp 0x4e84b
movq 0x38(%rsp), %rcx
cmpq 0x30(%rsp), %rcx
jae 0x4e8c9
cmpl $0x2b, %eax
je 0x4e6b3
cmpl $0x2d, %eax
jne 0x4ea65
movq %r13, %rdi
movl %r12d, %esi
callq 0x4ffcf
callq 0xb060
andl $0x0, (%rax)
cmpq $0x0, 0x48(%rsp)
je 0x4e977
movq 0x28(%rsp), %rdi
movq %r13, %rsi
callq 0x4fed2
movq %rax, 0x70(%rsp)
movl 0x4b0(%rsp), %ebx
movq 0x38(%rsp), %r13
movq 0x30(%rsp), %r12
movb 0x5(%rsp), %r15b
leaq 0x168(%rsp), %rdi
leaq 0x363ef(%rip), %rbp     # 0x84af8
movq %rbp, %rsi
callq 0xb7b0
leaq 0x190(%rsp), %r14
movq %r14, %rdi
movq %rbp, %rsi
callq 0xb7b0
xorl %r9d, %r9d
cmpb $0x2b, %r15b
sete %r9b
leaq 0xd8(%rsp), %r15
movq %r15, %rdi
movq %rbx, %rsi
leaq 0x8(%rsp), %rdx
movq %r13, %rcx
movq %r12, %r8
pushq %r14
leaq 0x170(%rsp), %rax
pushq %rax
pushq $0x0
pushq $0x0
callq 0x4bca4
addq $0x20, %rsp
movq 0x70(%rsp), %rdi
movq %r15, %rbp
movq %r15, %rsi
callq 0x4ff38
movq 0x68(%rsp), %rbx
leaq 0x4b8(%rsp), %r14
leaq 0x250(%rsp), %r15
pushq $0x5f
popq %r12
leaq 0x40(%rsp), %r13
movq %rbp, %rdi
callq 0x4ff50
leaq 0x190(%rsp), %rdi
callq 0xbb68
leaq 0x168(%rsp), %rdi
callq 0xbb68
movq %r13, %rdi
callq 0xbb68
leaq 0x8(%rsp), %rdi
callq 0xbb68
leaq 0x98(%rsp), %rdi
callq 0xbb68
jmp 0x4e501
leaq 0x365ad(%rip), %rdi     # 0x84d88
callq 0xba60
testl %eax, %eax
je 0x4e5fe
leaq 0x36419(%rip), %rdi     # 0x84c08
callq 0x1d260
leaq -0x314b1(%rip), %rdi    # 0x1d34a
leaq 0x36406(%rip), %rsi     # 0x84c08
leaq 0x35daf(%rip), %rdx     # 0x845b8
callq 0xb500
leaq 0x36573(%rip), %rdi     # 0x84d88
callq 0xb3e0
leaq 0x4b8(%rsp), %r14
leaq 0x40(%rsp), %r13
jmp 0x4e5fe
leaq 0x250(%rsp), %rdi
callq 0x1d368
addq $0x4f8, %rsp            # imm = 0x4F8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
pushq $0x10
popq %rdi
callq 0xb300
movq %rax, %r15
leaq 0x1086b(%rip), %rdx     # 0x5f0c8
leaq 0x78(%rsp), %rdi
leaq 0x98(%rsp), %rsi
callq 0x1c88d
leaq 0xb8(%rsp), %rdi
movl %r14d, %esi
callq 0x1caa3
leaq 0xd8(%rsp), %rdi
leaq 0x78(%rsp), %rsi
leaq 0xb8(%rsp), %rdx
callq 0x1ca3c
movb $0x1, %bpl
leaq 0xd8(%rsp), %rsi
movq %r15, %rdi
callq 0xb940
xorl %ebp, %ebp
movq 0x35733(%rip), %rsi     # 0x83fe8
movq 0x356a4(%rip), %rdx     # 0x83f60
movq %r15, %rdi
callq 0xb9d0
jmp 0x4eae9
pushq $0x10
popq %rdi
callq 0xb300
movq %rax, %r14
leaq 0x109a8(%rip), %rdx     # 0x5f283
leaq 0xd8(%rsp), %rdi
leaq 0x98(%rsp), %rsi
callq 0x1c88d
movb $0x1, %bpl
leaq 0xd8(%rsp), %rsi
movq %r14, %rdi
callq 0xb940
xorl %ebp, %ebp
movq 0x356dc(%rip), %rsi     # 0x83fe8
movq 0x3564d(%rip), %rdx     # 0x83f60
movq %r14, %rdi
callq 0xb9d0
jmp 0x4eae9
pushq $0x10
popq %rdi
callq 0xb300
movq %rax, %r14
leaq 0x10925(%rip), %rdx     # 0x5f257
leaq 0xd8(%rsp), %rdi
leaq 0x98(%rsp), %rsi
callq 0x1c88d
movb $0x1, %bpl
leaq 0xd8(%rsp), %rsi
movq %r14, %rdi
callq 0xb940
xorl %ebp, %ebp
movq 0x35685(%rip), %rsi     # 0x83fe8
movq 0x355f6(%rip), %rdx     # 0x83f60
movq %r14, %rdi
callq 0xb9d0
jmp 0x4eae9
callq 0xb6c0
testl %eax, %eax
jne 0x4ea5d
leaq 0x10557(%rip), %rsi     # 0x5eee2
leaq 0x210(%rsp), %rdi
leaq 0x7(%rsp), %rdx
callq 0x1b7b6
leaq 0x1f0(%rsp), %rdi
movl $0x198, %esi            # imm = 0x198
callq 0x1caa3
leaq 0x230(%rsp), %rdi
leaq 0x210(%rsp), %rsi
leaq 0x1f0(%rsp), %rdx
callq 0x1ca3c
leaq 0xb210(%rip), %rdx      # 0x59be3
leaq 0xb8(%rsp), %rdi
leaq 0x230(%rsp), %rsi
callq 0x1b92d
leaq 0x108b3(%rip), %rsi     # 0x5f2a2
leaq 0x1b0(%rsp), %rdi
leaq 0x6(%rsp), %rdx
callq 0x1b7b6
leaq 0xcf36(%rip), %rdx      # 0x5b93e
leaq 0x1d0(%rsp), %rdi
leaq 0x1b0(%rsp), %rsi
callq 0x1b92d
leaq 0x78(%rsp), %rdi
leaq 0xb8(%rsp), %rsi
leaq 0x1d0(%rsp), %rdx
callq 0x1ca3c
leaq 0x107ee(%rip), %rdx     # 0x5f22c
leaq 0xd8(%rsp), %rdi
leaq 0x78(%rsp), %rsi
callq 0x1b92d
leaq 0xd8(%rsp), %rdi
callq 0x224fc
pushq $0x1
popq %rdi
callq 0xb6d0
pushq $0x10
popq %rdi
callq 0xb300
movq %rax, %r14
leaq 0x106f8(%rip), %rdx     # 0x5f16f
leaq 0xd8(%rsp), %rdi
leaq 0x98(%rsp), %rsi
callq 0x1c88d
movb $0x1, %bpl
leaq 0xd8(%rsp), %rsi
movq %r14, %rdi
callq 0xb940
xorl %ebp, %ebp
movq 0x35540(%rip), %rsi     # 0x83fe8
movq 0x354b1(%rip), %rdx     # 0x83f60
movq %r14, %rdi
callq 0xb9d0
jmp 0x4eae9
pushq $0x10
popq %rdi
callq 0xb300
movq %rax, %r14
leaq 0x10778(%rip), %rsi     # 0x5f243
movq %rax, %rdi
callq 0xb260
movq 0x3550e(%rip), %rsi     # 0x83fe8
movq 0x3547f(%rip), %rdx     # 0x83f60
movq %r14, %rdi
callq 0xb9d0
movq %rax, %rbx
leaq 0x36295(%rip), %rdi     # 0x84d88
callq 0xb3d0
jmp 0x4ecd6
movq %rax, %rbx
leaq 0xd8(%rsp), %rdi
callq 0xbb68
jmp 0x4eb12
movq %rax, %rbx
leaq 0x78(%rsp), %rdi
callq 0xbb68
jmp 0x4eb21
movq %rax, %rbx
leaq 0x1d0(%rsp), %rdi
callq 0xbb68
jmp 0x4eb33
movq %rax, %rbx
leaq 0x1b0(%rsp), %rdi
callq 0xbb68
jmp 0x4eb45
movq %rax, %rbx
leaq 0xb8(%rsp), %rdi
callq 0xbb68
jmp 0x4eb57
movq %rax, %rbx
leaq 0x230(%rsp), %rdi
callq 0xbb68
jmp 0x4eb7b
jmp 0x4eb8a
movq %rax, %rbx
movq %r14, %rdi
callq 0xb470
jmp 0x4ed04
movq %rax, %rbx
leaq 0x1f0(%rsp), %rdi
callq 0xbb68
jmp 0x4eb95
movq %rax, %rbx
jmp 0x4ed04
movq %rax, %rbx
leaq 0x210(%rsp), %rdi
jmp 0x4ec47
movq %rax, %rbx
leaq 0xd8(%rsp), %rdi
callq 0xbb68
testb %bpl, %bpl
je 0x4ecd6
jmp 0x4ec01
jmp 0x4ebfe
jmp 0x4ecc6
movq %rax, %rbx
leaq 0xd8(%rsp), %rdi
callq 0xbb68
testb %bpl, %bpl
jne 0x4ebe1
jmp 0x4ecd6
movq %rax, %rbx
jmp 0x4ec01
movq %rax, %rbx
leaq 0xd8(%rsp), %rdi
callq 0xbb68
testb %bpl, %bpl
je 0x4ecd6
jmp 0x4ec01
movq %rax, %rbx
movq %r14, %rdi
jmp 0x4ecd1
movq %rax, %rbx
leaq 0xd8(%rsp), %rdi
callq 0x4ff50
jmp 0x4ec1e
movq %rax, %rbx
leaq 0x190(%rsp), %rdi
callq 0xbb68
jmp 0x4ec3f
movq %rax, %rbx
jmp 0x4ec7a
jmp 0x4ecc6
movq %rax, %rbx
jmp 0x4ec61
movq %rax, %rbx
leaq 0x168(%rsp), %rdi
callq 0xbb68
jmp 0x4ecd6
movq %rax, %rbx
leaq 0xd8(%rsp), %rdi
callq 0xbb68
leaq 0x78(%rsp), %rdi
callq 0xbb68
jmp 0x4ec70
movq %rax, %rbx
leaq 0x8(%rsp), %rdi
callq 0xbb68
leaq 0x40(%rsp), %rdi
jmp 0x4ecf2
jmp 0x4ecaa
movq %rax, %rbx
leaq 0xd8(%rsp), %rdi
callq 0xbb68
jmp 0x4ec9b
movq %rax, %rbx
movb $0x1, %bpl
leaq 0xb8(%rsp), %rdi
callq 0xbb68
jmp 0x4ecb5
movq %rax, %rbx
jmp 0x4ecf7
movq %rax, %rbx
movb $0x1, %bpl
leaq 0x78(%rsp), %rdi
callq 0xbb68
testb %bpl, %bpl
jne 0x4ecce
jmp 0x4ecd6
movq %rax, %rbx
jmp 0x4ecd6
movq %rax, %rbx
movq %r15, %rdi
callq 0xb470
leaq 0x40(%rsp), %rdi
callq 0xbb68
leaq 0x8(%rsp), %rdi
callq 0xbb68
leaq 0x98(%rsp), %rdi
callq 0xbb68
leaq 0x250(%rsp), %rdi
callq 0x1d368
movq 0x60(%rsp), %rdi
addq $0x38, %rdi
callq 0x1be2a
movq 0x28(%rsp), %rdi
callq 0x5003e
movq %rbx, %rdi
callq 0xba30