// File: /workspace/github_cpp_makefile_star2_O1/millanek[P]evo/./process_vcf_annotation_tools.h
// Function: Annotation::getAnnotationPerGeneDetails(std::vector<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>>>>, std::allocator<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>>>>>> const&)
void getAnnotationPerGeneDetails(const std::vector<std::vector<string> >& scaffoldAnnotation) {
        int thisGeneTranscriptCount;
        string previousGeneName = "";
        for (std::vector<string>::size_type i = 0; i != scaffoldAnnotation.size(); i++) {
            std::vector<string> annotLineVec = split(scaffoldAnnotation[i][0], '\t');
            int numDots = (int)std::count(annotLineVec[4].begin(), annotLineVec[4].end(), '.');
            std::string geneName;
            if (numDots == 4)  geneName = geneFromTranscript(annotLineVec[4]);
            else geneName = annotLineVec[4];
            if (previousGeneName == geneName) {
                thisGeneTranscriptCount++;
            } else {
                geneTranscriptCounts[previousGeneName] = thisGeneTranscriptCount;
                thisGeneTranscriptCount = 1;
                previousGeneName = geneName;
            }
            if (i == (scaffoldAnnotation.size()-1)) {   // Add the final gene in the scaffold
                geneTranscriptCounts[previousGeneName] = thisGeneTranscriptCount;
            }
        }
    }

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x78, %rsp
movq %rsi, %rbx
movq %rdi, %r14
leaq 0x30(%rsp), %rax
movq %rax, -0x10(%rax)
leaq 0x93179(%rip), %rdx     # 0xd1c7f
leaq 0x20(%rsp), %rdi
movq %rdx, %rsi
callq 0x28952
movq (%rbx), %rax
cmpq %rax, 0x8(%rbx)
je 0x3ecb8
addq $0x30, %r14
xorl %r12d, %r12d
leaq 0x60(%rsp), %r15
leaq (%r12,%r12,2), %rcx
movq (%rax,%rcx,8), %rsi
movq %r15, %rbp
movq %r15, %rdi
movl $0x9, %edx
callq 0x50624
movq 0x60(%rsp), %rcx
leaq 0x80(%rcx), %rsi
movq 0x88(%rcx), %rax
testq %rax, %rax
je 0x3ebcf
movq 0x80(%rcx), %rdx
xorl %edi, %edi
xorl %ecx, %ecx
xorl %r8d, %r8d
cmpb $0x2e, (%rdx,%rdi)
sete %r8b
addq %r8, %rcx
incq %rdi
cmpq %rdi, %rax
jne 0x3eb67
leaq 0x10(%rsp), %rax
movq %rax, (%rsp)
movq $0x0, 0x8(%rsp)
movb $0x0, 0x10(%rsp)
cmpl $0x4, %ecx
jne 0x3ebe6
leaq 0x40(%rsp), %r15
movq %r15, %rdi
callq 0x3ed36
movq %rsp, %rdi
movq %r15, %rsi
callq 0x8540
movq 0x40(%rsp), %rdi
leaq 0x50(%rsp), %rax
cmpq %rax, %rdi
je 0x3ebee
movq 0x50(%rsp), %rsi
incq %rsi
callq 0x8480
jmp 0x3ebee
leaq 0x10(%rsp), %rax
movq %rax, (%rsp)
movq $0x0, 0x8(%rsp)
movb $0x0, 0x10(%rsp)
movq %rsp, %rdi
callq 0x8270
movq 0x28(%rsp), %rdx
cmpq 0x8(%rsp), %rdx
jne 0x3ec11
testq %rdx, %rdx
je 0x3ec36
movq (%rsp), %rsi
movq 0x20(%rsp), %rdi
callq 0x8490
testl %eax, %eax
je 0x3ec36
movq %r14, %rdi
leaq 0x20(%rsp), %rsi
callq 0x3f0a2
movl %r13d, (%rax)
movl $0x1, %r13d
leaq 0x20(%rsp), %rdi
movq %rsp, %rsi
callq 0x8270
jmp 0x3ec39
incl %r13d
movq 0x8(%rbx), %rax
subq (%rbx), %rax
sarq $0x3, %rax
movabsq $-0x5555555555555555, %rcx # imm = 0xAAAAAAAAAAAAAAAB
imulq %rcx, %rax
decq %rax
cmpq %rax, %r12
jne 0x3ec6a
movq %r14, %rdi
leaq 0x20(%rsp), %rsi
callq 0x3f0a2
movl %r13d, (%rax)
movq (%rsp), %rdi
leaq 0x10(%rsp), %rax
cmpq %rax, %rdi
je 0x3ec85
movq 0x10(%rsp), %rsi
incq %rsi
callq 0x8480
movq %rbp, %rdi
callq 0x3123c
movq %rbp, %r15
incq %r12
movq (%rbx), %rax
movq 0x8(%rbx), %rcx
subq %rax, %rcx
sarq $0x3, %rcx
movabsq $-0x5555555555555555, %rdx # imm = 0xAAAAAAAAAAAAAAAB
imulq %rdx, %rcx
cmpq %rcx, %r12
jne 0x3eb2c
movq 0x20(%rsp), %rdi
leaq 0x30(%rsp), %rax
cmpq %rax, %rdi
je 0x3ecd4
movq 0x30(%rsp), %rsi
incq %rsi
callq 0x8480
addq $0x78, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
jmp 0x3ecea
movq %rax, %rbx
jmp 0x3ed12
movq %rax, %rbx
movq (%rsp), %rdi
leaq 0x10(%rsp), %rax
cmpq %rax, %rdi
je 0x3ed08
movq 0x10(%rsp), %rsi
incq %rsi
callq 0x8480
leaq 0x60(%rsp), %rdi
callq 0x3123c
movq 0x20(%rsp), %rdi
leaq 0x30(%rsp), %rax
cmpq %rax, %rdi
je 0x3ed2e
movq 0x30(%rsp), %rsi
incq %rsi
callq 0x8480
movq %rbx, %rdi
callq 0x8840