// File: /workspace/github_cpp_makefile_star2_O3/millanek[P]evo/./process_vcf_annotation_tools.h
// Function: Annotation::loadAnnotationMap[abi:cxx11](std::basic_ifstream<char, std::char_traits<char>>*&, bool)
std::map<string, std::vector<std::vector<string> > > loadAnnotationMap(std::ifstream*& geneFile, const bool bUsePartial) {
        std::map<string, std::vector<std::vector<string> > > annotationMap;
        std::vector<std::vector<string> > annotation;
        string line;
        std::vector<string> currentTranscript;
        getline(*geneFile, line);
        currentTranscript.push_back(line);
        std::vector<string> annotLineVec = split(line, '\t');
        std::vector<string> findIfPartial = split(annotLineVec[4], '-');
        string currentScaffold = annotLineVec[0];
        bool bThisTranscriptPartial; string currentTranscriptName = getTranscriptName(annotLineVec[4], bThisTranscriptPartial);
        while (getline(*geneFile, line)) {
            std::vector<string> annotLineVec = split(line, '\t');
            bool bCurrentLinePartial = false; string currentLineTranscriptName = getTranscriptName(annotLineVec[4], bCurrentLinePartial);
            if (bCurrentLinePartial)
                bThisTranscriptPartial = true;
            if (annotLineVec[0] == currentScaffold) {
                if (currentLineTranscriptName == currentTranscriptName) {
                    currentTranscript.push_back(line);
                } else {
                    if (!bThisTranscriptPartial || bUsePartial)
                        annotation.push_back(currentTranscript);
                    currentTranscript.clear();
                    currentTranscript.push_back(line);
                    currentTranscriptName = currentLineTranscriptName;
                    bThisTranscriptPartial = bCurrentLinePartial;
                }
            } else {
                if (!bThisTranscriptPartial || bUsePartial)
                    annotation.push_back(currentTranscript);
                annotationMap[currentScaffold] = annotation;
                annotation.clear();
                currentTranscript.clear();
                currentTranscript.push_back(line);
                currentScaffold = annotLineVec[0];
                currentTranscriptName = currentLineTranscriptName;
                bThisTranscriptPartial = bCurrentLinePartial;
            }
        }
        return annotationMap;
    }

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x128, %rsp            # imm = 0x128
movl %ecx, 0xc(%rsp)
movq %rsi, 0x50(%rsp)
leaq 0x8(%rdi), %rax
movl $0x0, 0x8(%rdi)
xorl %ecx, %ecx
movq %rcx, 0x10(%rdi)
movq %rax, 0x18(%rdi)
movq %rax, 0x20(%rdi)
movq %rdi, 0x28(%rsp)
movq %rcx, 0x28(%rdi)
movq %rcx, 0x40(%rsp)
xorps %xmm0, %xmm0
movaps %xmm0, 0x30(%rsp)
leaq 0x88(%rsp), %rax
movq %rax, -0x10(%rax)
movq %rcx, -0x8(%rax)
movb $0x0, (%rax)
movq %rcx, 0x20(%rsp)
movaps %xmm0, 0x10(%rsp)
movq %rdx, 0xd8(%rsp)
movq (%rdx), %rbx
movq (%rbx), %rax
movq -0x18(%rax), %rdi
addq %rbx, %rdi
movl $0xa, %esi
callq 0x8450
movsbl %al, %edx
leaq 0x78(%rsp), %rsi
movq %rbx, %rdi
callq 0x8870
leaq 0x10(%rsp), %rdi
leaq 0x78(%rsp), %rsi
callq 0x3133c
leaq 0xe0(%rsp), %rdi
leaq 0x78(%rsp), %rsi
movl $0x9, %edx
callq 0x4d650
movq 0xe0(%rsp), %rsi
subq $-0x80, %rsi
leaq 0x110(%rsp), %rdi
movl $0x2d, %edx
callq 0x4d650
movq 0xe0(%rsp), %rax
leaq 0x68(%rsp), %rcx
movq %rcx, -0x10(%rcx)
movq (%rax), %rsi
movq 0x8(%rax), %rdx
addq %rsi, %rdx
leaq 0x58(%rsp), %rdi
callq 0x2ba06
movq 0xe0(%rsp), %rdx
subq $-0x80, %rdx
leaq 0xb8(%rsp), %rdi
leaq 0xa(%rsp), %rcx
movq 0x50(%rsp), %rsi
callq 0x3bae8
leaq 0x78(%rsp), %r12
leaq 0xf8(%rsp), %r13
leaq 0x98(%rsp), %rbx
movq 0xd8(%rsp), %rax
movq (%rax), %rbp
movq (%rbp), %rax
movq -0x18(%rax), %rdi
addq %rbp, %rdi
movl $0xa, %esi
callq 0x8450
movsbl %al, %edx
movq %rbp, %rdi
movq %r12, %rsi
callq 0x8870
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
testb $0x5, 0x20(%rax,%rcx)
jne 0x3b90c
movq %r13, %rdi
movq %r12, %rsi
movl $0x9, %edx
callq 0x4d650
movb $0x0, 0xb(%rsp)
movq 0xf8(%rsp), %rdx
subq $-0x80, %rdx
movq %rbx, %rdi
movq 0x50(%rsp), %rsi
leaq 0xb(%rsp), %rcx
callq 0x3bae8
cmpb $0x1, 0xb(%rsp)
jne 0x3b713
movb $0x1, 0xa(%rsp)
movq 0xf8(%rsp), %rax
movq 0x8(%rax), %rdx
cmpq 0x60(%rsp), %rdx
jne 0x3b744
testq %rdx, %rdx
je 0x3b815
movq 0x58(%rsp), %rsi
movq (%rax), %rdi
callq 0x8490
testl %eax, %eax
je 0x3b815
movb 0xa(%rsp), %al
xorb $0x1, %al
orb 0xc(%rsp), %al
cmpb $0x1, %al
jne 0x3b761
leaq 0x30(%rsp), %rdi
leaq 0x10(%rsp), %rsi
callq 0x2f876
movq 0x28(%rsp), %rdi
leaq 0x58(%rsp), %rsi
callq 0x2f908
movq %rax, %rdi
leaq 0x30(%rsp), %rsi
callq 0x2f984
movq 0x30(%rsp), %r14
movq 0x38(%rsp), %r15
cmpq %r14, %r15
je 0x3b7a5
movq %r14, %rbp
movq %rbp, %rdi
callq 0x2e784
addq $0x18, %rbp
cmpq %r15, %rbp
jne 0x3b78f
movq %r14, 0x38(%rsp)
movq 0x10(%rsp), %rbp
movq 0x18(%rsp), %r15
cmpq %rbp, %r15
je 0x3b7e1
leaq 0x10(%rbp), %r14
movq -0x10(%r14), %rdi
cmpq %rdi, %r14
je 0x3b7cc
movq (%r14), %rsi
incq %rsi
callq 0x8480
leaq 0x20(%r14), %rax
addq $0x10, %r14
cmpq %r15, %r14
movq %rax, %r14
jne 0x3b7b8
movq %rbp, 0x18(%rsp)
leaq 0x10(%rsp), %rdi
movq %r12, %rsi
callq 0x3133c
movq 0xf8(%rsp), %rsi
leaq 0x58(%rsp), %rdi
callq 0x8270
leaq 0xb8(%rsp), %rdi
movq %rbx, %rsi
callq 0x8270
jmp 0x3b8c3
movq 0xa0(%rsp), %rdx
cmpq 0xc0(%rsp), %rdx
jne 0x3b84d
testq %rdx, %rdx
je 0x3b8fd
movq 0xb8(%rsp), %rsi
movq 0x98(%rsp), %rdi
callq 0x8490
testl %eax, %eax
je 0x3b8fd
movb 0xa(%rsp), %al
xorb $0x1, %al
orb 0xc(%rsp), %al
cmpb $0x1, %al
jne 0x3b86a
leaq 0x30(%rsp), %rdi
leaq 0x10(%rsp), %rsi
callq 0x2f876
movq 0x10(%rsp), %rbp
movq 0x18(%rsp), %r15
cmpq %rbp, %r15
je 0x3b8a6
leaq 0x10(%rbp), %r14
movq -0x10(%r14), %rdi
cmpq %rdi, %r14
je 0x3b891
movq (%r14), %rsi
incq %rsi
callq 0x8480
leaq 0x20(%r14), %rax
addq $0x10, %r14
cmpq %r15, %r14
movq %rax, %r14
jne 0x3b87d
movq %rbp, 0x18(%rsp)
leaq 0x10(%rsp), %rdi
movq %r12, %rsi
callq 0x3133c
leaq 0xb8(%rsp), %rdi
movq %rbx, %rsi
callq 0x8270
movb 0xb(%rsp), %al
movb %al, 0xa(%rsp)
movq 0x98(%rsp), %rdi
leaq 0xa8(%rsp), %rax
cmpq %rax, %rdi
je 0x3b8f0
movq 0xa8(%rsp), %rsi
incq %rsi
callq 0x8480
movq %r13, %rdi
callq 0x2e784
jmp 0x3b694
leaq 0x10(%rsp), %rdi
movq %r12, %rsi
callq 0x3133c
jmp 0x3b8cb
leaq 0xc8(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x3b92d
movq 0xc8(%rsp), %rsi
incq %rsi
callq 0x8480
movq 0x58(%rsp), %rdi
leaq 0x68(%rsp), %rax
cmpq %rax, %rdi
je 0x3b949
movq 0x68(%rsp), %rsi
incq %rsi
callq 0x8480
leaq 0x110(%rsp), %rdi
callq 0x2e784
leaq 0xe0(%rsp), %rdi
callq 0x2e784
leaq 0x10(%rsp), %rdi
callq 0x2e784
movq 0x78(%rsp), %rdi
leaq 0x88(%rsp), %rax
cmpq %rax, %rdi
je 0x3b98f
movq 0x88(%rsp), %rsi
incq %rsi
callq 0x8480
leaq 0x30(%rsp), %rdi
callq 0x2efec
movq 0x28(%rsp), %rax
addq $0x128, %rsp            # imm = 0x128
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %rbx
jmp 0x3ba31
movq %rax, %rbx
jmp 0x3ba4d
movq %rax, %rbx
jmp 0x3ba5a
jmp 0x3b9c7
movq %rax, %rbx
jmp 0x3ba67
movq %rax, %rbx
jmp 0x3ba03
jmp 0x3b9d6
movq %rax, %rbx
jmp 0x3ba10
movq %rax, %rbx
movq 0x98(%rsp), %rdi
leaq 0xa8(%rsp), %rax
cmpq %rax, %rdi
je 0x3ba03
movq 0xa8(%rsp), %rsi
incq %rsi
callq 0x8480
leaq 0xf8(%rsp), %rdi
callq 0x2e784
leaq 0xc8(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x3ba31
movq 0xc8(%rsp), %rsi
incq %rsi
callq 0x8480
movq 0x58(%rsp), %rdi
leaq 0x68(%rsp), %rax
cmpq %rax, %rdi
je 0x3ba4d
movq 0x68(%rsp), %rsi
incq %rsi
callq 0x8480
leaq 0x110(%rsp), %rdi
callq 0x2e784
leaq 0xe0(%rsp), %rdi
callq 0x2e784
leaq 0x10(%rsp), %rdi
callq 0x2e784
movq 0x78(%rsp), %rdi
leaq 0x88(%rsp), %rax
cmpq %rax, %rdi
je 0x3ba93
movq 0x88(%rsp), %rsi
incq %rsi
callq 0x8480
leaq 0x30(%rsp), %rdi
callq 0x2efec
movq 0x28(%rsp), %rdi
callq 0x30870
movq %rbx, %rdi
callq 0x8840
nop