LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/./process_vcf_annotation_tools.h
// Function: Annotation::getTranscriptName(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, bool&)
std::string getTranscriptName(const string& geneColumn, bool& bPartial) {
        string thisTranscriptName;
        std::vector<string> findIfPartial = split(geneColumn, '-');
        if (findIfPartial.size() == 2) {
            bPartial = true;
            thisTranscriptName = findIfPartial[1];
        } else if (findIfPartial.size() == 1) {
            thisTranscriptName = geneColumn;
        }
        return thisTranscriptName;
    }

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
subq $0x20, %rsp
movq %rcx, %r15
movq %rdx, %r14
movq %rdi, %rbx
leaq 0x10(%rdi), %rax
movq %rax, (%rdi)
andq $0x0, 0x8(%rdi)
movb $0x0, 0x10(%rdi)
leaq 0x8(%rsp), %rdi
pushq $0x2d
popq %rdx
movq %r14, %rsi
callq 0x40349
movq 0x8(%rsp), %rax
movq 0x10(%rsp), %rcx
subq %rax, %rcx
sarq $0x5, %rcx
cmpq $0x1, %rcx
je 0x3263c
cmpq $0x2, %rcx
jne 0x32647
movb $0x1, (%r15)
addq $0x20, %rax
movq %rax, %r14
movq %rbx, %rdi
movq %r14, %rsi
callq 0x82a0
leaq 0x8(%rsp), %rdi
callq 0x28a08
movq %rbx, %rax
addq $0x20, %rsp
popq %rbx
popq %r14
popq %r15
retq
movq %rax, %r14
leaq 0x8(%rsp), %rdi
callq 0x28a08
jmp 0x32670
movq %rax, %r14
movq %rbx, %rdi
callq 0x8978
movq %r14, %rdi
callq 0x8870
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_cbs.cpp
// Function: numToStringVector[abi:cxx11](std::vector<int, std::allocator<int>>&)
std::vector<string> numToStringVector(std::vector<int>& vec) {
    std::vector<string> converted;
    for (std::vector<int>::size_type i = 0; i != vec.size(); i++) {
        converted.push_back(numToString(vec[i]));
    }
    return converted;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %rsi, %r14
movq %rdi, %rbx
andq $0x0, 0x10(%rdi)
xorps %xmm0, %xmm0
movups %xmm0, (%rdi)
xorl %r12d, %r12d
leaq 0x8(%rsp), %r15
movq (%r14), %rax
movq 0x8(%r14), %rcx
subq %rax, %rcx
sarq $0x2, %rcx
cmpq %rcx, %r12
je 0x38b3e
movl (%rax,%r12,4), %esi
movq %r15, %rdi
callq 0x28ad3
movq %rbx, %rdi
movq %r15, %rsi
callq 0x3490e
movq %r15, %rdi
callq 0x8978
incq %r12
jmp 0x38b07
movq %rbx, %rax
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
movq %rax, %r14
jmp 0x38b5f
movq %rax, %r14
leaq 0x8(%rsp), %rdi
callq 0x8978
movq %rbx, %rdi
callq 0x28a08
movq %r14, %rdi
callq 0x8870
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_cbs.cpp
// Function: numToStringMinFilterVector[abi:cxx11](std::vector<int, std::allocator<int>>&, int)
std::vector<string> numToStringMinFilterVector(std::vector<int>& vec, int min) {
    std::vector<string> converted;
    for (std::vector<int>::size_type i = 0; i != vec.size(); i++) {
        if (vec[i] >= min)
            converted.push_back(numToString(vec[i]));
    }
    return converted;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x20, %rsp
movl %edx, %ebp
movq %rsi, %r14
movq %rdi, %rbx
andq $0x0, 0x10(%rdi)
xorps %xmm0, %xmm0
movups %xmm0, (%rdi)
xorl %r12d, %r12d
movq %rsp, %r15
movq (%r14), %rax
movq 0x8(%r14), %rcx
subq %rax, %rcx
sarq $0x2, %rcx
cmpq %rcx, %r12
je 0x38bcf
movl (%rax,%r12,4), %esi
cmpl %ebp, %esi
jl 0x38bca
movq %r15, %rdi
callq 0x28ad3
movq %rbx, %rdi
movq %r15, %rsi
callq 0x3490e
movq %r15, %rdi
callq 0x8978
incq %r12
jmp 0x38b94
movq %rbx, %rax
addq $0x20, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %r14
jmp 0x38bef
movq %rax, %r14
movq %rsp, %rdi
callq 0x8978
movq %rbx, %rdi
callq 0x28a08
movq %r14, %rdi
callq 0x8870
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_cbs.cpp
// Function: cbsMain(int, char**)
int cbsMain(int argc, char** argv) {
    parseCbsOptions(argc, argv);
    
    if (!opt::vcfFile.empty()) {
        std::cerr << "Calculating the lenghts of cbs tracts from: " << opt::vcfFile << std::endl;
        std::cerr << "and using information about scaffold lengths and the location of undetermined regions from: " << opt::undeterminedLociFile << std::endl;
        calculateCbs();
    } else if (!opt::genomeFile.empty()) {
        std::cerr << "Looking for undetermined regions (runs of Ns) in the reference genome: " << std::endl;
        std::cerr << opt::genomeFile << std::endl;
        findUndeterminedRegions();
    } else {
        assert(false);
    }
    
    return 0;
}

// Assembly:
pushq %rbx
callq 0x3a2f8
cmpq $0x0, 0xa3e45(%rip)     # 0xde078
jne 0x3a281
cmpq $0x0, 0xa3e5b(%rip)     # 0xde098
je 0x3a2d9
movq 0xa2d9e(%rip), %rbx     # 0xdcfe8
leaq 0x63e54(%rip), %rsi     # 0x9e0a5
movq %rbx, %rdi
callq 0x8480
movq %rax, %rdi
callq 0x8230
leaq 0xa3e28(%rip), %rsi     # 0xde090
movq %rbx, %rdi
callq 0x8430
movq %rax, %rdi
callq 0x8230
callq 0x387dc
xorl %eax, %eax
popq %rbx
retq
movq 0xa2d60(%rip), %rbx     # 0xdcfe8
leaq 0x63d8c(%rip), %rsi     # 0x9e01b
movq %rbx, %rdi
callq 0x8480
leaq 0xa3dd2(%rip), %rsi     # 0xde070
movq %rax, %rdi
callq 0x8430
movq %rax, %rdi
callq 0x8230
leaq 0x63d93(%rip), %rsi     # 0x9e048
movq %rbx, %rdi
callq 0x8480
leaq 0xa3e4c(%rip), %rsi     # 0xde110
movq %rax, %rdi
callq 0x8430
movq %rax, %rdi
callq 0x8230
callq 0x38c14
leaq 0x63e0d(%rip), %rdi     # 0x9e0ed
leaq 0x63c21(%rip), %rsi     # 0x9df08
leaq 0x63e05(%rip), %rcx     # 0x9e0f3
movl $0x176, %edx            # imm = 0x176
callq 0x82f0
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/./process_vcf_seq_utils.h
// Function: readScaffold(std::basic_ifstream<char, std::char_traits<char>>*&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>&)
inline std::string readScaffold(std::ifstream*& genomeFile, std::string& nextScaffoldName) {
    std::string scaffoldString;
    scaffoldString.reserve(100000000);
    std::string line = "";
    while (getline(*genomeFile, line) && line[0] != '>') {
        scaffoldString.append(line);
    }
    if (line[0] == '>')
        nextScaffoldName = split(line,' ')[0];
    else
        nextScaffoldName = "";
    return scaffoldString;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x38, %rsp
movq %rdx, %r14
movq %rsi, %r15
movq %rdi, %rbx
leaq 0x10(%rdi), %rax
movq %rax, (%rdi)
andq $0x0, 0x8(%rdi)
movb $0x0, 0x10(%rdi)
movl $0x5f5e100, %esi        # imm = 0x5F5E100
callq 0x8700
leaq 0x5f8af(%rip), %rsi     # 0x99e1f
leaq 0x18(%rsp), %rdi
movq %rsp, %rdx
callq 0x21904
leaq 0x18(%rsp), %r12
movq (%r15), %rdi
movq %r12, %rsi
callq 0x80a0
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
testb $0x5, 0x20(%rax,%rcx)
movq 0x18(%rsp), %rax
movb (%rax), %al
jne 0x3a5b3
cmpb $0x3e, %al
je 0x3a5b7
movq %rbx, %rdi
movq %r12, %rsi
callq 0x8920
jmp 0x3a582
cmpb $0x3e, %al
jne 0x3a5dd
movq %rsp, %rdi
leaq 0x18(%rsp), %rsi
pushq $0x20
popq %rdx
callq 0x40349
movq (%rsp), %rsi
movq %r14, %rdi
callq 0x82a0
movq %rsp, %rdi
callq 0x28a08
jmp 0x3a5ec
leaq 0x5f83b(%rip), %rsi     # 0x99e1f
movq %r14, %rdi
callq 0x88f0
leaq 0x18(%rsp), %rdi
callq 0x8978
movq %rbx, %rax
addq $0x38, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
jmp 0x3a61d
movq %rax, %r14
movq %rsp, %rdi
callq 0x28a08
jmp 0x3a620
jmp 0x3a61d
jmp 0x3a618
movq %rax, %r14
jmp 0x3a62a
movq %rax, %r14
leaq 0x18(%rsp), %rdi
callq 0x8978
movq %rbx, %rdi
callq 0x8978
movq %r14, %rdi
callq 0x8870
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/./process_vcf_utils.h
// Function: void print_matrix<std::vector<std::vector<double, std::allocator<double>>, std::allocator<std::vector<double, std::allocator<double>>>> const&>(std::vector<std::vector<double, std::allocator<double>>, std::allocator<std::vector<double, std::allocator<double>>>> const&, std::ostream&)
void print_matrix(T matrix, std::ostream& outFile) {
    for (int i = 0; i < matrix.size(); i++) {
        for (int j = 0; j < matrix[i].size(); j++) {
            if (j == (matrix[i].size()-1))
                outFile << matrix[i][j] << std::endl;
            else 
                outFile << matrix[i][j] << "\t";
        }    
    }    
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
movq (%rdi), %rcx
xorl %esi, %esi
leaq 0x514d4(%rip), %r15     # 0x99e1e
movq 0x8(%r14), %rax
subq %rcx, %rax
cqto
pushq $0x18
popq %rdi
idivq %rdi
cmpq %rsi, %rax
jbe 0x489b7
movq %rsi, (%rsp)
imulq $0x18, %rsi, %rbp
xorl %r13d, %r13d
movq (%rcx,%rbp), %rax
movq 0x8(%rcx,%rbp), %r12
subq %rax, %r12
sarq $0x3, %r12
cmpq %r13, %r12
jbe 0x489ae
decq %r12
movsd (%rax,%r13,8), %xmm0
movq %rbx, %rdi
callq 0x8750
movq %rax, %rdi
cmpq %r12, %r13
jne 0x4899e
callq 0x8230
jmp 0x489a6
movq %r15, %rsi
callq 0x8480
incq %r13
movq (%r14), %rcx
jmp 0x48969
movq (%rsp), %rsi
incq %rsi
jmp 0x4894a
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/./process_vcf_stats_utils.h
// Function: factorial(double)
inline double factorial(double num) {
    if (num < 0) {
        std::cerr << "Can't compute factorial of a negative number " << num << std::endl;
        exit(1);
    }
    return tgamma(num+1);
}

// Assembly:
xorpd %xmm1, %xmm1
ucomisd %xmm0, %xmm1
ja 0x3c287
addsd 0x5b36e(%rip), %xmm0    # 0x975f0
jmp 0x8080
pushq %rax
movq 0xa0d59(%rip), %rdi     # 0xdcfe8
leaq 0x61edd(%rip), %rsi     # 0x9e173
movsd %xmm0, (%rsp)
callq 0x8480
movq %rax, %rdi
movsd (%rsp), %xmm0
callq 0x88d0
movq %rax, %rdi
callq 0x8230
pushq $0x1
popq %rdi
callq 0x8540
nop
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/./process_vcf_IUPAC.h
// Function: returnHetIUPAC[abi:cxx11](char)
inline std::string returnHetIUPAC(char IUPACbase) {
    char firstBase; char secondBase;
    switch (std::toupper(IUPACbase))
    {
        case 'K': firstBase = 'T'; secondBase = 'G'; break;
        case 'M': firstBase = 'C'; secondBase = 'A'; break;
        case 'R': firstBase = 'G'; secondBase = 'A'; break;
        case 'S': firstBase = 'G'; secondBase = 'C'; break;
        case 'W': firstBase = 'T'; secondBase = 'A'; break;
        case 'Y': firstBase = 'T'; secondBase = 'C'; break;
        default: assert(false);
    }
    std::string bases = ""; bases = firstBase + secondBase;
    return bases;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
movl %esi, %edi
callq 0x88b0
addl $-0x4b, %eax
cmpl $0xf, %eax
jae 0x3f835
movl $0x5185, %ecx           # imm = 0x5185
btl %eax, %ecx
jae 0x3f835
movl %eax, %r14d
leaq 0x5f6d2(%rip), %r15     # 0x9eeca
leaq 0x5f6da(%rip), %rax     # 0x9eed9
movb (%r14,%rax), %bpl
leaq 0x5a615(%rip), %rsi     # 0x99e1f
leaq 0x7(%rsp), %rdx
movq %rbx, %rdi
callq 0x21904
addb (%r14,%r15), %bpl
movsbl %bpl, %esi
movq %rbx, %rdi
callq 0x87b0
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
leaq 0x5e8b1(%rip), %rdi     # 0x9e0ed
leaq 0x5f3a7(%rip), %rsi     # 0x9ebea
leaq 0x5f3b6(%rip), %rcx     # 0x9ec00
pushq $0x32
popq %rdx
callq 0x82f0
movq %rax, %r14
movq %rbx, %rdi
callq 0x8978
movq %r14, %rdi
callq 0x8870
nop
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_join_multiFasta.cpp
// Function: processMultiFastaMain(int, char**)
int processMultiFastaMain(int argc, char** argv) {
    parseMultiFastaOptions(argc, argv);
    
    string allSequences = readMultiFastaToOneString(opt::fastaFile, 500000000);
    
    if (opt::out.empty()) {
        print80bpPerLineStdOut(std::cout, allSequences);
    } else {
        string outFN = opt::out + ".joined.fa";
        std::ofstream* outAncestralFile = new std::ofstream(outFN.c_str());
        print80bpPerLineFile(outAncestralFile, allSequences);
    }
    
    return 0;
}

// Assembly:
pushq %r14
pushq %rbx
subq $0x88, %rsp
callq 0x3f9cb
leaq 0x9e92e(%rip), %rsi     # 0xde1e8
leaq 0x8(%rsp), %rdi
movl $0x1dcd6500, %edx       # imm = 0x1DCD6500
callq 0x42ce0
cmpq $0x0, 0x9e93f(%rip)     # 0xde210
je 0x3f939
leaq 0x9e92e(%rip), %rsi     # 0xde208
leaq 0x5f607(%rip), %rdx     # 0x9eee8
leaq 0x48(%rsp), %rdi
callq 0x28806
movl $0x200, %edi            # imm = 0x200
callq 0x8490
movq %rax, %r14
movq 0x48(%rsp), %rsi
pushq $0x10
popq %rdx
movq %rax, %rdi
callq 0x84e0
movq %r14, (%rsp)
leaq 0x28(%rsp), %rdi
leaq 0x8(%rsp), %rsi
callq 0x8600
movq %rsp, %rdi
leaq 0x28(%rsp), %rsi
callq 0x42730
leaq 0x28(%rsp), %rdi
callq 0x8978
leaq 0x48(%rsp), %rdi
jmp 0x3f95e
leaq 0x68(%rsp), %rdi
leaq 0x8(%rsp), %rsi
callq 0x8600
movq 0x9d669(%rip), %rdi     # 0xdcfb8
leaq 0x68(%rsp), %rsi
callq 0x426a5
leaq 0x68(%rsp), %rdi
callq 0x8978
leaq 0x8(%rsp), %rdi
callq 0x8978
xorl %eax, %eax
addq $0x88, %rsp
popq %rbx
popq %r14
retq
movq %rax, %rbx
leaq 0x68(%rsp), %rdi
jmp 0x3f9b4
jmp 0x3f9a7
movq %rax, %rbx
leaq 0x28(%rsp), %rdi
callq 0x8978
jmp 0x3f9af
movq %rax, %rbx
movl $0x200, %esi            # imm = 0x200
movq %r14, %rdi
callq 0x84a0
jmp 0x3f9af
movq %rax, %rbx
jmp 0x3f9b9
movq %rax, %rbx
leaq 0x48(%rsp), %rdi
callq 0x8978
leaq 0x8(%rsp), %rdi
callq 0x8978
movq %rbx, %rdi
callq 0x8870
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_join_multiFasta.cpp
// Function: parseMultiFastaOptions(int, char**)
void parseMultiFastaOptions(int argc, char** argv) {
    bool die = false;
    for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;)
    {
        std::istringstream arg(optarg != NULL ? optarg : "");
        switch (c)
        {
            case '?': die = true; break;
            case 'o': arg >> opt::out; break;
            case 'h':
                std::cout << MULTI_FASTA_USAGE_MESSAGE;
                exit(EXIT_SUCCESS);
        }
    }
    if (argc - optind < 1) {
        std::cerr << "missing arguments\n";
        die = true;
    }
    else if (argc - optind > 1)
    {
        std::cerr << "too many arguments\n";
        die = true;
    }
    
    if (die) {
        std::cout << "\n" << MULTI_FASTA_USAGE_MESSAGE;
        exit(EXIT_FAILURE);
    }
    
    // Parse the input filenames
    opt::fastaFile = argv[optind++];
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x1b8, %rsp            # imm = 0x1B8
movq %rsi, %rbx
movl %edi, %ebp
movq $0x0, 0x10(%rsp)
leaq 0x18(%rsp), %r12
leaq 0x38(%rsp), %r14
pushq $0x8
popq %r15
movl %ebp, %edi
movq %rbx, %rsi
leaq 0x5d435(%rip), %rdx     # 0x9ce39
leaq 0x9b485(%rip), %rcx     # 0xdae90
xorl %r8d, %r8d
callq 0x8790
movl %eax, %r13d
shll $0x18, %eax
cmpl $0xff000000, %eax       # imm = 0xFF000000
je 0x3fa98
movq 0x9d569(%rip), %rax     # 0xdcf90
movq (%rax), %rsi
testq %rsi, %rsi
leaq 0x5a3eb(%rip), %rax     # 0x99e1f
cmoveq %rax, %rsi
movq %r12, %rdi
leaq 0xf(%rsp), %rdx
callq 0x21904
movq %r14, %rdi
movq %r12, %rsi
movl %r15d, %edx
callq 0x87e0
movsbl %r13b, %r13d
movq %r12, %rdi
callq 0x8978
cmpl $0x3f, %r13d
je 0x3fa84
cmpl $0x6f, %r13d
je 0x3fa73
cmpl $0x68, %r13d
jne 0x3fa8b
jmp 0x3fad9
movq %r14, %rdi
leaq 0x9e78b(%rip), %rsi     # 0xde208
callq 0x8570
jmp 0x3fa8b
movb $0x1, %al
movq %rax, 0x10(%rsp)
movq %r14, %rdi
callq 0x8220
jmp 0x3f9f8
movq 0x9d521(%rip), %rax     # 0xdcfc0
movslq (%rax), %rcx
subl %ecx, %ebp
jle 0x3faf3
cmpl $0x1, %ebp
jne 0x3fafc
testb $0x1, 0x10(%rsp)
jne 0x3fb0f
leal 0x1(%rcx), %edx
movl %edx, (%rax)
movq (%rbx,%rcx,8), %rsi
leaq 0x9e726(%rip), %rdi     # 0xde1e8
callq 0x88f0
addq $0x1b8, %rsp            # imm = 0x1B8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x9d4d8(%rip), %rdi     # 0xdcfb8
leaq 0x5f40c(%rip), %rsi     # 0x9eef3
callq 0x8480
xorl %edi, %edi
callq 0x8540
leaq 0x56828(%rip), %rsi     # 0x96322
jmp 0x3fb03
leaq 0x56832(%rip), %rsi     # 0x96335
movq 0x9d4de(%rip), %rdi     # 0xdcfe8
callq 0x8480
movq 0x9d4a2(%rip), %rdi     # 0xdcfb8
leaq 0x53e30(%rip), %rsi     # 0x9394d
callq 0x8480
leaq 0x5f3ca(%rip), %rsi     # 0x9eef3
movq %rax, %rdi
callq 0x8480
pushq $0x1
popq %rdi
callq 0x8540
jmp 0x3fb3b
movq %rax, %rbx
leaq 0x38(%rsp), %rdi
callq 0x8220
jmp 0x3fb5c
movq %rax, %rbx
jmp 0x3fb5c
movq %rax, %rbx
leaq 0x18(%rsp), %rdi
callq 0x8978
movq %rbx, %rdi
callq 0x8870
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: GeneralSetCounts::getSetVariantCountsSimple(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&, std::map<unsigned long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>>>> const&)
void GeneralSetCounts::getSetVariantCountsSimple(const std::vector<std::string>& genotypes, const std::map<size_t, string>& posToSpeciesMap) {
    // std::cerr << fields[0] << "\t" << fields[1] << std::endl;
    getBasicCounts(genotypes, posToSpeciesMap);
    
    // Now fill in the allele frequencies
    for(std::map<string,int>::iterator it = setAltCounts.begin(); it != setAltCounts.end(); ++it) {
        if (setAlleleCounts.at(it->first) > 0) {
            setAAFs[it->first] = (double)setAltCounts.at(it->first)/setAlleleCounts.at(it->first);
        }
    }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rdi, %rbx
callq 0x3fde8
leaq 0x38(%rbx), %r14
movq 0x50(%rbx), %r12
leaq 0x40(%rbx), %rbp
leaq 0x68(%rbx), %r15
addq $0xe0, %rbx
cmpq %rbp, %r12
je 0x3fffa
leaq 0x20(%r12), %r13
movq %r15, %rdi
movq %r13, %rsi
callq 0x43738
cmpl $0x0, (%rax)
jle 0x3ffed
movq %r14, %rdi
movq %r13, %rsi
callq 0x43738
cvtsi2sdl (%rax), %xmm0
movsd %xmm0, (%rsp)
movq %r15, %rdi
movq %r13, %rsi
callq 0x43738
cvtsi2sdl (%rax), %xmm0
movsd (%rsp), %xmm1
divsd %xmm0, %xmm1
movsd %xmm1, (%rsp)
movq %rbx, %rdi
movq %r13, %rsi
callq 0x4377e
movsd (%rsp), %xmm0
movsd %xmm0, (%rax)
movq %r12, %rdi
callq 0x8340
movq %rax, %r12
jmp 0x3ff8e
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
nop
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: GeneralSetCountsWithComplements::getComplementCounts(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 GeneralSetCountsWithComplements::getComplementCounts(const std::vector<string>& populationsToUse) {
    // Now fill in the allele frequencies
    for(std::map<string,int>::iterator it = setAltCounts.begin(); it != setAltCounts.end(); ++it) {
        int complementAAFCount = 0; int complementTotalAlleleCount = 0;
        for (int i = 0; i < populationsToUse.size(); i++) {
            if (it->first != populationsToUse[i]) {
                complementAAFCount += setAltCounts.at(populationsToUse[i]);
                complementTotalAlleleCount += setAlleleCounts.at(populationsToUse[i]);
            }
        }
        setAAFsComplement[it->first] = (double)complementAAFCount/complementTotalAlleleCount;
        setAlleleCountsComplement[it->first] = complementTotalAlleleCount;
    }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x38, %rsp
movq %rsi, %rbx
leaq 0x38(%rdi), %rax
movq %rax, 0x30(%rsp)
movq 0x50(%rdi), %rcx
leaq 0x40(%rdi), %rax
movq %rax, 0x10(%rsp)
leaq 0x68(%rdi), %rax
movq %rax, 0x28(%rsp)
leaq 0x240(%rdi), %rax
movq %rax, (%rsp)
addq $0x2a0, %rdi            # imm = 0x2A0
movq %rdi, 0x8(%rsp)
cmpq 0x10(%rsp), %rcx
je 0x4010d
movq %rcx, 0x20(%rsp)
leaq 0x20(%rcx), %r13
xorl %ebp, %ebp
xorl %r12d, %r12d
xorl %r15d, %r15d
xorl %r14d, %r14d
movq (%rbx), %rsi
movq 0x8(%rbx), %rax
subq %rsi, %rax
sarq $0x5, %rax
cmpq %r12, %rax
jbe 0x400c1
addq %rbp, %rsi
movq %r13, %rdi
callq 0x311fd
testb %al, %al
je 0x400b8
movq (%rbx), %rsi
addq %rbp, %rsi
movq 0x30(%rsp), %rdi
callq 0x43738
addl (%rax), %r15d
movq (%rbx), %rsi
addq %rbp, %rsi
movq 0x28(%rsp), %rdi
callq 0x43738
addl (%rax), %r14d
incq %r12
addq $0x20, %rbp
jmp 0x40070
cvtsi2sd %r15d, %xmm1
cvtsi2sd %r14d, %xmm0
divsd %xmm0, %xmm1
movsd %xmm1, 0x18(%rsp)
movq (%rsp), %rdi
movq %r13, %rsi
callq 0x4377e
movsd 0x18(%rsp), %xmm0
movsd %xmm0, (%rax)
movq 0x8(%rsp), %rdi
movq %r13, %rsi
callq 0x32a8a
movl %r14d, (%rax)
movq 0x20(%rsp), %rdi
callq 0x8340
movq %rax, %rcx
jmp 0x40051
addq $0x38, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: split(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, char, 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 split(const std::string &s, char delim, std::vector<std::string> &elems) {
    std::stringstream ss(s);
    std::string item;
    while (std::getline(ss, item, delim)) {
        elems.push_back(item);
    }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
subq $0x1a8, %rsp            # imm = 0x1A8
movq %rdx, %rbx
movl %esi, %ebp
movq %rdi, %rsi
leaq 0x20(%rsp), %r14
pushq $0x18
popq %rdx
movq %r14, %rdi
callq 0x8720
leaq 0x10(%rsp), %rax
movq %rax, -0x10(%rax)
andq $0x0, -0x8(%rax)
movb $0x0, (%rax)
movsbl %bpl, %ebp
movq %rsp, %r15
movq %r14, %rdi
movq %r15, %rsi
movl %ebp, %edx
callq 0x88a0
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
testb $0x5, 0x20(%rax,%rcx)
jne 0x40181
movq %rbx, %rdi
movq %r15, %rsi
callq 0x2b0a4
jmp 0x40159
movq %rsp, %rdi
callq 0x8978
leaq 0x20(%rsp), %rdi
callq 0x83b0
addq $0x1a8, %rsp            # imm = 0x1A8
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %rbx
movq %rsp, %rdi
callq 0x8978
leaq 0x20(%rsp), %rdi
callq 0x83b0
movq %rbx, %rdi
callq 0x8870
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: splitToDouble(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, char, std::vector<double, std::allocator<double>>&)
void splitToDouble(const std::string &s, char delim, std::vector<double> &elems) {
    std::stringstream ss(s);
    std::string item;
    while (std::getline(ss, item, delim)) {
        elems.push_back(stringToDouble(item));
    }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x1d8, %rsp            # imm = 0x1D8
movq %rdx, %rbx
movl %esi, %ebp
movq %rdi, %rsi
leaq 0x50(%rsp), %r14
pushq $0x18
popq %rdx
movq %r14, %rdi
callq 0x8720
leaq 0x20(%rsp), %rax
movq %rax, -0x10(%rax)
andq $0x0, -0x8(%rax)
movb $0x0, (%rax)
movsbl %bpl, %ebp
leaq 0x10(%rsp), %r15
leaq 0x30(%rsp), %r12
leaq 0x8(%rsp), %r13
movq %r14, %rdi
movq %r15, %rsi
movl %ebp, %edx
callq 0x88a0
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
testb $0x5, 0x20(%rax,%rcx)
jne 0x40254
movq %r12, %rdi
movq %r15, %rsi
callq 0x8600
movq %r12, %rdi
callq 0x402aa
movsd %xmm0, 0x8(%rsp)
movq %rbx, %rdi
movq %r13, %rsi
callq 0x2af10
movq %r12, %rdi
callq 0x8978
jmp 0x4020b
leaq 0x10(%rsp), %rdi
callq 0x8978
leaq 0x50(%rsp), %rdi
callq 0x83b0
addq $0x1d8, %rsp            # imm = 0x1D8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
jmp 0x4027c
movq %rax, %rbx
jmp 0x4028e
movq %rax, %rbx
leaq 0x30(%rsp), %rdi
callq 0x8978
leaq 0x10(%rsp), %rdi
callq 0x8978
leaq 0x50(%rsp), %rdi
callq 0x83b0
movq %rbx, %rdi
callq 0x8870
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: stringToDouble(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>)
double stringToDouble(std::string s) {
    double d;
    std::stringstream ss(s); //turn the string into a stream
    ss >> d; //convert
    return d;
}

// Assembly:
pushq %rbx
subq $0x1a0, %rsp            # imm = 0x1A0
movq %rdi, %rsi
leaq 0x18(%rsp), %rbx
pushq $0x18
popq %rdx
movq %rbx, %rdi
callq 0x8720
leaq 0x10(%rsp), %rsi
movq %rbx, %rdi
callq 0x8300
movsd 0x10(%rsp), %xmm0
movsd %xmm0, 0x8(%rsp)
leaq 0x18(%rsp), %rdi
callq 0x83b0
movsd 0x8(%rsp), %xmm0
addq $0x1a0, %rsp            # imm = 0x1A0
popq %rbx
retq
movq %rax, %rbx
leaq 0x18(%rsp), %rdi
callq 0x83b0
movq %rbx, %rdi
callq 0x8870
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: initialize_matrix_double(std::vector<std::vector<double, std::allocator<double>>, std::allocator<std::vector<double, std::allocator<double>>>>&, int, int)
void initialize_matrix_double(std::vector<std::vector<double> >& m, int m_rows, int m_columns) {
    if (m_columns == 0)
        m_columns = m_rows;
    for (int i = 0; i < m_columns; i++) {
        std::vector<double> v(m_rows,0);
        m.push_back(v);
    }       
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %rdi, %rbx
testl %edx, %edx
cmovel %esi, %edx
xorl %ebp, %ebp
testl %edx, %edx
cmovgl %edx, %ebp
movslq %esi, %r14
leaq 0x10(%rsp), %r15
leaq 0x8(%rsp), %r12
leaq 0x7(%rsp), %r13
subl $0x1, %ebp
jb 0x403e6
andq $0x0, 0x8(%rsp)
movq %r15, %rdi
movq %r14, %rsi
movq %r12, %rdx
movq %r13, %rcx
callq 0x4381e
movq %rbx, %rdi
movq %r15, %rsi
callq 0x43874
movq %r15, %rdi
callq 0x2b43c
jmp 0x403b5
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %rbx
leaq 0x10(%rsp), %rdi
callq 0x2b43c
movq %rbx, %rdi
callq 0x8870
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: initialize_matrix_int(std::vector<std::vector<int, std::allocator<int>>, std::allocator<std::vector<int, std::allocator<int>>>>&, int, int)
void initialize_matrix_int(std::vector<std::vector<int> >& m, int m_rows, int m_columns) {
    if (m_columns == 0)
        m_columns = m_rows;
    for (int i = 0; i < m_columns; i++) {
        std::vector<int> v(m_rows,0);
        m.push_back(v);
    }       
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %rdi, %rbx
testl %edx, %edx
cmovel %esi, %edx
xorl %ebp, %ebp
testl %edx, %edx
cmovgl %edx, %ebp
movslq %esi, %r14
leaq 0x10(%rsp), %r15
leaq 0xc(%rsp), %r12
leaq 0xb(%rsp), %r13
subl $0x1, %ebp
jb 0x40469
andl $0x0, 0xc(%rsp)
movq %r15, %rdi
movq %r14, %rsi
movq %r12, %rdx
movq %r13, %rcx
callq 0x438a0
movq %rbx, %rdi
movq %r15, %rsi
callq 0x3b5c4
movq %r15, %rdi
callq 0x2aef2
jmp 0x40439
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %rbx
leaq 0x10(%rsp), %rdi
callq 0x2aef2
movq %rbx, %rdi
callq 0x8870
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: stripPath(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&)
std::string stripPath(const std::string& filename)
{
    size_t slashPos = filename.find_last_of('/');
    if(slashPos == std::string::npos)
        return filename; // no path
    else
        return filename.substr(slashPos+1);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %r14
movq %rdi, %rbx
pushq $0x2f
popq %rsi
pushq $-0x1
popq %rdx
movq %r14, %rdi
callq 0x8940
cmpq $-0x1, %rax
je 0x404c1
incq %rax
pushq $-0x1
popq %rcx
movq %rbx, %rdi
movq %r14, %rsi
movq %rax, %rdx
callq 0x84b0
jmp 0x404cc
movq %rbx, %rdi
movq %r14, %rsi
callq 0x8600
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: stripExtension(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&)
std::string stripExtension(const std::string& filename)
{
    size_t suffixPos = filename.find_last_of('.');
    if(suffixPos == std::string::npos)
        return filename; // no suffix
    else
        return filename.substr(0, suffixPos);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %r14
movq %rdi, %rbx
pushq $0x2e
popq %rsi
pushq $-0x1
popq %rdx
movq %r14, %rdi
callq 0x8940
movq %rbx, %rdi
movq %r14, %rsi
cmpq $-0x1, %rax
je 0x40507
xorl %edx, %edx
movq %rax, %rcx
callq 0x84b0
jmp 0x4050c
callq 0x8600
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: calculateInbreedingCoefficient(std::vector<int, std::allocator<int>>&)
double calculateInbreedingCoefficient(std::vector<int>& individualsWithVariant) {
    int naa = 0; int nAa = 0; int nAA = 0;
    for (std::vector<int>::size_type i = 0; i != individualsWithVariant.size(); i++) {
        if (individualsWithVariant[i] == 0) naa++;
        if (individualsWithVariant[i] == 1) nAa++;
        if (individualsWithVariant[i] == 2) nAA++;
    }
    
    // Get the proportions of alt-hom and hets
    double pAA = (double)nAA / individualsWithVariant.size();
    double pAa = (double)nAa / individualsWithVariant.size();
    
    // Allele frequencies
    double p = pAA + (0.5 * pAa);
    double q = 1 - p;
    
    // Get the Hardy-Weinberg prediction for expected number of heterozygotes:
    double HWAa = 2*p*q;

    
    // Get the inbreeding coefficient
    double F = (HWAa - pAa) / HWAa;
    return F;
}

// Assembly:
movq (%rdi), %rdx
movq 0x8(%rdi), %rcx
subq %rdx, %rcx
sarq $0x2, %rcx
xorl %esi, %esi
xorl %edi, %edi
xorl %eax, %eax
cmpq %rsi, %rcx
je 0x405b5
movl (%rdx,%rsi,4), %r8d
xorl %r9d, %r9d
cmpl $0x1, %r8d
sete %r9b
addl %r9d, %eax
xorl %r9d, %r9d
cmpl $0x2, %r8d
sete %r9b
addl %r9d, %edi
incq %rsi
jmp 0x4058b
cvtsi2sd %edi, %xmm0
movq %rcx, %xmm1
punpckldq 0x51c7a(%rip), %xmm1 # xmm1 = xmm1[0],mem[0],xmm1[1],mem[1]
subpd 0x51c82(%rip), %xmm1    # 0x92250
movapd %xmm1, %xmm2
unpckhpd %xmm1, %xmm2            # xmm2 = xmm2[1],xmm1[1]
addsd %xmm1, %xmm2
divsd %xmm2, %xmm0
cvtsi2sd %eax, %xmm1
divsd %xmm2, %xmm1
movsd 0x57012(%rip), %xmm2    # 0x97600
mulsd %xmm1, %xmm2
addsd %xmm0, %xmm2
movsd 0x56ff2(%rip), %xmm0    # 0x975f0
subsd %xmm2, %xmm0
addsd %xmm2, %xmm2
mulsd %xmm0, %xmm2
movapd %xmm2, %xmm0
subsd %xmm1, %xmm0
divsd %xmm2, %xmm0
retq
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: randomisePhase(char&, char&)
void randomisePhase(char& v1, char& v2) {
    if (v1 != v2) {
        char temp;
        double r = ((double) rand() / (RAND_MAX));
        if (r > 0.5) {
            temp = v1;
            v1 = v2; v2 = temp;
        }
    }
}

// Assembly:
movb (%rdi), %al
cmpb (%rsi), %al
je 0x4085b
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
callq 0x8160
cvtsi2sd %eax, %xmm0
divsd 0x518e0(%rip), %xmm0    # 0x92120
ucomisd 0x56db8(%rip), %xmm0    # 0x97600
jbe 0x40854
movb (%r14), %al
movb (%rbx), %cl
movb %cl, (%r14)
movb %al, (%rbx)
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: MultiallelicCounts::getHeterozygosityThisVariant()
double MultiallelicCounts::getHeterozygosityThisVariant() {
    
    std::vector<int> nonMissingHets = individualsHets;
    nonMissingHets.erase(std::remove(nonMissingHets.begin(), nonMissingHets.end(), -1), nonMissingHets.end());
    
    int numNonMisInds = (int) nonMissingHets.size();
    int numHets = vector_sum(nonMissingHets);
    
    double hetThisVar = (double)numHets/(double)numNonMisInds;
    return hetThisVar;
}

// Assembly:
pushq %r14
pushq %rbx
subq $0x48, %rsp
leaq 0x20(%rdi), %rsi
leaq 0x18(%rsp), %rbx
movq %rbx, %rdi
callq 0x2c6d4
movq (%rbx), %rdi
movq 0x8(%rbx), %rsi
leaq 0x14(%rsp), %rdx
orl $-0x1, (%rdx)
callq 0x451ae
leaq 0x18(%rsp), %rdi
movq 0x8(%rdi), %rdx
movq %rax, %rsi
callq 0x439ba
leaq 0x18(%rsp), %rsi
movq (%rsi), %rbx
movq 0x8(%rsi), %r14
leaq 0x30(%rsp), %rdi
callq 0x2c6d4
subq %rbx, %r14
shrq $0x2, %r14
leaq 0x30(%rsp), %rbx
movq %rbx, %rdi
callq 0x2c6ac
movaps %xmm0, (%rsp)
movq %rbx, %rdi
callq 0x2aef2
cvttpd2dq (%rsp), %xmm0
cvtdq2pd %xmm0, %xmm1
cvtsi2sd %r14d, %xmm0
divsd %xmm0, %xmm1
movapd %xmm1, (%rsp)
leaq 0x18(%rsp), %rdi
callq 0x2aef2
movaps (%rsp), %xmm0
addq $0x48, %rsp
popq %rbx
popq %r14
retq
jmp 0x40a16
jmp 0x40a16
movq %rax, %rbx
leaq 0x18(%rsp), %rdi
callq 0x2aef2
movq %rbx, %rdi
callq 0x8870
nop
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: MultiallelicCounts::getPiThisVariant()
double MultiallelicCounts::getPiThisVariant() {
    
    std::vector<int> nonMissingHaplotypeVars = haplotypeVariants;
    nonMissingHaplotypeVars.erase(std::remove(nonMissingHaplotypeVars.begin(), nonMissingHaplotypeVars.end(), -1), nonMissingHaplotypeVars.end());
    
    int countedNumComparisons = 0;  // TEST
    int numDiffs = 0; int numHaplotypes = (int) nonMissingHaplotypeVars.size();
    for (std::vector<std::string>::size_type i = 0; i !=  numHaplotypes - 1; i++) {
        for (std::vector<std::string>::size_type j = i+1; j != numHaplotypes; j++) {
            if (nonMissingHaplotypeVars[i] != nonMissingHaplotypeVars[j]) {
                numDiffs++;
            }
            countedNumComparisons++;
        }
    }
    int numComparisons = (numHaplotypes * (numHaplotypes -1)) / 2;
    assert(numComparisons == countedNumComparisons);
    
    double piThisVar = (double)numDiffs/(double)numComparisons;
    
    return piThisVar;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
subq $0x28, %rsp
leaq 0x38(%rdi), %rsi
leaq 0x8(%rsp), %rbx
movq %rbx, %rdi
callq 0x2c6d4
movq (%rbx), %rdi
movq 0x8(%rbx), %rsi
leaq 0x24(%rsp), %rdx
orl $-0x1, (%rdx)
callq 0x451ae
leaq 0x8(%rsp), %rdi
movq 0x8(%rdi), %rdx
movq %rax, %rsi
callq 0x439ba
movq 0x8(%rsp), %rdx
movq 0x10(%rsp), %rcx
subq %rdx, %rcx
shrq $0x2, %rcx
leal -0x1(%rcx), %eax
movslq %eax, %r8
movslq %ecx, %r9
leaq 0x4(%rdx), %r10
decq %r9
xorl %esi, %esi
xorl %edi, %edi
xorl %r11d, %r11d
cmpq %r8, %r11
je 0x40acb
leaq 0x1(%r11), %rbx
xorl %r14d, %r14d
cmpq %r14, %r9
je 0x40abc
movl (%rdx,%r11,4), %ebp
xorl %r15d, %r15d
cmpl (%r10,%r14,4), %ebp
setne %r15b
addl %r15d, %esi
incq %r14
jmp 0x40aa0
addl %r14d, %edi
addq $0x4, %r10
decq %r9
movq %rbx, %r11
jmp 0x40a94
imull %ecx, %eax
pushq $0x2
popq %rcx
cltd
idivl %ecx
cmpl %edi, %eax
jne 0x40b03
cvtsi2sd %esi, %xmm1
cvtsi2sd %edi, %xmm0
divsd %xmm0, %xmm1
movsd %xmm1, (%rsp)
leaq 0x8(%rsp), %rdi
callq 0x2aef2
movsd (%rsp), %xmm0
addq $0x28, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
leaq 0x5e68c(%rip), %rdi     # 0x9f196
leaq 0x5e6ad(%rip), %rsi     # 0x9f1be
leaq 0x5e6bc(%rip), %rcx     # 0x9f1d4
movl $0x15e, %edx            # imm = 0x15E
callq 0x82f0
jmp 0x40b24
movq %rax, %rbx
leaq 0x8(%rsp), %rdi
callq 0x2aef2
movq %rbx, %rdi
callq 0x8870
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: testOverallReadDepth(int, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&)
bool testOverallReadDepth(const int maxReadDepth,const int minReadDepth, const std::string& infoField) {
    std::vector<std::string> info = split(infoField, ';');
    if (info[0] == "INDEL") {
        split(info[1], '=', info);
    } else {
        split(info[0], '=', info);
    }
    int DP = atoi((info.back()).c_str());
    if (DP <= maxReadDepth && DP >= minReadDepth) { return true; }
    else { return false; }
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
subq $0x20, %rsp
movl %esi, %ebx
movl %edi, %ebp
leaq 0x8(%rsp), %r14
pushq $0x3b
popq %rax
movq %r14, %rdi
movq %rdx, %rsi
movl %eax, %edx
callq 0x40349
movq (%r14), %rdi
leaq 0x55723(%rip), %rsi     # 0x976ba
callq 0x2193f
movzbl %al, %edi
shll $0x5, %edi
addq (%r14), %rdi
pushq $0x3d
popq %rsi
movq %r14, %rdx
callq 0x4011c
leaq 0x8(%rsp), %r14
movq 0x8(%r14), %rax
movq -0x20(%rax), %rdi
callq 0x86f0
cmpl %ebp, %eax
setle %cl
cmpl %ebx, %eax
setge %bl
andb %cl, %bl
movq %r14, %rdi
callq 0x28a08
movl %ebx, %eax
addq $0x20, %rsp
popq %rbx
popq %r14
popq %rbp
retq
movq %rax, %rbx
leaq 0x8(%rsp), %rdi
callq 0x28a08
movq %rbx, %rdi
callq 0x8870
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: testMaxNumHet(FilterResult&, std::vector<int, std::allocator<int>>&, std::vector<int, std::allocator<int>>&, std::vector<int, std::allocator<int>>&, int, std::vector<std::vector<int, std::allocator<int>>, std::allocator<std::vector<int, std::allocator<int>>>>&)
bool testMaxNumHet(FilterResult& result, std::vector<int>& depthsHetFailed, std::vector<int>& depthsHetPassed, std::vector<int>& numVariantsPerHetCount, int maxNumHet, std::vector<std::vector<int> >& num_indiv_het_vs_depth) {
    // filter out sites where more than MAX_NUM_HET individuals are heterozygous
    int num_hets = 0;
    for (std::vector<std::vector<int> >::size_type i = 0; i < result.counts.individualsWithVariant.size(); i++) {
        if (result.counts.individualsWithVariant[i] == 1)
            num_hets++;
    }
    numVariantsPerHetCount[num_hets]++;
    
    // Randomly sample 1% of sites for num_indiv_het vs depth scatterplot
    double rn = ((double) rand() / RAND_MAX);
    if (rn < 0.01) {
        std::vector<int> this_num_het_depth; this_num_het_depth.push_back(num_hets); this_num_het_depth.push_back(result.counts.overallDepth); 
        num_indiv_het_vs_depth.push_back(this_num_het_depth);
    }
    
    if (num_hets > maxNumHet) {
        depthsHetFailed.push_back(result.counts.overallDepth);
        return false;
    } else {
        depthsHetPassed.push_back(result.counts.overallDepth);
        return true;
    }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %r9, %r12
movl %r8d, %ebp
movq %rdx, %rbx
andl $0x0, 0xc(%rsp)
movq %rsi, %r15
movq %rdi, %r14
movq 0x78(%rdi), %rax
movq 0x80(%rdi), %rdx
subq %rax, %rdx
sarq $0x2, %rdx
xorl %r13d, %r13d
xorl %esi, %esi
cmpq %rdx, %rsi
jae 0x42047
cmpl $0x1, (%rax,%rsi,4)
jne 0x42042
incl %r13d
movl %r13d, 0xc(%rsp)
incq %rsi
jmp 0x4202f
movslq %r13d, %rax
movq (%rcx), %rcx
incl (%rcx,%rax,4)
callq 0x8160
cvtsi2sd %eax, %xmm0
divsd 0x500bf(%rip), %xmm0    # 0x92120
movsd 0x5d037(%rip), %xmm1    # 0x9f0a0
ucomisd %xmm0, %xmm1
jbe 0x420b5
xorpd %xmm0, %xmm0
leaq 0x10(%rsp), %rdi
movapd %xmm0, (%rdi)
andq $0x0, 0x10(%rdi)
leaq 0xc(%rsp), %rsi
callq 0x3aca4
leaq 0x10(%r14), %rsi
leaq 0x10(%rsp), %rdi
callq 0x3aca4
leaq 0x10(%rsp), %rsi
movq %r12, %rdi
callq 0x3b5c4
leaq 0x10(%rsp), %rdi
callq 0x2aef2
movl 0xc(%rsp), %r13d
addq $0x10, %r14
cmpl %ebp, %r13d
setle %bpl
cmovleq %rbx, %r15
movq %r15, %rdi
movq %r14, %rsi
callq 0x3aca4
movl %ebp, %eax
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %rbx
leaq 0x10(%rsp), %rdi
callq 0x2aef2
movq %rbx, %rdi
callq 0x8870
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: tabulateVector(std::vector<int, std::allocator<int>>&)
std::map<int, int> tabulateVector(std::vector<int>& vec) {
    std::vector<int> vecCopy(vec); 
    std::sort(vecCopy.begin(), vecCopy.end());
    std::vector<int>::iterator it = std::unique(vecCopy.begin(), vecCopy.end());
    vecCopy.resize(std::distance(vecCopy.begin(), it));
    
    std::map<int, int>  table;
    //int pos = 0;
    for (std::vector<int>::size_type i = 0; i != vecCopy.size(); i++) {
        int mycount = std::count(vec.begin(), vec.end(), vecCopy[i]);
        table[vecCopy[i]] = mycount;
        //pos = pos + mycount;
    }
    return table;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x20, %rsp
movq %rsi, %r14
movq %rdi, %rbx
leaq 0x8(%rsp), %r15
movq %r15, %rdi
callq 0x2c6d4
movq (%r15), %rdi
movq 0x8(%r15), %rsi
callq 0x45b51
movq 0x8(%rsp), %rdi
movq 0x10(%rsp), %rsi
callq 0x45f51
leaq 0x8(%rsp), %rdi
subq (%rdi), %rax
sarq $0x2, %rax
movq %rax, %rsi
callq 0x43aec
leaq 0x8(%rbx), %rax
andl $0x0, 0x8(%rbx)
andq $0x0, 0x10(%rbx)
movq %rax, 0x18(%rbx)
movq %rax, 0x20(%rbx)
andq $0x0, 0x28(%rbx)
xorl %r12d, %r12d
xorl %r13d, %r13d
movq 0x8(%rsp), %rdx
movq 0x10(%rsp), %rax
subq %rdx, %rax
sarq $0x2, %rax
cmpq %rax, %r13
je 0x421a8
movq (%r14), %rdi
movq 0x8(%r14), %rsi
addq %r12, %rdx
callq 0x460cb
movq %rax, %r15
movq 0x8(%rsp), %rsi
addq %r12, %rsi
movq %rbx, %rdi
callq 0x43b1e
movl %r15d, (%rax)
incq %r13
addq $0x4, %r12
jmp 0x42164
leaq 0x8(%rsp), %rdi
callq 0x2aef2
movq %rbx, %rax
addq $0x20, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
jmp 0x421c5
movq %rax, %r14
jmp 0x421d5
movq %rax, %r14
movq %rbx, %rdi
callq 0x44472
leaq 0x8(%rsp), %rdi
callq 0x2aef2
movq %r14, %rdi
callq 0x8870
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: rearrange_doubletons(std::vector<std::vector<int, std::allocator<int>>, std::allocator<std::vector<int, std::allocator<int>>>>&)
void rearrange_doubletons(std::vector<std::vector<int> >& doubletons){
    for (std::vector<std::vector<int> >::size_type i = 0; i < doubletons.size(); i++) {
        for (int j = 0; j < i; j++) {
            doubletons[i][j] = doubletons[i][j] + doubletons[j][i];
            doubletons[j][i] = 0;
        }    
    }
}

// Assembly:
movq (%rdi), %rcx
movq 0x8(%rdi), %rax
subq %rcx, %rax
pushq $0x18
popq %rsi
cqto
idivq %rsi
xorl %edx, %edx
cmpq %rax, %rdx
je 0x42233
imulq $0x18, %rdx, %rsi
addq %rcx, %rsi
movq %rcx, %rdi
xorl %r8d, %r8d
cmpq %r8, %rdx
je 0x4222e
movq (%rsi), %r9
movq (%rdi), %r10
movl (%r10,%rdx,4), %r11d
addl %r11d, (%r9,%r8,4)
andl $0x0, (%r10,%rdx,4)
incq %r8
addq $0x18, %rdi
jmp 0x4220d
incq %rdx
jmp 0x421fb
retq
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: readSampleNamesFromTextFile(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&)
std::vector<string> readSampleNamesFromTextFile(const std::string& sampleNameFile) {
    std::vector<string> sampleNames;
    std::ifstream* sampleFile = new std::ifstream(sampleNameFile.c_str());
    string line;
    while (getline(*sampleFile, line)) {
        sampleNames.push_back(line);
    }
    return sampleNames;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
subq $0x20, %rsp
movq %rsi, %r15
movq %rdi, %rbx
xorps %xmm0, %xmm0
movups %xmm0, (%rdi)
andq $0x0, 0x10(%rdi)
movl $0x208, %edi            # imm = 0x208
callq 0x8490
movq %rax, %r14
movq (%r15), %rsi
pushq $0x8
popq %rdx
movq %rax, %rdi
callq 0x8890
leaq 0x10(%rsp), %rax
movq %rax, -0x10(%rax)
andq $0x0, -0x8(%rax)
movb $0x0, (%rax)
movq %rsp, %r15
movq %r14, %rdi
movq %r15, %rsi
callq 0x80a0
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
testb $0x5, 0x20(%rax,%rcx)
jne 0x423eb
movq %rbx, %rdi
movq %r15, %rsi
callq 0x2b0a4
jmp 0x423c5
movq %rsp, %rdi
callq 0x8978
movq %rbx, %rax
addq $0x20, %rsp
popq %rbx
popq %r14
popq %r15
retq
movq %rax, %r15
movl $0x208, %esi            # imm = 0x208
movq %r14, %rdi
callq 0x84a0
jmp 0x42422
movq %rax, %r15
jmp 0x42422
movq %rax, %r15
movq %rsp, %rdi
callq 0x8978
movq %rbx, %rdi
callq 0x28a08
movq %r15, %rdi
callq 0x8870
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: isGzip(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&)
bool isGzip(const std::string& filename)
{
    size_t suffix_length = sizeof(GZIP_EXT) - 1;
    
    // Assume files without an extension are not compressed
    if(filename.length() < suffix_length)
        return false;
    
    std::string extension = suffix(filename, suffix_length);
    return extension == GZIP_EXT;
}

// Assembly:
pushq %r14
pushq %rbx
subq $0x28, %rsp
cmpq $0x3, 0x8(%rdi)
jae 0x42480
xorl %ebx, %ebx
jmp 0x424ac
movq %rdi, %rsi
leaq 0x8(%rsp), %r14
pushq $0x3
popq %rdx
movq %r14, %rdi
callq 0x42432
leaq 0x5c633(%rip), %rsi     # 0x9eacd
movq %r14, %rdi
callq 0x2193f
movl %eax, %ebx
movq %r14, %rdi
callq 0x8978
movl %ebx, %eax
addq $0x28, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: createReader(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, std::_Ios_Openmode)
std::istream* createReader(const std::string& filename, std::ios_base::openmode mode)
{
    if(isGzip(filename))
    {
        igzstream* pGZ = new igzstream(filename.c_str(), mode);
        assertGZOpen(*pGZ, filename);
        return pGZ;
    }
    else
    {
        std::ifstream* pReader = new std::ifstream(filename.c_str(), mode);
        assertFileOpen(*pReader, filename);
        return pReader;
    }
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movl %esi, %ebp
movq %rdi, %r14
callq 0x4246e
testb %al, %al
je 0x425c7
movl $0x2a0, %edi            # imm = 0x2A0
callq 0x8490
movq %rax, %rbx
movq (%r14), %rsi
movq %rax, %rdi
movl %ebp, %edx
callq 0x43b6c
movq %rbx, %rdi
movq %r14, %rsi
callq 0x42546
addq $0x188, %rbx            # imm = 0x188
jmp 0x425ec
movl $0x208, %edi            # imm = 0x208
callq 0x8490
movq %rax, %rbx
movq (%r14), %rsi
movq %rax, %rdi
movl %ebp, %edx
callq 0x8890
movq %rbx, %rdi
movq %r14, %rsi
callq 0x424b6
movq %rbx, %rax
popq %rbx
popq %r14
popq %rbp
retq
movq %rax, %r14
movl $0x208, %esi            # imm = 0x208
jmp 0x42606
movq %rax, %r14
movl $0x2a0, %esi            # imm = 0x2A0
movq %rbx, %rdi
callq 0x84a0
movq %r14, %rdi
callq 0x8870
// File: /workspace/github_cpp_makefile_star2_O2/millanek[P]evo/process_vcf_utils.cpp
// Function: createWriter(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, std::_Ios_Openmode)
std::ostream* createWriter(const std::string& filename,
                           std::ios_base::openmode mode)
{
    if(isGzip(filename))
    {
        ogzstream* pGZ = new ogzstream(filename.c_str(), mode);
        assertGZOpen(*pGZ, filename);
        return pGZ;
    }
    else
    {
        std::ofstream* pWriter = new std::ofstream(filename.c_str(), mode);
        assertFileOpen(*pWriter, filename);
        return pWriter;
    }
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movl %esi, %ebp
movq %rdi, %r14
callq 0x4246e
testb %al, %al
je 0x42656
movl $0x298, %edi            # imm = 0x298
callq 0x8490
movq %rax, %rbx
movq (%r14), %rsi
movq %rax, %rdi
movl %ebp, %edx
callq 0x43c26
movq %rbx, %rdi
movq %r14, %rsi
callq 0x42546
addq $0x188, %rbx            # imm = 0x188
jmp 0x4267b
movl $0x200, %edi            # imm = 0x200
callq 0x8490
movq %rax, %rbx
movq (%r14), %rsi
movq %rax, %rdi
movl %ebp, %edx
callq 0x84e0
movq %rbx, %rdi
movq %r14, %rsi
callq 0x424fe
movq %rbx, %rax
popq %rbx
popq %r14
popq %rbp
retq
movq %rax, %r14
movl $0x200, %esi            # imm = 0x200
jmp 0x42695
movq %rax, %r14
movl $0x298, %esi            # imm = 0x298
movq %rbx, %rdi
callq 0x84a0
movq %r14, %rdi
callq 0x8870