LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/sparseSA.cpp
// Function: sparseSA::collectAllSMAMs(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, int, interval_t, std::vector<match_t, std::allocator<match_t>>&, int, int, int) const
void sparseSA::collectAllSMAMs(const string &P, int prefix,
        interval_t xmi, vector<match_t> &matches, int min_len, int maxCount, int maxLeft) const {
  // All of the suffixes in xmi's interval are right maximal.
  if(xmi.size() <= maxCount)
        for(long i = xmi.start; i <= xmi.end; i++) 
            find_LmaximalStrict(P, prefix, SA[i], xmi.depth, matches, min_len, maxLeft);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x48, %rsp
movl %r9d, 0x4(%rsp)
movq %r8, 0x18(%rsp)
movl %edx, %ebp
movq %rsi, 0x30(%rsp)
movq %rdi, 0x28(%rsp)
movslq 0x80(%rsp), %rdi
movq (%rcx), %r14
movq %rcx, 0x8(%rsp)
movq 0x8(%rcx), %rax
movq %rax, %rdx
subq %r14, %rdx
leaq 0x1(%rdx), %rdx
setl %sil
cmpq %rdi, %rdx
setg %cl
orb %sil, %cl
jne 0x1351b
movl 0x88(%rsp), %ebx
movslq %ebp, %r12
movl %r12d, %ecx
movq %rcx, 0x10(%rsp)
leaq -0x1(%r12), %rcx
movq %rcx, 0x20(%rsp)
negq %r12
testl %ebx, %ebx
jle 0x1350b
movq 0x8(%rsp), %rcx
movl 0x10(%rcx), %esi
movq 0x28(%rsp), %rcx
movq 0x50(%rcx), %r8
movq 0x70(%rcx), %rcx
movl (%rcx,%r14,4), %edi
cmpl %ebp, %edi
movl %ebp, %edx
cmovbl %edi, %edx
movl %ebp, %ecx
subl %edx, %ecx
addl %esi, %edx
movq 0x30(%rsp), %r9
movq (%r9), %r10
addq 0x20(%rsp), %r10
leaq (%r8,%rdi), %r11
decq %r11
movl %ebx, %r13d
xorl %r9d, %r9d
leaq (%rdi,%r9), %r8
cmpq %r9, %r12
je 0x134dd
testq %r8, %r8
je 0x134dd
movb (%r10,%r9), %r15b
cmpb (%r11,%r9), %r15b
jne 0x134d0
decq %r9
decl %ebx
jne 0x134ac
movl %r13d, %ebx
jmp 0x1350b
movq 0x10(%rsp), %rcx
addl %r9d, %ecx
subl %r9d, %esi
movl %esi, %edx
cmpl 0x4(%rsp), %edx
movl %r13d, %ebx
jl 0x1350b
movq %r8, 0x38(%rsp)
movl %ecx, 0x40(%rsp)
movl %edx, 0x44(%rsp)
movq 0x18(%rsp), %rdi
leaq 0x38(%rsp), %rsi
callq 0x16a7a
movq 0x8(%rsp), %rax
movq 0x8(%rax), %rax
leaq 0x1(%r14), %rcx
cmpq %rax, %r14
movq %rcx, %r14
jl 0x13464
addq $0x48, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/sparseSA.h
// Function: vec_uchar::set(unsigned long, int)
void set(size_t idx, int v){
    if(v >= std::numeric_limits<unsigned char>::max()) {
        vec.at(idx) = std::numeric_limits<unsigned char>::max();
        M.push_back(item_t(idx, v));
    }
    else { vec.at(idx) = (unsigned char)v; }
  }

// Assembly:
subq $0x18, %rsp
movl %edx, %eax
movq (%rdi), %rcx
movq 0x8(%rdi), %rdx
subq %rcx, %rdx
cmpl $0xff, %eax
jge 0x159c1
cmpq %rsi, %rdx
jbe 0x159ff
movb %al, (%rcx,%rsi)
jmp 0x159fa
cmpq %rsi, %rdx
jbe 0x159ff
movb $-0x1, (%rcx,%rsi)
movq %rsi, 0x8(%rsp)
movl %eax, 0x10(%rsp)
movq 0x20(%rdi), %rsi
cmpq 0x28(%rdi), %rsi
je 0x159ec
movups 0x8(%rsp), %xmm0
movups %xmm0, (%rsi)
addq $0x10, 0x20(%rdi)
jmp 0x159fa
addq $0x18, %rdi
leaq 0x8(%rsp), %rdx
callq 0x1688a
addq $0x18, %rsp
retq
leaq 0x2a9fd(%rip), %rdi     # 0x40403
xorl %eax, %eax
callq 0x74e0
nop
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/fasta.cpp
// Function: trim(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>&, long&, long&)
void trim(string &line, long &start, long &end) {
  // Trim leading spaces.
  for(long i = start; i < (int)line.length(); i++) {
    if(line[i] != ' ') { start = i; break; }
  }
  // Trim trailing spaces.
  for(long i = line.length() - 1; i >= 0; i--) {
    if(line[i] != ' ') { end = i; break; }
    if(i == 0) break;
  }
}

// Assembly:
movq (%rsi), %rcx
movq 0x8(%rdi), %rax
movslq %eax, %r8
cmpq %r8, %rcx
jge 0x196f2
movq (%rdi), %r9
cmpb $0x20, (%r9,%rcx)
jne 0x196eb
incq %rcx
cmpq %rcx, %r8
jne 0x196da
jmp 0x196f2
movq %rcx, (%rsi)
movq 0x8(%rdi), %rax
movq (%rdi), %rcx
decq %rax
testq %rax, %rax
js 0x19709
cmpb $0x20, (%rcx,%rax)
jne 0x1970a
addq $-0x1, %rax
jb 0x196f8
retq
movq %rax, (%rdx)
retq
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/fasta.cpp
// Function: fastqInputReader::fastqInputReader(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, bool)
fastqInputReader::fastqInputReader(const string& fName, bool nucOnly): 
        nucleotidesOnly(nucOnly), filename(fName) {
    pthread_mutex_init(&readLock_, NULL);
    fp = gzopen(fName.c_str(),"r");
    if(fp == NULL){
        fprintf(stderr, "ERROR: file %s could not be read.", fName.c_str());
        exit(1);
    }
    seq = kseq_init(fp);
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %r14
movq %rdi, %rbx
movb %dl, 0x14(%rdi)
leaq 0x18(%rdi), %r15
leaq 0x28(%rdi), %r12
movq %r12, 0x18(%rdi)
movq (%rsi), %rsi
movq 0x8(%r14), %rdx
addq %rsi, %rdx
movq %r15, %rdi
callq 0xc1d8
leaq 0x38(%rbx), %rdi
xorl %esi, %esi
callq 0x74d0
movq (%r14), %rdi
leaq 0x27b17(%rip), %rsi     # 0x4170b
callq 0x74b0
movq %rax, (%rbx)
testq %rax, %rax
je 0x19c19
movq %rax, %rdi
callq 0x19c40
movq %rax, 0x8(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
movq %r14, %rdi
callq 0x7953
movq %rax, %rbx
movq (%r15), %rdi
cmpq %r12, %rdi
je 0x19c38
movq (%r12), %rsi
incq %rsi
callq 0x72f0
movq %rbx, %rdi
callq 0x7600
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/fasta.cpp
// Function: fastqInputReader::open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, bool)
void fastqInputReader::open(const string& fileName, bool nucOnly){
    nucleotidesOnly = nucOnly;
    filename = fileName;
    fp = gzopen(fileName.c_str(),"r");
    if(fp == NULL){
        fprintf(stderr, "ERROR: file %s could not be read.", fileName.c_str());
        exit(1);
    }
    seq = kseq_init(fp);
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %r14
movq %rdi, %rbx
movb %dl, 0x14(%rdi)
addq $0x18, %rdi
callq 0x7170
movq (%r14), %rdi
leaq 0x27a61(%rip), %rsi     # 0x4170b
callq 0x74b0
movq %rax, (%rbx)
testq %rax, %rax
je 0x19ccb
movq %rax, %rdi
callq 0x19c40
movq %rax, 0x8(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r14
retq
movq %r14, %rdi
callq 0x797a
nop
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/dp.cpp
// Function: dp_scores::updateScoreMatrixDna()
void dp_scores::updateScoreMatrixDna(){//presumes match/mismatch has been added correctly
    for(int i = 0; i < 127; i++)
        for(int j = 0; j < 127; j++)
            //set to value that is small enough to be used with large reads and not cause overflow with current score
            scoreMatrix[i][j] = -200000;
    for(int i = 'A'; i <= 'Z'; i++)
        for(int j = 'A'; j <= 'Z'; j++)
            scoreMatrix[i][j] = i==j ? match : mismatch;
    for(int i = 'a'; i <= 'z'; i++)
        for(int j = 'a'; j <= 'z'; j++)
            scoreMatrix[i][j] = i==j ? match : mismatch;
}

// Assembly:
leaq 0x1c(%rdi), %rax
xorl %ecx, %ecx
movdqa 0x29e26(%rip), %xmm0    # 0x44270
movdqa 0x29dfe(%rip), %xmm1    # 0x44250
movdqa 0x25be6(%rip), %xmm2    # 0x40040
movdqa 0x2a41e(%rip), %xmm3    # 0x44880
pshufd $0xf5, %xmm3, %xmm4     # xmm4 = xmm3[1,1,3,3]
movdqa 0x2a421(%rip), %xmm5    # 0x44890
xorl %edx, %edx
movdqa %xmm1, %xmm6
movdqa %xmm0, %xmm7
movdqa %xmm6, %xmm8
pxor %xmm2, %xmm8
movdqa %xmm3, %xmm9
pcmpgtd %xmm8, %xmm9
pshufd $0xf5, %xmm8, %xmm8     # xmm8 = xmm8[1,1,3,3]
pcmpeqd %xmm4, %xmm8
pand %xmm9, %xmm8
movd %xmm8, %esi
testb $0x1, %sil
je 0x1a4b0
movl $0xfffcf2c0, -0xc(%rax,%rdx,4) # imm = 0xFFFCF2C0
pextrw $0x4, %xmm8, %esi
testb $0x1, %sil
je 0x1a4c4
movl $0xfffcf2c0, -0x8(%rax,%rdx,4) # imm = 0xFFFCF2C0
movdqa %xmm7, %xmm8
pxor %xmm2, %xmm8
movdqa %xmm3, %xmm9
pcmpgtd %xmm8, %xmm9
pshufd $0xf5, %xmm8, %xmm8     # xmm8 = xmm8[1,1,3,3]
pcmpeqd %xmm4, %xmm8
pand %xmm9, %xmm8
pextrw $0x0, %xmm8, %esi
testb $0x1, %sil
je 0x1a4fc
movl $0xfffcf2c0, -0x4(%rax,%rdx,4) # imm = 0xFFFCF2C0
pextrw $0x4, %xmm8, %esi
testb $0x1, %sil
je 0x1a50f
movl $0xfffcf2c0, (%rax,%rdx,4) # imm = 0xFFFCF2C0
addq $0x4, %rdx
paddq %xmm5, %xmm6
paddq %xmm5, %xmm7
cmpq $0x80, %rdx
jne 0x1a479
incq %rcx
addq $0x1fc, %rax            # imm = 0x1FC
cmpq $0x7f, %rcx
jne 0x1a46f
leaq 0x8210(%rdi), %rax
movl $0x41, %ecx
xorl %edx, %edx
xorl %esi, %esi
xorl %r8d, %r8d
cmpq %rsi, %rdx
setne %r8b
movl (%rdi,%r8,4), %r8d
movl %r8d, (%rax,%rsi,4)
incq %rsi
cmpq $0x1a, %rsi
jne 0x1a54b
incq %rcx
incq %rdx
addq $0x1fc, %rax            # imm = 0x1FC
cmpq $0x5b, %rcx
jne 0x1a549
leaq 0xc210(%rdi), %rax
movl $0x61, %ecx
xorl %edx, %edx
xorl %esi, %esi
xorl %r8d, %r8d
cmpq %rsi, %rdx
setne %r8b
movl (%rdi,%r8,4), %r8d
movl %r8d, (%rax,%rsi,4)
incq %rsi
cmpq $0x1a, %rsi
jne 0x1a588
incq %rcx
incq %rdx
addq $0x1fc, %rax            # imm = 0x1FC
cmpq $0x7b, %rcx
jne 0x1a586
retq
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/dp.cpp
// Function: dynProg::initDPMatrix(int, int, bool)
void dynProg::initDPMatrix(int dimensionL2, int dimensionL1, bool affine){
    DP_L2 = dimensionL2;
    DP_L1 = dimensionL1;
    M = new int * [DP_L2];
    for(int i = 0; i < DP_L2; i++){
        M[i] = new int[DP_L1];
    }
    if(affine){
        UP = new int * [DP_L1];
        LEFT = new int * [DP_L1];
        for(int i = 0; i < DP_L2; i++){
            UP[i] = new int[DP_L1];
            LEFT[i] = new int[DP_L1];
        }
    }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movl %ecx, 0x4(%rsp)
movl %edx, %ebp
movl %esi, %r14d
movq %rdi, %rbx
movl %esi, 0x18(%rdi)
movl %edx, 0x1c(%rdi)
movl %esi, %r13d
leaq (,%r13,8), %rdi
testl %esi, %esi
movq $-0x1, %r15
cmovsq %r15, %rdi
callq 0x7030
movq %rax, (%rbx)
testl %r14d, %r14d
jle 0x1a61f
movl %ebp, %r12d
shlq $0x2, %r12
testl %ebp, %ebp
cmovsq %r15, %r12
xorl %r15d, %r15d
movq %r12, %rdi
callq 0x7030
movq (%rbx), %rcx
movq %rax, (%rcx,%r15,8)
incq %r15
cmpq %r15, %r13
jne 0x1a608
cmpb $0x0, 0x4(%rsp)
je 0x1a697
movslq %ebp, %r15
leaq (,%r15,8), %r12
testl %ebp, %ebp
movq $-0x1, %rax
cmovsq %rax, %r12
movq %r12, %rdi
callq 0x7030
movq %rax, 0x8(%rbx)
movq %r12, %rdi
callq 0x7030
movq %rax, 0x10(%rbx)
testl %r14d, %r14d
jle 0x1a697
shlq $0x2, %r15
testl %ebp, %ebp
movq $-0x1, %rax
cmovsq %rax, %r15
xorl %r14d, %r14d
movq %r15, %rdi
callq 0x7030
movq 0x8(%rbx), %rcx
movq %rax, (%rcx,%r14,8)
movq %r15, %rdi
callq 0x7030
movq 0x10(%rbx), %rcx
movq %rax, (%rcx,%r14,8)
incq %r14
cmpq %r14, %r13
jne 0x1a66f
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/dp.cpp
// Function: dynProg::deleteDPMatrix(bool)
void dynProg::deleteDPMatrix(bool affine){
    for(int i = 0; i < DP_L2; i++)
        delete[] M[ i ];
    delete[] M;
    if(affine){
        for(int i = 0; i < DP_L2; i++){
            delete[] UP[ i ];
            delete[] LEFT[ i ];
        }
        delete[] UP;
        delete[] LEFT;
    }
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movl %esi, %ebp
movq %rdi, %rbx
movl 0x18(%rdi), %eax
testl %eax, %eax
jle 0x1a6ec
xorl %r14d, %r14d
movq (%rbx), %rcx
movq (%rcx,%r14,8), %rdi
testq %rdi, %rdi
je 0x1a6e1
callq 0x7400
movl 0x18(%rbx), %eax
incq %r14
movslq %eax, %rcx
cmpq %rcx, %r14
jl 0x1a6cd
movq (%rbx), %rdi
testq %rdi, %rdi
je 0x1a6f9
callq 0x7400
testb %bpl, %bpl
je 0x1a757
cmpl $0x0, 0x18(%rbx)
jle 0x1a737
xorl %r14d, %r14d
movq 0x8(%rbx), %rax
movq (%rax,%r14,8), %rdi
testq %rdi, %rdi
je 0x1a719
callq 0x7400
movq 0x10(%rbx), %rax
movq (%rax,%r14,8), %rdi
testq %rdi, %rdi
je 0x1a72b
callq 0x7400
incq %r14
movslq 0x18(%rbx), %rax
cmpq %rax, %r14
jl 0x1a707
movq 0x8(%rbx), %rdi
testq %rdi, %rdi
je 0x1a745
callq 0x7400
movq 0x10(%rbx), %rdi
testq %rdi, %rdi
je 0x1a757
popq %rbx
popq %r14
popq %rbp
jmp 0x7400
popq %rbx
popq %r14
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/utils.cpp
// Function: Utils::contains(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, long, long, char)
bool contains(const std::string & str,const long begin,const long end, const char c){
        bool contains = false;
        long i = begin;
        assert(begin >= 0 && end < (long)str.length());
        while(!contains && i <= end){
            contains = str[i] == c;
            i++;
        }
        return contains;
    }

// Assembly:
cmpq %rdx, %rsi
jle 0x1eb0b
xorl %eax, %eax
retq
movq (%rdi), %rdi
cmpb %cl, (%rdi,%rsi)
sete %al
je 0x1eb22
leaq 0x1(%rsi), %r8
cmpq %rdx, %rsi
movq %r8, %rsi
jl 0x1eb0e
retq
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/mapper.cpp
// Function: recoverCIGAR3from4(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>)
string recoverCIGAR3from4(string cigar4){
    stringstream ss(cigar4);
    stringstream cigar3;
    int i;
    char symbol;
    int matchLength = 0;
    while (ss >> i){
        ss.get(symbol);
        if(symbol == 'X' || symbol == '=')
            matchLength += i;
        else{
            //finish previous series of match/mismatch
            if(matchLength > 0){
                cigar3 << matchLength << 'M';
                matchLength = 0;
            }
            cigar3 << i << symbol;
        }
    }
    //finish possible last series of matches
    if(matchLength > 0)
        cigar3 << matchLength << 'M';
    return cigar3.str();
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x328, %rsp            # imm = 0x328
movq %rdi, 0x10(%rsp)
leaq 0x1a0(%rsp), %rdi
movl $0x18, %edx
callq 0x7550
leaq 0x18(%rsp), %rdi
callq 0x71e0
xorl %r15d, %r15d
leaq 0x28(%rsp), %r12
leaq 0x1a0(%rsp), %r14
leaq 0xc(%rsp), %r13
leaq 0xb(%rsp), %rbp
leaq 0xa(%rsp), %rbx
movq %r14, %rdi
movq %r13, %rsi
callq 0x7190
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
testb $0x5, 0x20(%rax,%rcx)
jne 0x1ecca
movq %r14, %rdi
movq %rbp, %rsi
callq 0x7440
movzbl 0xb(%rsp), %eax
cmpl $0x58, %eax
je 0x1ec72
cmpl $0x3d, %eax
jne 0x1ec79
addl 0xc(%rsp), %r15d
jmp 0x1ec3f
testl %r15d, %r15d
jle 0x1eca1
movq %r12, %rdi
movl %r15d, %esi
callq 0x75d0
movb $0x4d, 0xa(%rsp)
movl $0x1, %edx
movq %rax, %rdi
movq %rbx, %rsi
callq 0x7340
xorl %r15d, %r15d
movl 0xc(%rsp), %esi
movq %r12, %rdi
callq 0x75d0
movb 0xb(%rsp), %cl
movb %cl, 0xa(%rsp)
movl $0x1, %edx
movq %rax, %rdi
movq %rbx, %rsi
callq 0x7340
jmp 0x1ec3f
testl %r15d, %r15d
jle 0x1ecef
movq %r12, %rdi
movl %r15d, %esi
callq 0x75d0
leaq 0xa(%rsp), %rsi
movb $0x4d, (%rsi)
movl $0x1, %edx
movq %rax, %rdi
callq 0x7340
leaq 0x30(%rsp), %rsi
movq 0x10(%rsp), %rdi
callq 0x7540
movq 0x35293(%rip), %rbx     # 0x53f98
leaq 0x18(%rsp), %r12
movq %r12, %rdi
movq %rbx, %rsi
callq 0x7210
movl $0x80, %r15d
addq %r15, %r12
movq %r12, %rdi
callq 0x7100
movq %r14, %rdi
movq %rbx, %rsi
callq 0x7210
addq %r15, %r14
movq %r14, %rdi
callq 0x7100
movq 0x10(%rsp), %rax
addq $0x328, %rsp            # imm = 0x328
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %rbx
jmp 0x1ed7b
jmp 0x1ed5a
movq %rax, %rbx
movq 0x35234(%rip), %rsi     # 0x53f98
leaq 0x18(%rsp), %rdi
callq 0x7210
leaq 0x98(%rsp), %rdi
callq 0x7100
movq 0x35216(%rip), %rsi     # 0x53f98
leaq 0x1a0(%rsp), %rdi
callq 0x7210
leaq 0x220(%rsp), %rdi
callq 0x7100
movq %rbx, %rdi
callq 0x7600
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/mapper.cpp
// Function: alignment_t::setMate(alignment_t const*, bool, bool)
void alignment_t::setMate(const alignment_t * o, bool concordant, bool upstream){
    mate.flag.set(0,true);//positions for mate to be important: 0,1,5,6,7
    mate.flag.set(1,true);
    mate.flag.set(5,o->flag.test(4));
    mate.flag.set(6,upstream);
    mate.flag.set(7,!upstream);
    mate.concordant = concordant;
    mate.pnext = o->pos;
    mate.pnextGlob = o->refB;
    mate.tLength = max(refE,o->refE) - min(refB,o->refB) + 1;
    long firstPos = flag.test(4) ? refE : refB;
    long secondPos = o->flag.test(4) ? o->refE : o->refB;
    if(firstPos > secondPos) mate.tLength *= -1;
    mate.rnext = rname == o->rname ? "=" : o->rname;
    if(concordant)
        mate.alignmentScore = o->alignmentScore;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x20, %rsp
movl %edx, %ebp
movq %rsi, %r14
movq %rdi, %rbx
movq 0xa0(%rdi), %rax
movq %rax, %rdx
orq $0x3, %rdx
movq %rdx, 0xa0(%rdi)
orq $0x23, %rax
andq $-0xe1, %rdx
testb $0x10, 0x40(%rsi)
cmovneq %rax, %rdx
andq $-0xc1, %rdx
xorb $0x1, %cl
movzbl %cl, %eax
shll $0x6, %eax
addq %rdx, %rax
addq $0x40, %rax
movq %rax, 0xa0(%rdi)
movb %bpl, 0xdc(%rdi)
movq 0x18(%rsi), %rax
movq %rax, 0xc8(%rdi)
movq (%rsi), %rcx
movq %rcx, 0xd0(%rdi)
leaq 0x8(%rsi), %rdx
movq (%rdi), %rsi
movq 0x8(%rdi), %rdi
movq 0x8(%r14), %rax
cmpq %rax, %rdi
cmovgq %rdi, %rax
cmpq %rsi, %rcx
cmovgeq %rsi, %rcx
subl %ecx, %eax
leal 0x1(%rax), %ecx
movl %ecx, 0xd8(%rbx)
testb $0x10, 0x40(%rbx)
cmoveq %rsi, %rdi
testb $0x10, 0x40(%r14)
cmoveq %r14, %rdx
cmpq (%rdx), %rdi
jle 0x202c4
notl %eax
movl %eax, 0xd8(%rbx)
movq 0x50(%rbx), %rdx
movq 0x50(%r14), %r15
cmpq %r15, %rdx
jne 0x2030b
testq %rdx, %rdx
je 0x202ea
movq 0x48(%r14), %r12
movq 0x48(%rbx), %rdi
movq %r12, %rsi
callq 0x7300
testl %eax, %eax
jne 0x2030f
leaq 0x10(%rsp), %rax
movq %rax, -0x10(%rax)
leaq 0x20187(%rip), %rsi     # 0x40481
leaq 0x20181(%rip), %rdx     # 0x40482
movq %rsp, %rdi
callq 0xc2d0
jmp 0x20329
movq 0x48(%r14), %r12
leaq 0x10(%rsp), %rax
movq %rax, -0x10(%rax)
addq %r12, %r15
movq %rsp, %rdi
movq %r12, %rsi
movq %r15, %rdx
callq 0xc1d8
leaq 0xa8(%rbx), %rdi
movq %rsp, %rsi
callq 0x7170
leaq 0x10(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x20353
movq 0x10(%rsp), %rsi
incq %rsi
callq 0x72f0
testb %bpl, %bpl
je 0x20362
movl 0x70(%r14), %eax
movl %eax, 0xe0(%rbx)
addq $0x20, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %rbx
leaq 0x10(%rsp), %rax
movq -0x10(%rax), %rdi
cmpq %rax, %rdi
je 0x2038d
movq 0x10(%rsp), %rsi
incq %rsi
callq 0x72f0
movq %rbx, %rdi
callq 0x7600
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/mapper.cpp
// Function: coveredBases(lis_t&)
int coveredBases(lis_t& interval){
    //sort this candidate region by query position
    interval.sortByReadPos();
    vector<match_t> & seeds = interval.matches;
    int trueCover = seeds[0].len;
    int prevEnd = seeds[0].query + seeds[0].len-1;
    for(size_t i = 1; i < seeds.size(); i++ ){
        int start = max(seeds[i].query,prevEnd+1);
        int stop = max(prevEnd,seeds[i].query + seeds[i].len -1);
        prevEnd = stop;
        trueCover += max(0,stop-start+1);
    }
    return trueCover;
}

// Assembly:
pushq %rbx
movq %rdi, %rbx
callq 0x2b940
movq 0x20(%rbx), %rcx
movq 0x28(%rbx), %rdx
movl 0xc(%rcx), %eax
subq %rcx, %rdx
sarq $0x4, %rdx
cmpq $0x2, %rdx
jb 0x22394
movl 0x8(%rcx), %esi
addl %eax, %esi
decl %esi
decq %rdx
addq $0x1c, %rcx
movl %esi, %edi
leal 0x1(%rdi), %r8d
movl -0x4(%rcx), %esi
movl (%rcx), %r9d
cmpl %r8d, %esi
cmovgl %esi, %r8d
addl %r9d, %esi
decl %esi
cmpl %esi, %edi
cmovgl %edi, %esi
movl %esi, %edi
subl %r8d, %edi
jns 0x22387
movl $0xffffffff, %edi       # imm = 0xFFFFFFFF
addl %edi, %eax
incl %eax
addq $0x10, %rcx
decq %rdx
jne 0x2235e
popq %rbx
retq
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/mapper.cpp
// Function: filterLISwithAlignments(read_t&, std::vector<lis_t, std::allocator<lis_t>>&)
void filterLISwithAlignments(read_t & read, vector<lis_t> & lisIntervals){
    for(size_t i = 0; i < read.alignments.size(); i++){
        alignment_t * a = read.alignments[i];
        vector< lis_t >::iterator it = lisIntervals.begin();
        while(it != lisIntervals.end()) {
            //If alignment overlaps with LIS
            if(a->flag.test(4) != it->fw && a->refE >= it->refBegin && a->refB <= it->refEnd) 
                it = lisIntervals.erase(it);
            else 
                ++it;
        }
    }
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq 0xb0(%rdi), %rdx
movq 0xb8(%rdi), %rsi
cmpq %rdx, %rsi
je 0x24d7f
movq %rdi, %r14
movq 0x8(%rbx), %rcx
xorl %r15d, %r15d
movq (%rbx), %rax
cmpq %rcx, %rax
je 0x24d6d
movq (%rdx,%r15,8), %r12
movb 0x4(%rax), %dl
btl $0x4, 0x40(%r12)
sbbb $0x0, %dl
je 0x24d43
movq 0x8(%r12), %rdx
cmpq 0x8(%rax), %rdx
jl 0x24d43
movq (%r12), %rdx
cmpq 0x10(%rax), %rdx
jle 0x24d4e
addq $0x38, %rax
cmpq %rcx, %rax
jne 0x24d1f
jmp 0x24d5f
movq %rbx, %rdi
movq %rax, %rsi
callq 0x30bc2
movq 0x8(%rbx), %rcx
jmp 0x24d47
movq 0xb0(%r14), %rdx
movq 0xb8(%r14), %rsi
incq %r15
movq %rsi, %rax
subq %rdx, %rax
sarq $0x3, %rax
cmpq %rax, %r15
jb 0x24d13
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/mapper.cpp
// Function: unpairedCopy(alignment_t const*)
alignment_t * unpairedCopy(const alignment_t * a){
  alignment_t * newAln = new alignment_t();
  newAln->refB = a->refB;
  newAln->refE = a->refE;
  newAln->qB = a->qB;
  newAln->qE = a->qE;
  newAln->pos = a->pos;
  newAln->rname = a->rname;
  newAln->refLength = a->refLength;
  newAln->alignmentScore = a->alignmentScore;
  newAln->flag.set(4, a->flag.test(4));
  for(size_t i = 0; i < a->chain.size(); i++)
      newAln->chain.push_back(a->chain[i]);
  return newAln;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
movq %rdi, %r14
movl $0x100, %edi            # imm = 0x100
callq 0x72e0
movq %rax, %rbx
movq %rax, %rdi
callq 0x2c490
movups (%r14), %xmm0
movups %xmm0, (%rbx)
movq 0x10(%r14), %rax
movq %rax, 0x10(%rbx)
movq 0x18(%r14), %rax
movq %rax, 0x18(%rbx)
leaq 0x48(%r14), %rsi
leaq 0x48(%rbx), %rdi
callq 0x7170
movl 0x98(%r14), %eax
movl %eax, 0x98(%rbx)
movl 0x70(%r14), %eax
movl %eax, 0x70(%rbx)
movq 0x40(%r14), %rax
andl $0x10, %eax
movq 0x40(%rbx), %rcx
andq $-0x11, %rcx
orq %rax, %rcx
movq %rcx, 0x40(%rbx)
movq 0xe8(%r14), %rsi
cmpq %rsi, 0xf0(%r14)
je 0x258af
movq %rbx, %r15
addq $0xe8, %r15
xorl %r12d, %r12d
xorl %r13d, %r13d
addq %r12, %rsi
movq %r15, %rdi
callq 0x2b8f4
incq %r13
movq 0xe8(%r14), %rsi
movq 0xf0(%r14), %rax
subq %rsi, %rax
sarq $0x4, %rax
addq $0x10, %r12
cmpq %rax, %r13
jb 0x25883
movq %rbx, %rax
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
movq %rax, %r14
movl $0x100, %esi            # imm = 0x100
movq %rbx, %rdi
callq 0x72f0
movq %r14, %rdi
callq 0x7600
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/mapper.cpp
// Function: setPaired(sparseSA const&, read_t&, read_t&, int, int, bool)
void setPaired(const sparseSA& sa, read_t & mate1, read_t & mate2, int i, int j, bool concordant){
    mate1.alignments[i]->setLocalPos(sa);
    mate2.alignments[j]->setLocalPos(sa);
    int mate1index = i;
    int mate2index = j;
    if(mate1.alignments[mate1index]->paired()){
        alignment_t * newAln = unpairedCopy(mate1.alignments[mate1index]);
        mate1.alignments.push_back(newAln);
        mate1index = mate1.alignments.size()-1;
    }
    if(mate2.alignments[mate2index]->paired()){
        alignment_t * newAln = unpairedCopy(mate2.alignments[mate2index]);
        mate2.alignments.push_back(newAln);
        mate2index = mate2.alignments.size()-1;
    }
    mate1.pairedAlignmentCount++;
    mate2.pairedAlignmentCount++;
    setPaired(mate1.alignments[mate1index], mate2.alignments[mate2index], concordant);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movl %r9d, 0x1c(%rsp)
movl %r8d, 0x8(%rsp)
movl %ecx, %r12d
movq %rdx, %rbp
movq %rsi, %rbx
movq %rdi, %r13
movl $0xb0, %r15d
leaq (%rsi,%r15), %rax
movq %rax, (%rsp)
movslq %ecx, %r14
movq 0xb0(%rsi), %rax
movq (%rax,%r14,8), %rdi
movq %r13, %rsi
callq 0x2b7b8
addq %rbp, %r15
movq %r15, 0x20(%rsp)
movq %rbx, %r15
movslq 0x8(%rsp), %rbx
movq %rbp, 0x8(%rsp)
movq 0xb0(%rbp), %rax
movq (%rax,%rbx,8), %rdi
movq %r13, %rsi
callq 0x2b7b8
movq 0xb0(%r15), %rax
movq (%rax,%r14,8), %rdi
testb $0x1, 0x40(%rdi)
je 0x259e2
callq 0x257f4
movq %rax, 0x10(%rsp)
movq 0xb8(%r15), %rsi
cmpq 0xc0(%r15), %rsi
je 0x259bd
movq %rax, (%rsi)
movq 0xb8(%r15), %r12
addq $0x8, %r12
movq %r12, 0xb8(%r15)
movq (%rsp), %r14
jmp 0x259d5
leaq 0x10(%rsp), %rdx
movq (%rsp), %r14
movq %r14, %rdi
callq 0x30830
movq 0xb8(%r15), %r12
movq (%r14), %rax
subq %rax, %r12
shrq $0x3, %r12
decl %r12d
movq 0x20(%rsp), %r14
movq (%r14), %rcx
movq (%rcx,%rbx,8), %rsi
testb $0x1, 0x40(%rsi)
jne 0x259fb
movq 0x8(%rsp), %rbx
jmp 0x25a6e
movq %rsi, %rdi
callq 0x257f4
movq %rax, 0x10(%rsp)
movq 0x8(%rsp), %rbx
movq 0xb8(%rbx), %rsi
cmpq 0xc0(%rbx), %rsi
je 0x25a34
movq %rax, (%rsi)
movq 0xb8(%rbx), %rcx
addq $0x8, %rcx
movq %rcx, 0xb8(%rbx)
jmp 0x25a48
leaq 0x10(%rsp), %rdx
movq %r14, %rdi
callq 0x30830
movq 0xb8(%rbx), %rcx
movq (%rsp), %rax
movq (%r14), %rdx
subq %rdx, %rcx
movq (%rax), %rax
shlq $0x1d, %rcx
movabsq $-0x100000000, %rsi     # imm = 0xFFFFFFFF00000000
addq %rcx, %rsi
sarq $0x20, %rsi
movq (%rdx,%rsi,8), %rsi
incl 0xc8(%r15)
incl 0xc8(%rbx)
movslq %r12d, %rcx
movq (%rax,%rcx,8), %rdi
movzbl 0x1c(%rsp), %edx
callq 0x258d4
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/mapper.cpp
// Function: bestAlignmentInWindow(read_t const&, std::vector<alnScoreInfo_t, std::allocator<alnScoreInfo_t>> const&, bool, long, long, bool)
int bestAlignmentInWindow(const read_t & mate, const vector<alnScoreInfo_t> & mateAlns, 
        bool firstMate, long refB, long refE, bool fw){
    int bestAln = -1;
    int bestAlnScore = -1*mate.sequence.size();
    for(size_t i = 0; i < mateAlns.size(); i++){
        if(firstMate != mateAlns[i].firstMate){
            alignment_t * mateAln = mate.alignments[mateAlns[i].position];
            if(mateAln->refB >= refB && mateAln->refE <= refE && mateAln->flag.test(4) != fw && mateAln->alignmentScore > bestAlnScore){
                bestAln = mateAlns[i].position;
                bestAlnScore = mateAln->alignmentScore;
            }
        }
    }
    return bestAln;
}

// Assembly:
movq (%rsi), %r10
movq 0x8(%rsi), %rax
subq %r10, %rax
je 0x2606c
pushq %rbp
pushq %r14
pushq %rbx
sarq $0x2, %rax
movabsq $-0x5555555555555555, %rsi # imm = 0xAAAAAAAAAAAAAAAB
imulq %rax, %rsi
xorl %r11d, %r11d
subl 0x28(%rdi), %r11d
movq 0xb0(%rdi), %rdi
cmpq $0x1, %rsi
adcq $0x0, %rsi
addq $0x4, %r10
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
cmpb %dl, -0x4(%r10)
je 0x2605e
movslq (%r10), %rbx
movq (%rdi,%rbx,8), %r14
cmpq %rcx, (%r14)
jl 0x2605e
cmpq %r8, 0x8(%r14)
jg 0x2605e
movb 0x40(%r14), %bpl
andb $0x10, %bpl
shrb $0x4, %bpl
cmpb %r9b, %bpl
je 0x2605e
movl 0x70(%r14), %ebp
cmpl %r11d, %ebp
cmovgl %ebp, %r11d
cmovgl %ebx, %eax
addq $0xc, %r10
decq %rsi
jne 0x26027
popq %rbx
popq %r14
popq %rbp
retq
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
retq
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/mapper.h
// Function: alignment_t::setLocalPos(sparseSA const&)
void setLocalPos(const sparseSA& sa){
    if(rname.empty() || rname == "*"){
        long descIndex;
        refB++;
        sa.from_set(refB, descIndex, pos);
        refB--;
        rname = sa.descr[descIndex];
    }
  }

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %rsi, %r14
movq %rdi, %r15
leaq 0x48(%rdi), %rbx
cmpq $0x0, 0x50(%rdi)
je 0x2b7e4
leaq 0x148aa(%rip), %rsi     # 0x40082
movq %rbx, %rdi
callq 0x70f0
testl %eax, %eax
jne 0x2b815
movq (%r15), %rsi
incq %rsi
movq %rsi, (%r15)
leaq 0x18(%r15), %rcx
movq %rsp, %r12
movq %r14, %rdi
movq %r12, %rdx
callq 0x2e76e
decq (%r15)
movq (%r12), %rsi
shlq $0x5, %rsi
addq (%r14), %rsi
movq %rbx, %rdi
callq 0x7170
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/mapper.cpp
// Function: executeSeedType(sparseSA const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> const&, int, mum_t, int, int, std::vector<match_t, std::allocator<match_t>>&, int)
inline void executeSeedType(const sparseSA& sa, const string& P, int min_len, mum_t memType, int maxBranchWidth, int sparseSkip, vector<match_t>& matches, int maxSmemMemStart){
    if(memType == SMAM)
        sa.SMAM(P, matches, min_len, maxBranchWidth, sparseSkip);
    else if(memType == SMEM)
        sa.SMEM(P, matches, min_len, maxBranchWidth, sparseSkip, maxSmemMemStart);
    else if(memType == MEM)
        sa.MEM(P, matches, min_len, maxBranchWidth, sparseSkip);
    else if(memType == SMEMP)
        sa.SMEMP(P, matches, min_len, maxBranchWidth, sparseSkip, maxSmemMemStart);
}

// Assembly:
pushq %rax
addl $-0x2, %ecx
cmpl $0x3, %ecx
ja 0x2b86e
movl %edx, %eax
movl 0x18(%rsp), %r10d
movq 0x10(%rsp), %rdx
leaq 0x194c3(%rip), %r11     # 0x44d00
movslq (%r11,%rcx,4), %rcx
addq %r11, %rcx
jmpq *%rcx
movl %eax, %ecx
popq %rax
jmp 0x14b0c
movl %eax, %ecx
popq %rax
jmp 0x14b76
movl %r10d, (%rsp)
movl %eax, %ecx
callq 0x1536c
jmp 0x2b86e
movl %r10d, (%rsp)
movl %eax, %ecx
callq 0x14bf0
popq %rax
retq
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/performanceUtils.cpp
// Function: summaryLine_t::addAlignment(int, bool)
void summaryLine_t::addAlignment(int flag, bool mateFound){
    int score = 0;
    //set fields
    tempAlnCount++;
    alignmentCnt++;
    if(!(flag & (1<<2))){
        mappedAln++;
        score++;
        if(mateFound){
            mappedPaired++;
            score++;
            if(flag & (1<<1)){
                mappedPairedCorrect++;
                score++;
            }
        }
        if(flag & (1<<8)){
            secondAln++;
        }
    }
    tempReadResult = max(tempReadResult, score);
}

// Assembly:
incl 0x1dc(%rdi)
incq 0x38(%rdi)
xorl %eax, %eax
testb $0x4, %sil
jne 0x32cf5
incq 0x30(%rdi)
movl $0x1, %eax
testb %dl, %dl
je 0x32ceb
incq 0x28(%rdi)
movl $0x2, %eax
testb $0x2, %sil
je 0x32ceb
incq 0x20(%rdi)
movl $0x3, %eax
btl $0x8, %esi
jae 0x32cf5
incq 0x18(%rdi)
movl 0x1d8(%rdi), %ecx
cmpl %eax, %ecx
cmovgl %ecx, %eax
movl %eax, 0x1d8(%rdi)
retq
nop
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/performanceUtils.cpp
// Function: summaryLine_t::finishRead()
void summaryLine_t::finishRead(){
    if(tempReadResult==3)
        readPairedCorrect++;
    else if(tempReadResult ==2)
        readPaired++;
    else if(tempReadResult ==1)
        readMapped++;
    tempReadResult = 0;
    alnPerRead[min(tempAlnCount,101)]++;
    tempAlnCount = 0;
}

// Assembly:
movl 0x1d8(%rdi), %eax
movq %rdi, %rcx
cmpl $0x1, %eax
je 0x32d2a
cmpl $0x2, %eax
je 0x32d26
cmpl $0x3, %eax
jne 0x32d2d
leaq 0x10(%rdi), %rcx
jmp 0x32d2a
leaq 0x8(%rdi), %rcx
incq (%rcx)
xorl %eax, %eax
movl %eax, 0x1d8(%rdi)
movl 0x1dc(%rdi), %ecx
cmpl $0x65, %ecx
movl $0x65, %edx
cmovll %ecx, %edx
movslq %edx, %rcx
incl 0x40(%rdi,%rcx,4)
movl %eax, 0x1dc(%rdi)
retq
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/performanceUtils.cpp
// Function: getlijn2(std::basic_ifstream<char, std::char_traits<char>>&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>&)
void getlijn2(ifstream & input, string & lijn){
    //write windows version of getline
    getline(input, lijn, '\n'); // Load one line at a time.
    if(lijn.length() > 0 && lijn[lijn.length()-1]=='\r')
        lijn.erase(--lijn.end());
}

// Assembly:
pushq %rbx
movq %rsi, %rbx
movl $0xa, %edx
callq 0x7650
movq 0x8(%rbx), %rax
testq %rax, %rax
je 0x34a15
movq (%rbx), %rcx
cmpb $0xd, -0x1(%rcx,%rax)
jne 0x34a15
leaq (%rcx,%rax), %rsi
decq %rsi
subq %rcx, %rsi
movl $0x1, %edx
movq %rbx, %rdi
popq %rbx
jmp 0x7370
popq %rbx
retq
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/performanceUtils.cpp
// Function: std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>> printVector<int>(std::vector<int, std::allocator<int>>)
string printVector(vector<T> vec){
    stringstream ss;
    if(!vec.empty()){
        ss << vec[0];
        for(size_t i=1; i < vec.size(); i++)
            ss << "," << vec[i];
    }
    return ss.str();
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x190, %rsp            # imm = 0x190
movq %rsi, %r14
movq %rdi, %rbx
leaq 0x8(%rsp), %rdi
callq 0x71e0
movq (%r14), %rax
cmpq 0x8(%r14), %rax
je 0x3dbbf
leaq 0x18(%rsp), %r15
movl (%rax), %esi
movq %r15, %rdi
callq 0x75d0
movq 0x8(%r14), %rax
subq (%r14), %rax
cmpq $0x5, %rax
jb 0x3dbbf
movl $0x1, %r13d
leaq 0x7303(%rip), %r12      # 0x44e90
movl $0x1, %edx
movq %r15, %rdi
movq %r12, %rsi
callq 0x7340
movq (%r14), %rax
movl (%rax,%r13,4), %esi
movq %r15, %rdi
callq 0x75d0
incq %r13
movq 0x8(%r14), %rax
subq (%r14), %rax
sarq $0x2, %rax
cmpq %rax, %r13
jb 0x3db8d
leaq 0x20(%rsp), %rsi
movq %rbx, %rdi
callq 0x7540
movq 0x163c5(%rip), %rsi     # 0x53f98
leaq 0x8(%rsp), %rdi
callq 0x7210
leaq 0x88(%rsp), %rdi
callq 0x7100
movq %rbx, %rax
addq $0x190, %rsp            # imm = 0x190
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
jmp 0x3dc00
movq %rax, %rbx
movq 0x1638e(%rip), %rsi     # 0x53f98
leaq 0x8(%rsp), %rdi
callq 0x7210
leaq 0x88(%rsp), %rdi
callq 0x7100
movq %rbx, %rdi
callq 0x7600
nop
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/kthread.c
// Function: kt_for
void kt_for(int n_threads, int n, void (*func)(void*,int,int), void *data)
{
	int i;
	kt_for_t t;
	pthread_t *tid;
	t.func = func, t.data = data, t.n_threads = n_threads, t.n = n;
	t.w = (ktf_worker_t*)alloca(n_threads * sizeof(ktf_worker_t));
	tid = (pthread_t*)alloca(n_threads * sizeof(pthread_t));
	for (i = 0; i < n_threads; ++i)
		t.w[i].t = &t, t.w[i].i = i;
	for (i = 0; i < n_threads; ++i) pthread_create(&tid[i], 0, ktf_worker, &t.w[i]);
	for (i = 0; i < n_threads; ++i) pthread_join(tid[i], 0);
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x38, %rsp
movq %rdx, -0x48(%rbp)
movq %rcx, -0x40(%rbp)
movl %edi, -0x58(%rbp)
movl %esi, -0x54(%rbp)
movslq %edi, %rcx
movq %rcx, %rdx
shlq $0x4, %rdx
movq %rsp, %rax
subq %rdx, %rax
movq %rax, %rsp
movq %rax, -0x50(%rbp)
movq %rsp, %r15
leaq 0xf(,%rcx,8), %rdx
andq $-0x10, %rdx
subq %rdx, %r15
movq %r15, %rsp
testl %ecx, %ecx
jle 0x3f972
movl %edi, %r13d
addq $0x8, %rax
xorl %ecx, %ecx
leaq -0x58(%rbp), %rdx
movq %rdx, -0x8(%rax)
movl %ecx, (%rax)
incq %rcx
addq $0x10, %rax
cmpq %rcx, %r13
jne 0x3f904
testl %edi, %edi
jle 0x3f972
movl %edi, -0x2c(%rbp)
movq %r13, %rbx
shlq $0x4, %rbx
xorl %r12d, %r12d
leaq 0x53(%rip), %r14        # 0x3f981
movq %r15, -0x38(%rbp)
movq -0x50(%rbp), %rcx
addq %r12, %rcx
movq %r15, %rdi
xorl %esi, %esi
movq %r14, %rdx
callq 0x7630
addq $0x10, %r12
addq $0x8, %r15
cmpq %r12, %rbx
jne 0x3f932
cmpl $0x0, -0x2c(%rbp)
movq -0x38(%rbp), %r14
jle 0x3f972
xorl %ebx, %ebx
movq (%r14,%rbx,8), %rdi
xorl %esi, %esi
callq 0x7290
incq %rbx
cmpq %rbx, %r13
jne 0x3f95f
leaq -0x28(%rbp), %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/kthread.c
// Function: ktf_worker
static void *ktf_worker(void *data)
{
	ktf_worker_t *w = (ktf_worker_t*)data;
	int i;
	for (;;) {
		i = __sync_fetch_and_add(&w->i, w->t->n_threads);
		if (i >= w->t->n) break;
		w->t->func(w->t->data, i, w - w->t->w);
	}
	while ((i = ktf_steal_work(w->t)) >= 0)
		w->t->func(w->t->data, i, w - w->t->w);
	pthread_exit(0);
}

// Assembly:
pushq %rbp
pushq %rbx
pushq %rax
movq %rdi, %rbx
movq (%rdi), %rax
movl (%rax), %esi
lock
xaddl %esi, 0x8(%rdi)
movq (%rdi), %rax
cmpl 0x4(%rax), %esi
jge 0x3f9ba
movq 0x18(%rax), %rdi
movq %rbx, %rdx
subq 0x8(%rax), %rdx
shrq $0x4, %rdx
callq *0x10(%rax)
movq (%rbx), %rax
movl (%rax), %esi
lock
xaddl %esi, 0x8(%rbx)
movq (%rbx), %rax
jmp 0x3f994
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
movslq (%rax), %rsi
movq 0x8(%rax), %rcx
testq %rsi, %rsi
jle 0x3f9f9
leaq 0x8(%rcx), %rdx
movl $0x7fffffff, %edi       # imm = 0x7FFFFFFF
xorl %r8d, %r8d
xorl %r9d, %r9d
movl (%rdx), %r10d
cmpl %r10d, %edi
cmovgel %r10d, %edi
cmovgl %r8d, %r9d
incq %r8
addq $0x10, %rdx
cmpq %r8, %rsi
jne 0x3f9da
movslq %r9d, %rdx
jmp 0x3f9fb
xorl %edx, %edx
shlq $0x4, %rdx
lock
xaddl %esi, 0x8(%rcx,%rdx)
cmpl 0x4(%rax), %esi
cmovgel %ebp, %esi
testl %esi, %esi
js 0x3fa29
movq (%rbx), %rax
movq 0x18(%rax), %rdi
movq %rbx, %rdx
subq 0x8(%rax), %rdx
shrq $0x4, %rdx
callq *0x10(%rax)
movq (%rbx), %rax
jmp 0x3f9bf
xorl %edi, %edi
callq 0x7610
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/kthread.c
// Function: kt_init
kthread_t *kt_init(int n_threads)
{
	kthread_t *t;
	int i;
	t = (kthread_t*)calloc(1, sizeof(kthread_t));
	t->n_threads = n_threads;
	t->w = (kts_worker_t*)calloc(t->n_threads, sizeof(kts_worker_t));
	pthread_mutex_init(&t->lock, 0);
	pthread_cond_init(&t->cv, 0);
	for (i = 0; i < t->n_threads; ++i) {
		t->w[i].i = i, t->w[i].t = t, t->w[i].pending = -1;
		pthread_create(&t->w[i].tid, 0, kts_worker, &t->w[i]);
	}
	return t;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
movl %edi, %ebp
movl $0x1, %edi
movl $0x6070, %esi           # imm = 0x6070
callq 0x71a0
movq %rax, %rbx
movl %ebp, 0x8(%rax)
movslq %ebp, %rdi
movl $0x20, %esi
callq 0x71a0
movq %rax, (%rbx)
leaq 0x6018(%rbx), %rdi
xorl %esi, %esi
callq 0x74d0
leaq 0x6040(%rbx), %rdi
xorl %esi, %esi
callq 0x73a0
cmpl $0x0, 0x8(%rbx)
jle 0x3fac5
xorl %r15d, %r15d
leaq 0x46(%rip), %r14        # 0x3fad1
xorl %r12d, %r12d
movq (%rbx), %rcx
leaq (%rcx,%r15), %rdi
addq $0x10, %rdi
addq %r15, %rcx
movl %r12d, -0x8(%rdi)
movq %rbx, -0x10(%rdi)
movl $0xffffffff, 0x8(%rdi)  # imm = 0xFFFFFFFF
xorl %esi, %esi
movq %r14, %rdx
callq 0x7630
incq %r12
movslq 0x8(%rbx), %rax
addq $0x20, %r15
cmpq %rax, %r12
jl 0x3fa8e
movq %rbx, %rax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O3/readmapping[P]alfalfa/src/kthread.c
// Function: kt_sync
void kt_sync(kthread_t *t)
{
	int i;
	pthread_mutex_lock(&t->lock);
	t->to_sync = 1;
	pthread_cond_broadcast(&t->cv);
	pthread_mutex_unlock(&t->lock);
	for (i = 0; i < t->n_threads; ++i)
		pthread_join(t->w[i].tid, 0);
	free(t->w); free(t);
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %rdi, %rbx
leaq 0x6018(%rdi), %r14
movq %r14, %rdi
callq 0x74a0
movl $0x1, 0xc(%rbx)
leaq 0x6040(%rbx), %rdi
callq 0x7110
movq %r14, %rdi
callq 0x7220
cmpl $0x0, 0x8(%rbx)
jle 0x3fc8c
movl $0x10, %r14d
xorl %r15d, %r15d
movq (%rbx), %rax
movq (%rax,%r14), %rdi
xorl %esi, %esi
callq 0x7290
incq %r15
movslq 0x8(%rbx), %rax
addq $0x20, %r14
cmpq %rax, %r15
jl 0x3fc6e
movq (%rbx), %rdi
callq 0x7380
movq %rbx, %rdi
popq %rbx
popq %r14
popq %r15
jmp 0x7380
// File: /workspace/github_cpp_makefile_star2_O3/ArashPartow[P]exprtk-extras/exprtk_binomial_coefficient.cpp
// Function: double ncr_println<double>(double, double, double)
inline T ncr_println(T n, T r, T ncr)
{
   printf("ncr(%2d,%2d) = %2llu\n",
          static_cast<int>(n),
          static_cast<int>(r),
          static_cast<unsigned long long>(ncr));

   return T(0);
}

// Assembly:
pushq %rax
cvttsd2si %xmm0, %esi
cvttsd2si %xmm1, %edx
cvttsd2si %xmm2, %rax
movq %rax, %rdi
sarq $0x3f, %rdi
subsd 0x1913b0(%rip), %xmm2   # 0x2ab008
cvttsd2si %xmm2, %rcx
andq %rdi, %rcx
orq %rax, %rcx
leaq 0x195ec7(%rip), %rdi    # 0x2afb31
xorl %eax, %eax
callq 0x116050
xorpd %xmm0, %xmm0
popq %rax
retq
nop
// File: /workspace/github_cpp_makefile_star2_O3/white0dew[P]WebServer/http/http_conn.cpp
// Function: http_conn::parse_headers(char*)
http_conn::HTTP_CODE http_conn::parse_headers(char *text)
{
    //判断是空行还是请求头
    if (text[0] == '\0')
    {
        //判断是GET还是POST请求
        //!0 is POST
        if (m_content_length != 0)
        {
            //POST需要跳转到消息体处理状态
            m_check_state = CHECK_STATE_CONTENT;
            return NO_REQUEST;
        }
        //==0 is GET
        return GET_REQUEST;
    }
    //解析请求头部connection字段
    else if (strncasecmp(text, "Connection:", 11) == 0)
    {
        text += 11;

        //跳过空格和\t字符
        text += strspn(text, " \t");
        if (strcasecmp(text, "keep-alive") == 0)
        {
            //如果是长连接，则将linger标志设置为true
            m_linger = true;
        }
    }
    //解析请求头部Content-length字段
    else if (strncasecmp(text, "Content-length:", 15) == 0)
    {
        text += 15;
        text += strspn(text, " \t");
        m_content_length = atol(text);
    }
    //解析请求头部Host字段
    else if (strncasecmp(text, "Host:", 5) == 0)
    {
        text += 5;
        text += strspn(text, " \t");
        m_host = text;
    }
    else
    {
        LOG_INFO("oop!unknow header: %s", text);
    }
    return NO_REQUEST;
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movq %rdi, %rbx
cmpb $0x0, (%rsi)
je 0x49d8
movq %rsi, %r14
leaq 0x490e(%rip), %rsi      # 0x9258
movl $0xb, %edx
movq %r14, %rdi
callq 0x34a0
testl %eax, %eax
je 0x49ed
leaq 0x4909(%rip), %rsi      # 0x926f
movl $0xf, %edx
movq %r14, %rdi
callq 0x34a0
testl %eax, %eax
je 0x4a20
leaq 0x48fd(%rip), %rsi      # 0x927f
movl $0x5, %edx
movq %r14, %rdi
callq 0x34a0
testl %eax, %eax
je 0x4a4c
xorl %ebp, %ebp
cmpl $0x0, 0xe34(%rbx)
jne 0x4a6c
callq 0x58ba
leaq 0x48d3(%rip), %rdx      # 0x9285
xorl %ebp, %ebp
movq %rax, %rdi
movl $0x1, %esi
movq %r14, %rcx
xorl %eax, %eax
callq 0x6410
callq 0x58ba
movq %rax, %rdi
callq 0x6852
jmp 0x4a6c
cmpl $0x0, 0xd20(%rbx)
je 0x4a45
movl $0x2, 0xc38(%rbx)
jmp 0x4a6a
leaq 0xb(%r14), %rdi
leaq 0x482f(%rip), %rsi      # 0x9227
callq 0x3140
leaq (%r14,%rax), %rdi
addq $0xb, %rdi
leaq 0x4858(%rip), %rsi      # 0x9264
callq 0x33d0
xorl %ebp, %ebp
testl %eax, %eax
jne 0x4a6c
movb $0x1, 0xd24(%rbx)
jmp 0x4a6c
leaq 0xf(%r14), %rdi
leaq 0x47fc(%rip), %rsi      # 0x9227
callq 0x3140
leaq (%r14,%rax), %rdi
addq $0xf, %rdi
callq 0x3460
movl %eax, 0xd20(%rbx)
jmp 0x4a6a
movl $0x1, %ebp
jmp 0x4a6c
leaq 0x5(%r14), %rdi
leaq 0x47d0(%rip), %rsi      # 0x9227
callq 0x3140
addq %r14, %rax
addq $0x5, %rax
movq %rax, 0xd18(%rbx)
xorl %ebp, %ebp
movl %ebp, %eax
popq %rbx
popq %r14
popq %rbp
retq
nop
// File: /workspace/github_cpp_makefile_star2_O3/white0dew[P]WebServer/http/http_conn.cpp
// Function: http_conn::add_response(char const*, ...)
bool http_conn::add_response(const char *format, ...)
{
    //如果写入内容超出m_write_buf大小则报错
    if (m_write_idx >= WRITE_BUFFER_SIZE)
        return false;
    //定义可变参数列表
    va_list arg_list;
    //将变量arg_list初始化为传入参数
    va_start(arg_list, format);
    //将数据format从可变参数列表写入缓冲区写，返回写入数据的长度
    int len = vsnprintf(m_write_buf + m_write_idx, WRITE_BUFFER_SIZE - 1 - m_write_idx, format, arg_list);
    //如果写入的数据长度超过缓冲区剩余空间，则报错
    if (len >= (WRITE_BUFFER_SIZE - 1 - m_write_idx))
    {
        va_end(arg_list);
        return false;
    }
    //更新m_write_idx位置
    m_write_idx += len;
    //清空可变参列表
    va_end(arg_list);

    LOG_INFO("request:%s", m_write_buf);

    return true;
}

// Assembly:
pushq %rbp
pushq %rbx
subq $0xd8, %rsp
movq %r9, 0x48(%rsp)
testb %al, %al
je 0x5427
movaps %xmm0, 0x50(%rsp)
movaps %xmm1, 0x60(%rsp)
movaps %xmm2, 0x70(%rsp)
movaps %xmm3, 0x80(%rsp)
movaps %xmm4, 0x90(%rsp)
movaps %xmm5, 0xa0(%rsp)
movaps %xmm6, 0xb0(%rsp)
movaps %xmm7, 0xc0(%rsp)
movq %r8, 0x40(%rsp)
movq %rcx, 0x38(%rsp)
movq %rdx, 0x30(%rsp)
cmpl $0x3ff, 0xc34(%rdi)     # imm = 0x3FF
jle 0x5449
xorl %ebp, %ebp
jmp 0x54ed
movq %rsi, %r10
movq %rdi, %rbx
leaq 0x20(%rsp), %rax
movq %rsp, %rcx
movq %rax, 0x10(%rcx)
leaq 0xf0(%rsp), %rax
movq %rax, 0x8(%rcx)
movabsq $0x3000000010, %rax     # imm = 0x3000000010
movq %rax, (%rcx)
movslq 0xc34(%rdi), %rax
addq %rax, %rdi
addq $0x834, %rdi            # imm = 0x834
movl $0x3ff, %esi            # imm = 0x3FF
subq %rax, %rsi
movq %r10, %rdx
callq 0x3260
movl 0xc34(%rbx), %ecx
movl $0x3ff, %edx            # imm = 0x3FF
subl %ecx, %edx
cmpl %edx, %eax
setl %bpl
jge 0x54ed
addl %eax, %ecx
movl %ecx, 0xc34(%rbx)
cmpl $0x0, 0xe34(%rbx)
jne 0x54ed
addq $0x834, %rbx            # imm = 0x834
callq 0x58ba
leaq 0x3e6f(%rip), %rdx      # 0x933d
movq %rax, %rdi
movl $0x1, %esi
movq %rbx, %rcx
xorl %eax, %eax
callq 0x6410
callq 0x58ba
movq %rax, %rdi
callq 0x6852
movl %ebp, %eax
addq $0xd8, %rsp
popq %rbx
popq %rbp
retq
nop
// File: /workspace/github_cpp_makefile_star2_O3/white0dew[P]WebServer/././threadpool/threadpool.h
// Function: threadpool<http_conn>::run()
void threadpool<T>::run()
{
    while (true)
    {
        m_queuestat.wait();
        m_queuelocker.lock();
        if (m_workqueue.empty())
        {
            m_queuelocker.unlock();
            continue;
        }
        //
        T *request = m_workqueue.front();
        m_workqueue.pop_front();
        m_queuelocker.unlock();
        if (!request)
            continue;
        //Reactor
        if (1 == m_actor_model)
        {
            //IO事件类型：0为读
            if (0 == request->m_state)
            {
                if (request->read_once())
                {
                    request->improv = 1;
                    connectionRAII mysqlcon(&request->mysql, m_connPool);
                    request->process();
                }
                else
                {
                    request->improv = 1;
                    request->timer_flag = 1;
                }
            }
            else
            {
                if (request->write())
                {
                    request->improv = 1;
                }
                else
                {
                    request->improv = 1;
                    request->timer_flag = 1;
                }
            }
        }
        //default:Proactor，线程池不需要进行数据读取，而是直接开始业务处理
        //之前的操作已经将数据读取到http的read和write的buffer中了
        else
        {
            connectionRAII mysqlcon(&request->mysql, m_connPool);
            request->process();
        }
    }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rdi, %rbx
leaq 0x50(%rdi), %r14
leaq 0x28(%rdi), %r15
leaq 0x10(%rdi), %r12
movq %r14, %rdi
callq 0x3250
movq %r15, %rdi
callq 0x3500
movq (%r12), %rbp
cmpq %r12, %rbp
je 0x8577
movq 0x10(%rbp), %r13
decq 0x20(%rbx)
movq %rbp, %rdi
callq 0x3590
movl $0x18, %esi
movq %rbp, %rdi
callq 0x33a0
movq %r15, %rdi
callq 0x3300
testq %r13, %r13
je 0x8511
cmpl $0x1, 0x78(%rbx)
jne 0x8581
cmpl $0x0, 0x10(%r13)
je 0x85ab
movq %r13, %rdi
callq 0x51ee
movl $0x1, 0x4(%r13)
testb %al, %al
jne 0x8511
jmp 0x85de
movq %r15, %rdi
callq 0x3300
jmp 0x8511
leaq 0x8(%r13), %rsi
movq 0x70(%rbx), %rdx
leaq 0x8(%rsp), %rbp
movq %rbp, %rdi
callq 0x6fec
movq %r13, %rdi
callq 0x57e0
movq %rbp, %rdi
callq 0x7012
jmp 0x8511
movq %r13, %rdi
callq 0x46ba
movl $0x1, 0x4(%r13)
testb %al, %al
je 0x85de
leaq 0x8(%r13), %rsi
movq 0x70(%rbx), %rdx
leaq 0x8(%rsp), %rbp
movq %rbp, %rdi
callq 0x6fec
movq %r13, %rdi
callq 0x57e0
jmp 0x859e
movl $0x1, (%r13)
jmp 0x8511
jmp 0x85ed
movq %rax, %rbx
leaq 0x8(%rsp), %rdi
callq 0x7012
movq %rbx, %rdi
callq 0x35e0
nop
// File: /workspace/github_cpp_makefile_star2_O3/loadzero[P]geoloc/geoloc/geoloc.cpp
// Function: usage(char const*)
static void usage(const char* condition)
{
    if (condition)
    {
        fprintf(stderr, "%s\n", condition);
    }

    fprintf(stderr, "usage:");
    fprintf(stderr, "\tgeoloc -f file ... [--headers]\n");
    fprintf(stderr, "\tgeoloc -q ip ...\n");
    fprintf(stderr, "\n");
    fprintf(stderr, "This software includes GeoLite data created by MaxMind\n");
    fprintf(stderr, "available from http://www.maxmind.com\n");

    exit(1);
}

// Assembly:
pushq %rbx
testq %rdi, %rdi
je 0x40ea
movq %rdi, %rdx
movq 0xbeff(%rip), %rax      # 0xffd8
movq (%rax), %rdi
leaq 0x702d(%rip), %rsi      # 0xb110
xorl %eax, %eax
callq 0x32e0
movq 0xbee7(%rip), %rbx      # 0xffd8
movq (%rbx), %rcx
leaq 0x7099(%rip), %rdi      # 0xb194
movl $0x6, %esi
movl $0x1, %edx
callq 0x33a0
movq (%rbx), %rcx
leaq 0x7087(%rip), %rdi      # 0xb19b
movl $0x20, %esi
movl $0x1, %edx
callq 0x33a0
movq (%rbx), %rcx
leaq 0x708f(%rip), %rdi      # 0xb1bc
movl $0x12, %esi
movl $0x1, %edx
callq 0x33a0
movq (%rbx), %rsi
movl $0xa, %edi
callq 0x3290
movq (%rbx), %rcx
leaq 0x707c(%rip), %rdi      # 0xb1cf
movl $0x37, %esi
movl $0x1, %edx
callq 0x33a0
movq (%rbx), %rcx
leaq 0x709b(%rip), %rdi      # 0xb207
movl $0x26, %esi
movl $0x1, %edx
callq 0x33a0
movl $0x1, %edi
callq 0x3260