LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_cpp_makefile_star2_O2/iZhangHui[P]CppPrimer/CH10_GenericAlgorithms/examples/rcomma.cc
// Function: main
int main()
{
	string line;
	getline(cin, line);

	// find the first element in a comma-separated list
	auto comma = find(line.cbegin(), line.cend(), ',');
	cout << string(line.cbegin(), comma) << endl;
	
	// find the last element in a comma-separated list
	auto rcomma = find(line.crbegin(), line.crend(), ',');
	
	// WRONG: will generate the word in reverse order
	cout << string(line.crbegin(), rcomma) << endl;
	
	// ok: get a forward iterator and read to the end of line
	cout << string(rcomma.base(), line.cend()) << endl;

	return 0;
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %r14
pushq %rbx
subq $0x70, %rsp
leaq -0x48(%rbp), %rax
movq %rax, -0x10(%rax)
andq $0x0, -0x8(%rax)
movb $0x0, (%rax)
movq 0x2dc2(%rip), %rdi      # 0x3fe0
leaq -0x58(%rbp), %rsi
callq 0x1030
movq -0x58(%rbp), %rdi
movq -0x50(%rbp), %rsi
addq %rdi, %rsi
leaq -0x38(%rbp), %rdx
movb $0x2c, (%rdx)
callq 0x13c4
movq -0x58(%rbp), %rsi
leaq -0x28(%rbp), %r14
movq %r14, -0x10(%r14)
leaq -0x38(%rbp), %rdi
movq %rax, %rdx
callq 0x1456
movq 0x2d73(%rip), %rdi      # 0x3fd0
leaq -0x38(%rbp), %rsi
callq 0x1080
movq %rax, %rdi
callq 0x1050
leaq -0x38(%rbp), %rbx
movq %rbx, %rdi
callq 0x1040
movq -0x58(%rbp), %rax
movq -0x50(%rbp), %rcx
addq %rax, %rcx
leaq -0x80(%rbp), %rsi
movq %rcx, (%rsi)
leaq -0x78(%rbp), %rdx
movq %rax, (%rdx)
movb $0x2c, (%rbx)
leaq -0x60(%rbp), %rdi
leaq -0x38(%rbp), %rcx
callq 0x1367
movq -0x58(%rbp), %rax
addq -0x50(%rbp), %rax
leaq -0x70(%rbp), %rsi
movq %rax, (%rsi)
movq -0x60(%rbp), %rax
leaq -0x68(%rbp), %rdx
movq %rax, (%rdx)
leaq -0x38(%rbp), %rdi
leaq -0x11(%rbp), %rcx
callq 0x1396
movq 0x2cff(%rip), %rdi      # 0x3fd0
leaq -0x38(%rbp), %rsi
callq 0x1080
movq %rax, %rdi
callq 0x1050
movq %rbx, %rdi
callq 0x1040
movq -0x60(%rbp), %rsi
movq -0x58(%rbp), %rdx
addq -0x50(%rbp), %rdx
movq %r14, (%rbx)
leaq -0x38(%rbp), %rdi
callq 0x1456
movq 0x2cc7(%rip), %rdi      # 0x3fd0
leaq -0x38(%rbp), %rsi
callq 0x1080
movq %rax, %rdi
callq 0x1050
leaq -0x38(%rbp), %rdi
callq 0x1040
leaq -0x58(%rbp), %rdi
callq 0x1040
xorl %eax, %eax
addq $0x70, %rsp
popq %rbx
popq %r14
popq %rbp
retq
jmp 0x1341
jmp 0x1341
jmp 0x1341
jmp 0x1341
jmp 0x1341
movq %rax, %rbx
jmp 0x1356
jmp 0x134a
jmp 0x134a
movq %rax, %rbx
leaq -0x38(%rbp), %rdi
callq 0x1040
leaq -0x58(%rbp), %rdi
callq 0x1040
movq %rbx, %rdi
callq 0x10a0
// File: /workspace/github_cpp_makefile_star2_O2/nmmmnu[P]HM3/hm3/main/db_merge.cc
// Function: int merge<hm3::DiskTable>(hm3::DiskTable const&, char const*, bool)
int merge(const TABLE &table, const char *output_file, bool const keepTombstones){
	using DiskFileBuilder = hm3::diskfile::DiskFileBuilder;

	DiskFileBuilder df;

	df.createFromList(output_file, table, keepTombstones);

	return 0;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
subq $0x20, %rsp
movl %edx, %ebx
movq %rdi, %r14
leaq 0x10(%rsp), %r15
movq %r15, %rdi
callq 0x2922
leaq 0xf(%rsp), %rdi
movq %r15, %rsi
movq %r14, %rdx
movl %ebx, %ecx
callq 0x2b18
xorl %eax, %eax
addq $0x20, %rsp
popq %rbx
popq %r14
popq %r15
retq
// File: /workspace/github_cpp_makefile_star2_O2/nmmmnu[P]HM3/hm3/multitableiterator/dualiterator_impl.h
// Function: hm3::multitableiterator::DualIterator<hm3::DiskTable, hm3::DiskTable>::operator*() const
const Pair &DualIterator<TABLE1, TABLE2>::operator*() const{
	const Pair &pair1 = *it1_;
	const Pair &pair2 = *it2_;

	int const cmp = pair1.cmp(pair2);

	if (cmp != 0){
		// return smaller
		return  cmp < 0 ? pair1 : pair2;
	}else{
		// return newer
		return pair1.cmpTime(pair2) > 0 ? pair1 : pair2;
	}
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %r14
callq 0x3606
movq %rax, %rbx
addq $0x60, %r14
movq %r14, %rdi
callq 0x3606
movq %rax, %r14
movq %rbx, %rdi
movq %rax, %rsi
callq 0x362a
testl %eax, %eax
je 0x34ea
shrl $0x1f, %eax
jmp 0x34fa
movq %rbx, %rdi
movq %r14, %rsi
callq 0x4d90
testl %eax, %eax
setg %al
testb %al, %al
cmovneq %rbx, %r14
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
nop
// File: /workspace/github_cpp_makefile_star2_O2/nmmmnu[P]HM3/hm3/multitableiterator/dualiterator_impl.h
// Function: hm3::multitableiterator::DualIterator<hm3::DiskTable, hm3::DiskTable>::operator++()
auto DualIterator<TABLE1, TABLE2>::operator++() -> DualIterator &{
	const Pair &pair1 = *it1_;
	const Pair &pair2 = *it2_;

	const auto cmp = pair1.cmp(pair2);

	if (cmp <= 0)
		++it1_;

	if (cmp >= 0)
		++it2_;

	return *this;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
callq 0x3606
movq %rax, %r14
leaq 0x60(%rbx), %rdi
callq 0x3606
movq %r14, %rdi
movq %rax, %rsi
callq 0x362a
testl %eax, %eax
jg 0x353b
incq 0x8(%rbx)
testl %eax, %eax
js 0x353f
incq 0x68(%rbx)
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_cpp_makefile_star2_O2/nmmmnu[P]HM3/hm3/tableloader/argtableloader.cc
// Function: hm3::tableloader::ArgTableLoader::refresh_()
bool ArgTableLoader::refresh_(){
	container_.clear();

	if (argc_ < 0)
		return true;

	container_.reserve((container_type::size_type) argc_);

	for(const char *filename : ArrayRef<const char *>{ argv_, argc_ } ){
		DiskTable dt;
		dt.open(filename);
		container_.push_back( std::move(dt) );
	}

	return true;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x108, %rsp            # imm = 0x108
movq %rdi, %r14
addq $0x10, %rdi
movq %rdi, 0x8(%rsp)
callq 0x47e4
movslq (%r14), %rsi
testq %rsi, %rsi
js 0x47b8
movq 0x8(%rsp), %rdi
callq 0x47ec
movq 0x8(%r14), %rax
movq %rax, 0x10(%rsp)
movl (%r14), %r13d
xorl %ebp, %ebp
testl %r13d, %r13d
cmovlel %ebp, %r13d
leaq 0x30(%rsp), %rbx
shlq $0x3, %r13
leaq 0x18(%rsp), %r14
leaq 0x28(%rsp), %r15
xorl %r12d, %r12d
cmpq %r12, %r13
je 0x47b8
movq 0x10(%rsp), %rax
movq (%rax,%r12), %rsi
movb %bpl, 0x28(%rsp)
movb %bpl, 0x10(%rbx)
xorps %xmm0, %xmm0
movups %xmm0, (%rbx)
movups %xmm0, 0x28(%rbx)
andq $0x0, 0x38(%rbx)
movups %xmm0, 0x18(%rbx)
andl $0x0, 0x54(%rbx)
movups %xmm0, 0x44(%rbx)
movl $0x1, 0x8c(%rsp)
movups %xmm0, 0x60(%rbx)
andl $0x0, 0xbc(%rsp)
movups %xmm0, 0x74(%rbx)
andl $0x0, 0x84(%rbx)
movb $0x1, 0xc0(%rsp)
movups %xmm0, 0xc8(%rbx)
movups %xmm0, 0xb8(%rbx)
movups %xmm0, 0xa8(%rbx)
movups %xmm0, 0x98(%rbx)
movq %r14, %rdi
callq 0x2922
movq %r15, %rdi
movq %r14, %rsi
callq 0x53b4
movq 0x8(%rsp), %rdi
movq %r15, %rsi
callq 0x4aaa
movq %r15, %rdi
callq 0x298a
addq $0x8, %r12
jmp 0x470b
movb $0x1, %al
addq $0x108, %rsp            # imm = 0x108
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
jmp 0x47ce
movq %rax, %rbx
leaq 0x28(%rsp), %rdi
callq 0x298a
movq %rbx, %rdi
callq 0x22f0
nop
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/Cinterface.cpp
// Function: likeFixedMinor(double, double*, int, char*)
double likeFixedMinor(double p,double *likes,int numInds,char *keepInd){
  // should these actually be normed genotype likelihoods? Or not normed?
  // only used for checking minLrt
  // returns minus the log of the likelihood
  double totalLike=0;
  for(int i=0;i<numInds;i++){
    if(keepInd[i])
      totalLike+=log(likes[i*3+0]*(1-p)*(1-p)+likes[i*3+1]*2.0*p*(1-p)+likes[i*3+2]*p*p);
  }
  return -totalLike;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %rdx, %rbx
movl %esi, %r14d
movq %rdi, %r15
movsd 0x89e0(%rip), %xmm1     # 0xb008
movsd %xmm0, 0x20(%rsp)
subsd %xmm0, %xmm1
movsd %xmm1, 0x18(%rsp)
xorl %r12d, %r12d
testl %esi, %esi
cmovlel %r12d, %r14d
addq $0x10, %r15
xorpd %xmm0, %xmm0
cmpq %r12, %r14
je 0x26bc
cmpb $0x0, (%rbx,%r12)
je 0x26b3
movsd -0x10(%r15), %xmm1
movsd 0x18(%rsp), %xmm3
mulsd %xmm3, %xmm1
movapd %xmm0, (%rsp)
movsd -0x8(%r15), %xmm0
addsd %xmm0, %xmm0
movsd 0x20(%rsp), %xmm2
mulsd %xmm2, %xmm0
mulsd %xmm3, %xmm0
mulsd %xmm3, %xmm1
addsd %xmm0, %xmm1
movsd (%r15), %xmm0
mulsd %xmm2, %xmm0
mulsd %xmm2, %xmm0
addsd %xmm1, %xmm0
callq 0x21a0
movapd (%rsp), %xmm1
addsd %xmm0, %xmm1
movapd %xmm1, (%rsp)
movapd (%rsp), %xmm0
incq %r12
addq $0x18, %r15
jmp 0x2649
xorpd 0x897c(%rip), %xmm0     # 0xb040
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/Cinterface.cpp
// Function: filterMinMaf(bgl&, float)
void filterMinMaf(bgl &d,float minMaf){
  //  fprintf(stderr,"WARNING filtering minMaf=%f \n",minMaf);
  int posi =0;
  for(int s=0;s<d.nSites;s++){
    //    fprintf(stderr,"minmaf=%f mafs[%d]=%f lik=%f\n",minMaf,s,d.mafs[s],lik);
    if(d.mafs[s]>minMaf&&d.mafs[s]<1-minMaf){
      d.genos[posi] = d.genos[s];
      d.major[posi] = d.major[s];
      d.minor[posi] = d.minor[s];
      d.ids[posi] = d.ids[s];
      d.keeps[posi] = d.keeps[s];
      d.keepInd[posi] = d.keepInd[s];
      d.mafs[posi] = d.mafs[s];
      posi++;   
    }else{
      //      fprintf(stderr,"skippping\n");
    }
  }
  d.nSites=posi;
}

// Assembly:
movss 0x8306(%rip), %xmm1     # 0xb060
subss %xmm0, %xmm1
xorl %eax, %eax
xorl %ecx, %ecx
movslq 0x20(%rdi), %rdx
cmpq %rdx, %rax
jge 0x2ddd
movq 0x38(%rdi), %rdx
movss (%rdx,%rax,4), %xmm2
ucomiss %xmm0, %xmm2
jbe 0x2dd8
ucomiss %xmm2, %xmm1
jbe 0x2dd8
movq (%rdi), %rdx
movq (%rdx,%rax,8), %rsi
movslq %ecx, %r8
movq %rsi, (%rdx,%r8,8)
movq 0x8(%rdi), %rdx
movb (%rdx,%rax), %sil
movb %sil, (%rdx,%r8)
movq 0x10(%rdi), %rdx
movb (%rdx,%rax), %sil
movb %sil, (%rdx,%r8)
movq 0x18(%rdi), %rdx
movq (%rdx,%rax,8), %rsi
movq %rsi, (%rdx,%r8,8)
movq 0x28(%rdi), %rdx
movq (%rdx,%rax,8), %rsi
movq %rsi, (%rdx,%r8,8)
movq 0x30(%rdi), %rdx
movl (%rdx,%rax,4), %esi
movl %esi, (%rdx,%r8,4)
movq 0x38(%rdi), %rdx
movss (%rdx,%rax,4), %xmm2
movss %xmm2, (%rdx,%r8,4)
incl %ecx
incq %rax
jmp 0x2d62
movl %ecx, 0x20(%rdi)
retq
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/Cinterface.cpp
// Function: filterMiss(bgl&, int)
void filterMiss(bgl &d,int minInd){
  //  fprintf(stderr,"WARNING filtering mis=%d \n",minInd);
  int posi =0;
  for(int s=0;s<d.nSites;s++){
    if(d.keepInd[s]>minInd){
      d.genos[posi] = d.genos[s];
      d.major[posi] = d.major[s];
      d.minor[posi] = d.minor[s];
      d.ids[posi] = d.ids[s];
      d.keeps[posi] = d.keeps[s];
      d.keepInd[posi] = d.keepInd[s];
      d.mafs[posi] = d.mafs[s];
      posi++;   
    }else{
      // fprintf(stderr,"skippping\n");
    }
  }
  d.nSites=posi;
}

// Assembly:
xorl %eax, %eax
xorl %ecx, %ecx
movslq 0x20(%rdi), %rdx
cmpq %rdx, %rax
jge 0x2e57
movq 0x30(%rdi), %rdx
cmpl %esi, (%rdx,%rax,4)
jle 0x2e52
movq (%rdi), %rdx
movq (%rdx,%rax,8), %r8
movslq %ecx, %r9
movq %r8, (%rdx,%r9,8)
movq 0x8(%rdi), %rdx
movb (%rdx,%rax), %r8b
movb %r8b, (%rdx,%r9)
movq 0x10(%rdi), %rdx
movb (%rdx,%rax), %r8b
movb %r8b, (%rdx,%r9)
movq 0x18(%rdi), %rdx
movq (%rdx,%rax,8), %r8
movq %r8, (%rdx,%r9,8)
movq 0x28(%rdi), %rdx
movq (%rdx,%rax,8), %r8
movq %r8, (%rdx,%r9,8)
movq 0x30(%rdi), %rdx
movl (%rdx,%rax,4), %r8d
movl %r8d, (%rdx,%r9,4)
movq 0x38(%rdi), %rdx
movss (%rdx,%rax,4), %xmm0
movss %xmm0, (%rdx,%r9,4)
incl %ecx
incq %rax
jmp 0x2de5
movl %ecx, 0x20(%rdi)
retq
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/Cinterface.cpp
// Function: filterMinLrt(bgl&, float)
void filterMinLrt(bgl &d,float minLrt){
  //  fprintf(stderr,"WARNING filtering minlrt=%f \n",minLrt);
  int posi =0;
  for(int s=0;s<d.nSites;s++){
    float lik=likeFixedMinor(d.mafs[s],d.genos[s],d.nInd,d.keeps[s]);
    float lik0=likeFixedMinor(0.0,d.genos[s],d.nInd,d.keeps[s]);
    //    fprintf(stderr,"minlrt=%f mafs[%d]=%f lik=%f lik0=%f 2*(lik0-lik)=%f\n",minLrt,s,d.mafs[s],lik,lik0,2.0*(lik0-lik));
    if(2.0*(lik0-lik)>minLrt){
      d.genos[posi] = d.genos[s];
      d.major[posi] = d.major[s];
      d.minor[posi] = d.minor[s];
      d.ids[posi] = d.ids[s];
      d.keeps[posi] = d.keeps[s];
      d.keepInd[posi] = d.keepInd[s];
      d.mafs[posi] = d.mafs[s];
      posi++;   
    }else{
      //  fprintf(stderr,"skippping\n");
    }
  }
  d.nSites=posi;
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
subq $0x10, %rsp
movq %rdi, %rbx
cvtss2sd %xmm0, %xmm0
movsd %xmm0, 0x8(%rsp)
xorl %r14d, %r14d
xorl %ebp, %ebp
movslq 0x20(%rbx), %rax
cmpq %rax, %r14
jge 0x2f41
movq 0x38(%rbx), %rax
cvtss2sd (%rax,%r14,4), %xmm0
movq (%rbx), %rax
movq (%rax,%r14,8), %rdi
movl 0x24(%rbx), %esi
movq 0x28(%rbx), %rax
movq (%rax,%r14,8), %rdx
callq 0x260c
cvtsd2ss %xmm0, %xmm0
movss %xmm0, 0x4(%rsp)
movq (%rbx), %rax
movq (%rax,%r14,8), %rdi
movl 0x24(%rbx), %esi
movq 0x28(%rbx), %rax
movq (%rax,%r14,8), %rdx
xorps %xmm0, %xmm0
callq 0x260c
cvtsd2ss %xmm0, %xmm0
subss 0x4(%rsp), %xmm0
cvtss2sd %xmm0, %xmm0
addsd %xmm0, %xmm0
ucomisd 0x8(%rsp), %xmm0
jbe 0x2f39
movq (%rbx), %rax
movq (%rax,%r14,8), %rcx
movslq %ebp, %rdx
movq %rcx, (%rax,%rdx,8)
movq 0x8(%rbx), %rax
movb (%rax,%r14), %cl
movb %cl, (%rax,%rdx)
movq 0x10(%rbx), %rax
movb (%rax,%r14), %cl
movb %cl, (%rax,%rdx)
movq 0x18(%rbx), %rax
movq (%rax,%r14,8), %rcx
movq %rcx, (%rax,%rdx,8)
movq 0x28(%rbx), %rax
movq (%rax,%r14,8), %rcx
movq %rcx, (%rax,%rdx,8)
movq 0x30(%rbx), %rax
movl (%rax,%r14,4), %ecx
movl %ecx, (%rax,%rdx,4)
movq 0x38(%rbx), %rax
movss (%rax,%r14,4), %xmm0
movss %xmm0, (%rax,%rdx,4)
incl %ebp
incq %r14
jmp 0x2e75
movl %ebp, 0x20(%rbx)
addq $0x10, %rsp
popq %rbx
popq %r14
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/Cinterface.cpp
// Function: dalloc(bgl&)
void dalloc(bgl &b){
  for(int i=0;i<b.nSites;i++){
    delete [] b.genos[i];
    free(b.ids[i]);
  }
  delete [] b.minor;
  delete [] b.major;
  delete [] b.genos;
  delete [] b.ids;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %rbx
xorl %r14d, %r14d
movslq 0x20(%rbx), %rax
cmpq %rax, %r14
jge 0x2f83
movq (%rbx), %rax
movq (%rax,%r14,8), %rdi
testq %rdi, %rdi
je 0x2f71
callq 0x22d0
movq 0x18(%rbx), %rax
movq (%rax,%r14,8), %rdi
callq 0x2270
incq %r14
jmp 0x2f57
movq 0x10(%rbx), %rdi
testq %rdi, %rdi
je 0x2f91
callq 0x22d0
movq 0x8(%rbx), %rdi
testq %rdi, %rdi
je 0x2f9f
callq 0x22d0
movq (%rbx), %rdi
testq %rdi, %rdi
je 0x2fac
callq 0x22d0
movq 0x18(%rbx), %rdi
addq $0x8, %rsp
testq %rdi, %rdi
je 0x2fc1
popq %rbx
popq %r14
jmp 0x22d0
popq %rbx
popq %r14
retq
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/Cinterface.cpp
// Function: getK(char const*)
int getK(const char*fname){
  const char*delims=" \n";
  FILE *fp = NULL;
  if((fp=fopen(fname,"r"))==NULL){
    fprintf(stderr,"can't open:%s\n",fname);
    exit(0);
  }
  int lens=100000 ;
  char buf[lens];
  if(NULL==fgets(buf,lens,fp)){
    fprintf(stderr,"Increase buffer\n");
    exit(0);
  }
  strtok(buf,delims);
  int K=1;
  while(strtok(NULL,delims))
    K++;
  fclose(fp);

  return(K);
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movq %rdi, %r14
leaq 0x7dd4(%rip), %rsi      # 0xb0f7
callq 0x2260
testq %rax, %rax
je 0x338f
movq %rax, %rbx
movq %rsp, %r14
addq $-0x186a0, %r14         # imm = 0xFFFE7960
movq %r14, %rsp
movq %r14, %rdi
movl $0x186a0, %esi          # imm = 0x186A0
movq %rax, %rdx
callq 0x23c0
testq %rax, %rax
je 0x33ac
leaq 0x7d9b(%rip), %r15      # 0xb0f4
movq %r14, %rdi
movq %r15, %rsi
callq 0x23b0
xorl %r14d, %r14d
xorl %edi, %edi
movq %r15, %rsi
callq 0x23b0
incl %r14d
testq %rax, %rax
jne 0x3367
movq %rbx, %rdi
callq 0x2210
movl %r14d, %eax
leaq -0x18(%rbp), %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
movq 0xdc42(%rip), %rax      # 0x10fd8
movq (%rax), %rdi
leaq 0x7ee3(%rip), %rsi      # 0xb283
movq %r14, %rdx
xorl %eax, %eax
callq 0x2320
jmp 0x33c8
movq 0xdc25(%rip), %rax      # 0x10fd8
movq (%rax), %rcx
leaq 0x7f67(%rip), %rdi      # 0xb324
pushq $0x10
popq %rsi
pushq $0x1
popq %rdx
callq 0x2470
xorl %edi, %edi
callq 0x2280
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/Cinterface.cpp
// Function: allocFloat(unsigned long, unsigned long)
float **allocFloat(size_t x,size_t y){
  float **ret= new float*[x];
  for(size_t i=0;i<x;i++)
    ret[i] = new float[y];
  //printf("\t-> Tried to allocate: %.3f gig memory\n",(float)sizeof(float)*x*y/1000000000);
  return ret;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
movq %rsi, %r12
movq %rdi, %rbx
movq %rdi, %rax
shrq $0x3d, %rax
leaq (,%rdi,8), %rcx
xorl %r13d, %r13d
negq %rax
movl $0x0, %edi
sbbq %rdi, %rdi
orq %rcx, %rdi
callq 0x2030
movq %rax, %r14
movq %r12, %rax
shrq $0x3e, %rax
shlq $0x2, %r12
negq %rax
movl $0x0, %r15d
sbbq %r15, %r15
orq %r12, %r15
cmpq %r13, %rbx
je 0x3436
movq %r15, %rdi
callq 0x2030
movq %rax, (%r14,%r13,8)
incq %r13
jmp 0x3420
movq %r14, %rax
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/Cinterface.cpp
// Function: allocDouble(unsigned long, unsigned long)
double **allocDouble(size_t x,size_t y){
  double **ret= new double*[x];
  for(size_t i=0;i<x;i++)
    ret[i] = new double[y];
  //printf("\t-> Tried to allocate: %.3f gig memory\n",(float)sizeof(double)*x*y/1000000000);
  return ret;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
movq %rsi, %r12
movq %rdi, %rbx
movq %rdi, %rax
shrq $0x3d, %rax
leaq (,%rdi,8), %rcx
xorl %r13d, %r13d
negq %rax
movl $0x0, %edi
sbbq %rdi, %rdi
orq %rcx, %rdi
callq 0x2030
movq %rax, %r14
movq %r12, %rax
shrq $0x3d, %rax
shlq $0x3, %r12
negq %rax
movl $0x0, %r15d
sbbq %r15, %r15
orq %r12, %r15
cmpq %r13, %rbx
je 0x34aa
movq %r15, %rdi
callq 0x2030
movq %rax, (%r14,%r13,8)
incq %r13
jmp 0x3494
movq %r14, %rax
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/Cinterface.cpp
// Function: allocDouble3D(unsigned long, unsigned long, unsigned long)
double ***allocDouble3D(size_t x,size_t y,size_t z){
  double ***ret= new double**[x];
  for(size_t i=0;i<x;i++){
    ret[i] = new double*[y];
    for(size_t j=0; j<y;j++)
      ret[i][j] = new double[z];
  }
    return ret;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rdx, %rbp
movq %rsi, %rbx
movq %rdi, %rax
shrq $0x3d, %rax
movq %rdi, 0x10(%rsp)
leaq (,%rdi,8), %rcx
xorl %r14d, %r14d
negq %rax
movl $0x0, %edi
sbbq %rdi, %rdi
orq %rcx, %rdi
callq 0x2030
movq %rax, 0x8(%rsp)
movq %rbx, %rax
shrq $0x3d, %rax
leaq (,%rbx,8), %rcx
negq %rax
movl $0x0, %r12d
sbbq %r12, %r12
orq %rcx, %r12
movq %rbp, %rax
shrq $0x3d, %rax
shlq $0x3, %rbp
negq %rax
movl $0x0, %r13d
sbbq %r13, %r13
orq %rbp, %r13
cmpq 0x10(%rsp), %r14
je 0x356c
movq %r12, %rdi
callq 0x2030
movq %rax, %rbp
movq 0x8(%rsp), %rax
movq %rbp, (%rax,%r14,8)
xorl %r15d, %r15d
cmpq %r15, %rbx
je 0x3567
movq %r13, %rdi
callq 0x2030
movq %rax, (%rbp,%r15,8)
incq %r15
jmp 0x3550
incq %r14
jmp 0x3532
movq 0x8(%rsp), %rax
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/Cinterface.cpp
// Function: functionC(void*)
void *functionC(void *a) //the a means nothing
{
  int running_job;

  pthread_mutex_lock(&mutex1); // Protect so only one thread can edit jobs done
  
  while (jobs > 0) {
    running_job = jobs--;
    pthread_mutex_unlock(&mutex1);

    ////////////////////////////////////////////// not protected
    int c = NumJobs-running_job;
    eachPars p=allPars[c];
    myPars *pars=p.pars;
    int i=p.ind1;
    evalAdmix(p.cor,p.ind1u, p.ind1,pars->r,pars->mean_r,pars->genos,pars->K,pars->Q,pars->F,pars->nInd,pars->nSites,pars->nIts, pars->isMissing, pars->nIndUse, pars->useInds);
    
    //////////////////////////////////////////////


  }

  return NULL;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
leaq 0xdba8(%rip), %rbx      # 0x112a8
movq %rbx, %rdi
callq 0x2330
movslq 0xdbc5(%rip), %r14      # 0x112d4
testq %r14, %r14
jle 0x3798
leal -0x1(%r14), %eax
movl %eax, 0xdbb2(%rip)      # 0x112d4
movq %rbx, %rdi
callq 0x2170
movslq 0xdb9f(%rip), %rax      # 0x112d0
subq %r14, %rax
movq 0xdbb5(%rip), %rcx      # 0x112f0
imulq $0x18, %rax, %rdi
movq (%rcx,%rdi), %rax
movl 0x8(%rcx,%rdi), %edx
movl 0xc(%rcx,%rdi), %esi
movq 0x10(%rcx,%rdi), %rdi
movq 0x30(%rax), %rcx
movq 0x38(%rax), %r8
movl 0x44(%rax), %r10d
movq 0x18(%rax), %r9
movl 0x48(%rax), %r11d
movl 0x50(%rax), %r14d
movl 0x40(%rax), %r15d
movl 0x4c(%rax), %r12d
subq $0x8, %rsp
pushq 0x68(%rax)
pushq %r12
pushq 0x60(%rax)
pushq %r15
pushq %r14
pushq %r11
pushq 0x20(%rax)
pushq 0x28(%rax)
pushq %r10
callq 0xa448
addq $0x50, %rsp
jmp 0x3708
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/Cinterface.cpp
// Function: ngsfunctionC(void*)
void *ngsfunctionC(void *a) //the a means nothing
{
  int running_job;

  pthread_mutex_lock(&mutex1); // Protect so only one thread can edit jobs done
  
  while (jobs > 0) {
    running_job = jobs--;
    pthread_mutex_unlock(&mutex1);

    ////////////////////////////////////////////// not protected
    int c = NumJobs-running_job;
    eachNGSPars p=allNGSPars[c];
    myNGSPars *pars=p.pars;
    int i=p.ind1;

    ngsevalAdmix(p.cor,p.ind1u, p.ind1,pars->r,pars->mean_r,pars->genos,pars->K,pars->Q,pars->F,pars->nInd,pars->nSites,pars->nIts, pars->keeps, pars->nIndUse);
    
    //////////////////////////////////////////////


  }

  return NULL;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
leaq 0xdaf3(%rip), %rbx      # 0x112a8
movq %rbx, %rdi
callq 0x2330
movslq 0xdb10(%rip), %r14      # 0x112d4
testq %r14, %r14
jle 0x3841
leal -0x1(%r14), %eax
movl %eax, 0xdb01(%rip)      # 0x112d4
movq %rbx, %rdi
callq 0x2170
movslq 0xdaee(%rip), %rax      # 0x112d0
subq %r14, %rax
movq 0xdb0c(%rip), %rcx      # 0x112f8
imulq $0x18, %rax, %rdi
movq (%rcx,%rdi), %rax
movl 0x8(%rcx,%rdi), %edx
movl 0xc(%rcx,%rdi), %esi
movq 0x10(%rcx,%rdi), %rdi
movq 0x18(%rax), %rcx
movq 0x20(%rax), %r8
movl 0x2c(%rax), %r10d
movq (%rax), %r9
movl 0x30(%rax), %r11d
movl 0x38(%rax), %r14d
movl 0x28(%rax), %r15d
movl 0x34(%rax), %r12d
pushq %r12
pushq 0x48(%rax)
pushq %r15
pushq %r14
pushq %r11
pushq 0x8(%rax)
pushq 0x10(%rax)
pushq %r10
callq 0xac01
addq $0x40, %rsp
jmp 0x37bd
xorl %eax, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/Cinterface.cpp
// Function: fex(char const*)
void fex(const char* fileName){
  const char*delims=" \n";
  FILE *fp = NULL;
  if((fp=fopen(fileName,"r"))==NULL){
    fprintf(stderr,"can't open:%s\n",fileName);
    exit(0);
  }
  fclose(fp);
}

// Assembly:
pushq %rbx
movq %rdi, %rbx
leaq 0x789d(%rip), %rsi      # 0xb0f7
callq 0x2260
testq %rax, %rax
je 0x386d
movq %rax, %rdi
popq %rbx
jmp 0x2210
movq 0xd764(%rip), %rax      # 0x10fd8
movq (%rax), %rdi
leaq 0x7a05(%rip), %rsi      # 0xb283
movq %rbx, %rdx
xorl %eax, %eax
callq 0x2320
xorl %edi, %edi
callq 0x2280
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/filereader_and_conversions.cpp
// Function: to_string[abi:cxx11](int)
std::string to_string(int a){///@param a An integer to convert.
  std::string str;
  std::stringstream ss;
  ss<<a;
  if(!(ss>>str)){
    printf("Error converting :%d will exit\n",a);
    exit(0);
  }
  ss>>str;
  return str; ///@return Returns the string value.
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
subq $0x190, %rsp            # imm = 0x190
movl %esi, %ebp
movq %rdi, %rbx
leaq 0x10(%rdi), %rax
movq %rax, (%rdi)
andq $0x0, 0x8(%rdi)
movb $0x0, 0x10(%rdi)
leaq 0x8(%rsp), %rdi
callq 0x2140
leaq 0x18(%rsp), %rdi
movl %ebp, %esi
callq 0x2400
leaq 0x8(%rsp), %rdi
movq %rbx, %rsi
callq 0x22c0
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
testb $0x5, 0x20(%rax,%rcx)
jne 0x5c3c
leaq 0x8(%rsp), %rdi
movq %rbx, %rsi
callq 0x22c0
leaq 0x8(%rsp), %rdi
callq 0x2160
movq %rbx, %rax
addq $0x190, %rsp            # imm = 0x190
popq %rbx
popq %r14
popq %rbp
retq
leaq 0x632d(%rip), %rdi      # 0xbf70
movl %ebp, %esi
xorl %eax, %eax
callq 0x2040
xorl %edi, %edi
callq 0x2280
movq %rax, %r14
jmp 0x5c65
movq %rax, %r14
leaq 0x8(%rsp), %rdi
callq 0x2160
movq %rbx, %rdi
callq 0x20f0
movq %r14, %rdi
callq 0x2410
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/filereader_and_conversions.cpp
// Function: to_int(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>)
int to_int(std::string a){///@param a a String to convert.
  int str;
  float check;
  std::stringstream ss;
  std::stringstream ss2;
  if(!a.compare("NA")||!a.compare("Na")||!a.compare("na")){
    return 0;
  }
  ss<<a;
  if(!(ss>>str)){
    printf("Error converting :\"%s\" will exit\n",a.c_str());
    exit(0);
  }

  //now check if numberis really an int
  ss2<<a;
  if(!(ss2>>check)){
    printf("Error converting :\"%s\" will exit\n",a.c_str());
    exit(0);
  }

  if(check!=str){
    printf("String you want as in integer is not really an integer: \"%s\"\n",a.c_str());
    puts("Just a warning");
  }
  //check values
  /* this was commented in v. 0.983 since the chromosome file converter uses it.
  if(str<0||str>3){
    printf("Value in genotype is out of bounds, should be {0...3} value is:%d\n",str);
    exit(0);
  }
  */
  return str;///@return Function returns the integer value.
}

// Assembly:
pushq %rbp
pushq %rbx
subq $0x318, %rsp            # imm = 0x318
movq %rdi, %rbx
leaq 0x190(%rsp), %rdi
callq 0x2140
leaq 0x8(%rsp), %rdi
callq 0x2140
leaq 0x62f1(%rip), %rsi      # 0xbf90
movq %rbx, %rdi
callq 0x20a0
xorl %ebp, %ebp
testl %eax, %eax
je 0x5d6f
leaq 0x62db(%rip), %rsi      # 0xbf93
movq %rbx, %rdi
callq 0x20a0
testl %eax, %eax
je 0x5d6f
leaq 0x62c7(%rip), %rsi      # 0xbf96
movq %rbx, %rdi
callq 0x20a0
testl %eax, %eax
je 0x5d6f
leaq 0x1a0(%rsp), %rdi
movq %rbx, %rsi
callq 0x21d0
leaq 0x190(%rsp), %rdi
movq %rsp, %rsi
callq 0x2110
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
testb $0x5, 0x20(%rax,%rcx)
jne 0x5d92
leaq 0x18(%rsp), %rdi
movq %rbx, %rsi
callq 0x21d0
leaq 0x8(%rsp), %rdi
leaq 0x4(%rsp), %rsi
callq 0x2480
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
testb $0x5, 0x20(%rax,%rcx)
jne 0x5d92
movl (%rsp), %ebp
cvtsi2ss %ebp, %xmm0
movss 0x4(%rsp), %xmm1
ucomiss %xmm0, %xmm1
jne 0x5d4f
jnp 0x5d6f
movq (%rbx), %rsi
leaq 0x6262(%rip), %rdi      # 0xbfbb
xorl %eax, %eax
callq 0x2040
leaq 0x6292(%rip), %rdi      # 0xbff9
callq 0x2380
movl (%rsp), %ebp
leaq 0x8(%rsp), %rdi
callq 0x2160
leaq 0x190(%rsp), %rdi
callq 0x2160
movl %ebp, %eax
addq $0x318, %rsp            # imm = 0x318
popq %rbx
popq %rbp
retq
movq (%rbx), %rsi
leaq 0x61fd(%rip), %rdi      # 0xbf99
xorl %eax, %eax
callq 0x2040
xorl %edi, %edi
callq 0x2280
movq %rax, %rbx
leaq 0x8(%rsp), %rdi
callq 0x2160
jmp 0x5dbc
movq %rax, %rbx
leaq 0x190(%rsp), %rdi
callq 0x2160
movq %rbx, %rdi
callq 0x2410
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/filereader_and_conversions.cpp
// Function: to_float(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>)
float to_float(std::string a){///@param a is the string to convert.
  float str;
  std::stringstream ss;
  ss<<a;
  if(!(ss>>str)){
    printf("Error converting :\"%s\" will exit\n",a.c_str());
    exit(0);
  }
  ss>>str;
  return str;///@return The float value.
}

// Assembly:
pushq %rbx
subq $0x190, %rsp            # imm = 0x190
movq %rdi, %rbx
leaq 0x8(%rsp), %rdi
callq 0x2140
leaq 0x18(%rsp), %rdi
movq %rbx, %rsi
callq 0x21d0
leaq 0x8(%rsp), %rdi
movq %rsp, %rsi
callq 0x2480
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
testb $0x5, 0x20(%rax,%rcx)
jne 0x5e3f
leaq 0x8(%rsp), %rdi
movq %rsp, %rsi
callq 0x2480
movss (%rsp), %xmm0
movss %xmm0, 0x4(%rsp)
leaq 0x8(%rsp), %rdi
callq 0x2160
movss 0x4(%rsp), %xmm0
addq $0x190, %rsp            # imm = 0x190
popq %rbx
retq
movq (%rbx), %rsi
leaq 0x6150(%rip), %rdi      # 0xbf99
xorl %eax, %eax
callq 0x2040
xorl %edi, %edi
callq 0x2280
movq %rax, %rbx
leaq 0x8(%rsp), %rdi
callq 0x2160
movq %rbx, %rdi
callq 0x2410
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/filereader_and_conversions.cpp
// Function: to_double(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>)
double to_double(std::string a){///@param a is the string to convert.
  double str;
  std::stringstream ss;
  ss<<a;
  if(!(ss>>str)){
    printf("Error converting :\"%s\" will exit\n",a.c_str());
    exit(0);
  }
  ss>>str;
  return str;///@return The double value.
}

// Assembly:
pushq %rbx
subq $0x1a0, %rsp            # imm = 0x1A0
movq %rdi, %rbx
leaq 0x18(%rsp), %rdi
callq 0x2140
leaq 0x28(%rsp), %rdi
movq %rbx, %rsi
callq 0x21d0
leaq 0x18(%rsp), %rdi
leaq 0x8(%rsp), %rsi
callq 0x2120
movq (%rax), %rcx
movq -0x18(%rcx), %rcx
testb $0x5, 0x20(%rax,%rcx)
jne 0x5edf
leaq 0x18(%rsp), %rdi
leaq 0x8(%rsp), %rsi
callq 0x2120
movsd 0x8(%rsp), %xmm0
movsd %xmm0, 0x10(%rsp)
leaq 0x18(%rsp), %rdi
callq 0x2160
movsd 0x10(%rsp), %xmm0
addq $0x1a0, %rsp            # imm = 0x1A0
popq %rbx
retq
movq (%rbx), %rsi
leaq 0x60b0(%rip), %rdi      # 0xbf99
xorl %eax, %eax
callq 0x2040
xorl %edi, %edi
callq 0x2280
movq %rax, %rbx
leaq 0x18(%rsp), %rdi
callq 0x2160
movq %rbx, %rdi
callq 0x2410
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/filereader_and_conversions.cpp
// Function: get_lexemes(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<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>>>>&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>)
int get_lexemes(std::string str,std::vector<std::string> &lexems,const std::string delims){
  ///@param str The string to be splittet.
  ///@param lexems A reference to a list of strings in which the splittet string will be put as seperate elements. A queue.
  ///@param delims A string containing all the chars that the function will split by.
  char *token = strtok( const_cast<char*>( str.c_str() ),delims.c_str());
  int numToks = 0;
  while ( token != NULL ){
    numToks++;
    lexems.push_back( token);
    token = strtok( NULL,delims.c_str() );
  }
  return numToks;///@return The number of strings that has been splittet.
}

// Assembly:
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x30, %rsp
movq %rdx, %rbx
movq %rsi, %r14
movq (%rdi), %rdi
movq (%rdx), %rsi
callq 0x23b0
xorl %r15d, %r15d
leaq 0x10(%rsp), %r12
leaq 0xf(%rsp), %r13
testq %rax, %rax
je 0x5f6c
movq %r12, %rdi
movq %rax, %rsi
movq %r13, %rdx
callq 0x5646
movq %r14, %rdi
movq %r12, %rsi
callq 0x79b6
incl %r15d
movq %r12, %rdi
callq 0x20f0
movq (%rbx), %rsi
xorl %edi, %edi
callq 0x23b0
jmp 0x5f37
movl %r15d, %eax
addq $0x30, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
retq
movq %rax, %rbx
leaq 0x10(%rsp), %rdi
callq 0x20f0
movq %rbx, %rdi
callq 0x2410
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/filereader_and_conversions.cpp
// Function: typecast_stringarray_to_int_matrix(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&, iMatrix*)
void typecast_stringarray_to_int_matrix(const std::vector<std::string> &tokens,iMatrix *mat){
  int start=0;
  for (int i=0;i<mat->x;i++)
    for(int j=0;j<mat->y;j++){
      mat->matrix[i][j] = to_int( tokens.at(start++));

    }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %rsi, %rbx
movq %rdi, %r14
xorl %r12d, %r12d
leaq 0x8(%rsp), %r15
xorl %esi, %esi
movslq (%rbx), %rax
cmpq %rax, %r12
jge 0x6004
movslq %esi, %r13
xorl %ebp, %ebp
movq %r13, %rsi
addq %rbp, %rsi
movslq 0x4(%rbx), %rax
cmpq %rax, %rbp
jge 0x5fff
movq %r14, %rdi
callq 0x7954
movq %r15, %rdi
movq %rax, %rsi
callq 0x22f0
movq %r15, %rdi
callq 0x5c75
movq 0x8(%rbx), %rcx
movq (%rcx,%r12,8), %rcx
movl %eax, (%rcx,%rbp,4)
movq %r15, %rdi
callq 0x20f0
incq %rbp
jmp 0x5fbd
incq %r12
jmp 0x5fb0
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq %rax, %rbx
leaq 0x8(%rsp), %rdi
callq 0x20f0
movq %rbx, %rdi
callq 0x2410
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/filereader_and_conversions.cpp
// Function: typecast_stringarray_to_iArray(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&)
iArray *typecast_stringarray_to_iArray(const std::vector<std::string> &tokens){
  iArray *ary = allocIntArray(tokens.size());
  for (unsigned int i=0;i<tokens.size();i++)
    ary->array[i] = to_int( tokens.at(i));
  return ary;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %rdi, %rbx
movq 0x8(%rdi), %rdi
subq (%rbx), %rdi
sarq $0x5, %rdi
callq 0x967f
movq %rax, %r14
xorl %eax, %eax
leaq 0x8(%rsp), %r15
movl %eax, %r12d
movq 0x8(%rbx), %rax
subq (%rbx), %rax
sarq $0x5, %rax
cmpq %r12, %rax
jbe 0x6098
movq %rbx, %rdi
movq %r12, %rsi
callq 0x7954
movq %r15, %rdi
movq %rax, %rsi
callq 0x22f0
movq %r15, %rdi
callq 0x5c75
movq 0x8(%r14), %rcx
movl %eax, (%rcx,%r12,4)
movq %r15, %rdi
callq 0x20f0
leal 0x1(%r12), %eax
jmp 0x6050
movq %r14, %rax
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
movq %rax, %rbx
leaq 0x8(%rsp), %rdi
callq 0x20f0
movq %rbx, %rdi
callq 0x2410
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/filereader_and_conversions.cpp
// Function: typecast_stringarray_to_dArray(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&)
dArray *typecast_stringarray_to_dArray(const std::vector<std::string> &tokens){
  dArray *ary = allocDoubleArray(tokens.size());
  for (unsigned int i=0;i<tokens.size();i++)
    ary->array[i] = to_double( tokens.at(i));
  return ary;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %rdi, %rbx
movq 0x8(%rdi), %rdi
subq (%rbx), %rdi
shrq $0x5, %rdi
callq 0x97cc
movq %rax, %r14
xorl %eax, %eax
leaq 0x8(%rsp), %r15
movl %eax, %r12d
movq 0x8(%rbx), %rax
subq (%rbx), %rax
sarq $0x5, %rax
cmpq %r12, %rax
jbe 0x612e
movq %rbx, %rdi
movq %r12, %rsi
callq 0x7954
movq %r15, %rdi
movq %rax, %rsi
callq 0x22f0
movq %r15, %rdi
callq 0x5e6c
movq 0x8(%r14), %rax
movsd %xmm0, (%rax,%r12,8)
movq %r15, %rdi
callq 0x20f0
leal 0x1(%r12), %eax
jmp 0x60e4
movq %r14, %rax
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
movq %rax, %rbx
leaq 0x8(%rsp), %rdi
callq 0x20f0
movq %rbx, %rdi
callq 0x2410
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/filereader_and_conversions.cpp
// Function: readarray(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>>)
std::vector<std::string> readarray(std::string filename,const std::string delims=",;: \t"){
  ///@param filename The name of the file to open.
  ///@param delims A string of delimeters to split by.
  std::vector<std::string> tokens;

  const int SIZE = MAX_ELEMS_PER_LINE;
  char *buffer = new char[SIZE];
  std::ifstream pFile (filename.c_str(),std::ios::in);
  
  if(!pFile){
    fileError(filename);
    exit(0);
  }
  
  std::string tmp_string;
  //we are reading an array, so just keep reading until no more lines
  while(!pFile.eof()){
    pFile.getline(buffer,SIZE);
    tmp_string = std::string(buffer);
    get_lexemes(tmp_string,tokens,delims);
    
  }
  pFile.close();
  delete [] buffer;
  ///now we have a token array of string coerce the types now
  //typecast_stringarray(tokens);
  return tokens;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x2b8, %rsp            # imm = 0x2B8
movq %rdx, %r15
movq %rsi, %rbx
xorps %xmm0, %xmm0
movups %xmm0, (%rdi)
movq %rdi, 0x8(%rsp)
andq $0x0, 0x10(%rdi)
movl $0x4c4b40, %edi         # imm = 0x4C4B40
callq 0x2030
movq %rax, %r14
movq (%rbx), %rsi
leaq 0xb0(%rsp), %rdi
pushq $0x8
popq %rdx
callq 0x2450
movq 0xb0(%rsp), %rax
movq -0x18(%rax), %rax
testb $0x5, 0xd0(%rsp,%rax)
jne 0x62a7
leaq 0x20(%rsp), %rcx
movq %rcx, -0x10(%rcx)
andq $0x0, -0x8(%rcx)
movb $0x0, (%rcx)
leaq 0x90(%rsp), %r13
leaq 0x10(%rsp), %rbx
leaq 0x50(%rsp), %r12
leaq 0x30(%rsp), %rbp
testb $0x2, 0xd0(%rsp,%rax)
jne 0x6264
movl $0x4c4b40, %edx         # imm = 0x4C4B40
leaq 0xb0(%rsp), %rdi
movq %r14, %rsi
callq 0x20b0
movq %r13, %rdi
movq %r14, %rsi
leaq 0x7(%rsp), %rdx
callq 0x5646
movq %rbx, %rdi
movq %r13, %rsi
callq 0x2290
movq %r13, %rdi
callq 0x20f0
movq %r12, %rdi
movq %rbx, %rsi
callq 0x22f0
movq %rbp, %rdi
movq %r15, %rsi
callq 0x22f0
movq %r12, %rdi
movq 0x8(%rsp), %rsi
movq %rbp, %rdx
callq 0x5f0c
movq %rbp, %rdi
callq 0x20f0
movq %r12, %rdi
callq 0x20f0
movq 0xb0(%rsp), %rax
movq -0x18(%rax), %rax
jmp 0x61db
leaq 0xb0(%rsp), %rdi
callq 0x2050
movq %r14, %rdi
callq 0x22d0
leaq 0x10(%rsp), %rdi
callq 0x20f0
leaq 0xb0(%rsp), %rdi
callq 0x2070
movq 0x8(%rsp), %rax
addq $0x2b8, %rsp            # imm = 0x2B8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
leaq 0x70(%rsp), %rdi
movq %rbx, %rsi
callq 0x22f0
leaq 0x70(%rsp), %rbx
movq %rbx, %rdi
callq 0x590c
movq %rbx, %rdi
callq 0x20f0
xorl %edi, %edi
callq 0x2280
movq %rax, %rbx
jmp 0x630b
jmp 0x62fe
jmp 0x62d9
movq %rax, %rbx
jmp 0x6318
movq %rax, %rbx
leaq 0x30(%rsp), %rdi
callq 0x20f0
jmp 0x62f0
movq %rax, %rbx
leaq 0x50(%rsp), %rdi
callq 0x20f0
jmp 0x6301
jmp 0x62fe
movq %rax, %rbx
leaq 0x10(%rsp), %rdi
callq 0x20f0
leaq 0xb0(%rsp), %rdi
callq 0x2070
movq 0x8(%rsp), %rdi
callq 0x7976
movq %rbx, %rdi
callq 0x2410
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/filereader_and_conversions.cpp
// Function: getNext(iArray*, int)
int getNext(iArray *list,int i){
  if(i>=list->x)
    return -1;
  for(int j=i;j<list->x;j++){
    // printf("i:%d\tj:%d\tiar:%d\n",i,j,list->array[i]);
    if(list->array[j]==1)
      return j;
  }
  return -1;
}

// Assembly:
movslq (%rdi), %rcx
pushq $-0x1
popq %rax
cmpl %esi, %ecx
jle 0x6ce1
movslq %esi, %rdx
cmpq %rcx, %rdx
jge 0x6ce1
movq 0x8(%rdi), %rsi
cmpl $0x1, (%rsi,%rdx,4)
je 0x6cdf
incq %rdx
jmp 0x6ccb
movl %edx, %eax
retq
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/filereader_and_conversions.cpp
// Function: getTestIndividuals(char const*)
std::vector<iArray*> getTestIndividuals(const char *pName){
  iArray *testList = typecast_stringarray_to_iArray(readarray(std::string(pName)));
  
  int numTrues=0;
  for(int i=0;i<testList->x;i++)
    if(testList->array[i])
      numTrues++;
  //printf("numTrues:%d\n",numTrues);
  //testList->print("testlist",NULL);
  std::vector<iArray*> returnVal;
  int pos1 = getNext(testList,0);
  while(pos1!=-1){
    int pos2 = getNext(testList,pos1+1);
    while(pos2!=-1){
      if(pos2!=-1){
	//printf("p1:%d\tp2:%d\n",pos1,pos2);
	iArray *pr = allocIntArray(2);
	pr->array[0]=pos1;pr->array[1]=pos2;
	returnVal.push_back(pr);
      }
      pos2 = getNext(testList,pos2+1);
    }
    pos1 = getNext(testList,pos1+1);
  }
  killArray(testList);
  return returnVal;

}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x68, %rsp
movq %rdi, %rbx
leaq 0x48(%rsp), %rdi
leaq 0xb(%rsp), %rdx
callq 0x5646
leaq 0x54cf(%rip), %rsi      # 0xc1d8
leaq 0x28(%rsp), %rdi
leaq 0xa(%rsp), %rdx
callq 0x5646
leaq 0x10(%rsp), %rdi
leaq 0x48(%rsp), %rsi
leaq 0x28(%rsp), %rdx
callq 0x6152
leaq 0x10(%rsp), %rdi
callq 0x6028
movq %rax, %r14
leaq 0x10(%rsp), %r15
movq %r15, %rdi
callq 0x7976
leaq 0x28(%rsp), %rdi
callq 0x20f0
leaq 0x48(%rsp), %rdi
callq 0x20f0
andq $0x0, 0x10(%rbx)
xorps %xmm0, %xmm0
movups %xmm0, (%rbx)
movl $0x0, 0xc(%rsp)
pushq $0x2
popq %r12
movq %r14, %rdi
movl 0xc(%rsp), %esi
callq 0x6cbe
cmpl $-0x1, %eax
je 0x6dc4
movl %eax, %r13d
movl %eax, %ebp
incl %ebp
movl %ebp, 0xc(%rsp)
movq %r14, %rdi
movl %ebp, %esi
callq 0x6cbe
cmpl $-0x1, %eax
je 0x6d71
movl %eax, %ebp
movq %r12, %rdi
callq 0x967f
movq %rax, 0x10(%rsp)
movq 0x8(%rax), %rax
movl %r13d, (%rax)
movl %ebp, 0x4(%rax)
movq %rbx, %rdi
movq %r15, %rsi
callq 0x7998
incl %ebp
jmp 0x6d8d
movq %r14, %rdi
callq 0x93b4
movq %rbx, %rax
addq $0x68, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
jmp 0x6e12
movq %rax, %r14
leaq 0x10(%rsp), %rdi
callq 0x7976
jmp 0x6df2
movq %rax, %r14
leaq 0x28(%rsp), %rdi
callq 0x20f0
jmp 0x6e01
movq %rax, %r14
leaq 0x48(%rsp), %rdi
callq 0x20f0
jmp 0x6e1d
movq %rax, %r14
jmp 0x6e1d
movq %rax, %r14
movq %rbx, %rdi
callq 0x7bf8
movq %r14, %rdi
callq 0x2410
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/filereader_and_conversions.cpp
// Function: numberOfLines(char const*)
int numberOfLines(const char *filename){
  const int SIZE=500000;
  char buffer[SIZE];
  int numLines=0;
  std::ifstream pFile (filename,std::ios::in);
  
  if(!pFile){
fileError(filename);
    return 0;
  }
  while(!pFile.eof()){
    pFile.getline(buffer,SIZE);
    numLines++;
  }
  return numLines;
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
subq $0x7a350, %rsp          # imm = 0x7A350
movq %rdi, %rbx
leaq 0x28(%rsp), %r14
pushq $0x8
popq %rdx
movq %r14, %rdi
movq %rbx, %rsi
callq 0x2450
movq (%r14), %rax
movq -0x18(%rax), %rax
testb $0x5, 0x48(%rsp,%rax)
je 0x72a6
leaq 0x8(%rsp), %rdi
leaq 0x7(%rsp), %rdx
movq %rbx, %rsi
callq 0x5646
leaq 0x8(%rsp), %rbx
movq %rbx, %rdi
callq 0x590c
movq %rbx, %rdi
callq 0x20f0
xorl %ebx, %ebx
leaq 0x28(%rsp), %rdi
callq 0x2070
movl %ebx, %eax
addq $0x7a350, %rsp          # imm = 0x7A350
popq %rbx
popq %r14
popq %r15
retq
xorl %ebx, %ebx
leaq 0x28(%rsp), %r14
leaq 0x230(%rsp), %r15
testb $0x2, 0x48(%rsp,%rax)
jne 0x728d
movl $0x7a120, %edx          # imm = 0x7A120
movq %r14, %rdi
movq %r15, %rsi
callq 0x20b0
incl %ebx
movq 0x28(%rsp), %rax
movq -0x18(%rax), %rax
jmp 0x72b5
jmp 0x72db
movq %rax, %rbx
leaq 0x28(%rsp), %rdi
callq 0x2070
movq %rbx, %rdi
callq 0x2410
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/extractors.cpp
// Function: extractOK(iArray*, iMatrix*)
iMatrix *extractOK(iArray *okList,iMatrix *matr){
  iMatrix *returnMatrix = allocIntMatrix(matr->x,okList->x);
  for(int j=0;j<matr->x;j++)
    for(int i=0;i<okList->x;i++)
      returnMatrix->matrix[j][i] = matr->matrix [j] [okList->array[i]];
  return returnMatrix;

}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
movl (%rsi), %edi
movl (%r14), %esi
callq 0x90f4
xorl %ecx, %ecx
movslq (%rbx), %rdx
cmpq %rdx, %rcx
jge 0x811c
xorl %edx, %edx
movslq (%r14), %rsi
cmpq %rsi, %rdx
jge 0x8117
movq 0x8(%rbx), %rsi
movq (%rsi,%rcx,8), %rsi
movq 0x8(%r14), %rdi
movslq (%rdi,%rdx,4), %rdi
movl (%rsi,%rdi,4), %esi
movq 0x8(%rax), %rdi
movq (%rdi,%rcx,8), %rdi
movl %esi, (%rdi,%rdx,4)
incq %rdx
jmp 0x80ec
incq %rcx
jmp 0x80e2
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/extractors.cpp
// Function: extractOK(iArray*, usiMatrix*)
usiMatrix *extractOK(iArray *okList,usiMatrix *matr){
  usiMatrix *returnMatrix = allocUSIntMatrix(matr->x,okList->x);
  for(int j=0;j<matr->x;j++)
    for(int i=0;i<okList->x;i++)
      returnMatrix->matrix[j][i] = matr->matrix [j] [okList->array[i]];
  return returnMatrix;

}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
movl (%rsi), %edi
movl (%r14), %esi
callq 0x9238
movl (%rbx), %ecx
xorl %edx, %edx
testl %ecx, %ecx
cmovlel %edx, %ecx
xorl %esi, %esi
cmpq %rcx, %rsi
je 0x8184
movl (%r14), %edi
testl %edi, %edi
cmovlel %edx, %edi
xorl %r8d, %r8d
cmpq %r8, %rdi
je 0x817f
movq 0x8(%rbx), %r9
movq (%r9,%rsi,8), %r9
movq 0x8(%r14), %r10
movslq (%r10,%r8,4), %r10
movzwl (%r9,%r10,2), %r9d
movq 0x8(%rax), %r10
movq (%r10,%rsi,8), %r10
movw %r9w, (%r10,%r8,2)
incq %r8
jmp 0x8153
incq %rsi
jmp 0x8143
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/extractors.cpp
// Function: extractOK(iArray*, dMatrix*)
dMatrix *extractOK(iArray *okList,dMatrix *matr){
  dMatrix *returnMatrix = allocDoubleMatrix(matr->x,okList->x);
  for(int j=0;j<matr->x;j++)
    for(int i=0;i<okList->x;i++)
      returnMatrix->matrix[j][i] = matr->matrix [j] [okList->array[i]];
  return returnMatrix;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
movl (%rsi), %edi
movl (%r14), %esi
callq 0x9522
movl (%rbx), %ecx
xorl %edx, %edx
testl %ecx, %ecx
cmovlel %edx, %ecx
xorl %esi, %esi
cmpq %rcx, %rsi
je 0x81ee
movl (%r14), %edi
testl %edi, %edi
cmovlel %edx, %edi
xorl %r8d, %r8d
cmpq %r8, %rdi
je 0x81e9
movq 0x8(%rbx), %r9
movq (%r9,%rsi,8), %r9
movq 0x8(%r14), %r10
movslq (%r10,%r8,4), %r10
movsd (%r9,%r10,8), %xmm0
movq 0x8(%rax), %r9
movq (%r9,%rsi,8), %r9
movsd %xmm0, (%r9,%r8,8)
incq %r8
jmp 0x81bb
incq %rsi
jmp 0x81ab
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/extractors.cpp
// Function: extractOK(iArray*, iArray*)
iArray *extractOK(iArray *okList,iArray *array){
  iArray *returnArray = allocIntArray(okList->x);
  for(int j=0;j<okList->x;j++)
    returnArray->array[j] = array->array[okList->array[j]];
  return returnArray;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
movslq (%rdi), %rdi
callq 0x967f
xorl %ecx, %ecx
movslq (%r14), %rdx
cmpq %rdx, %rcx
jge 0x822d
movq 0x8(%rbx), %rdx
movq 0x8(%r14), %rsi
movslq (%rsi,%rcx,4), %rsi
movl (%rdx,%rsi,4), %edx
movq 0x8(%rax), %rsi
movl %edx, (%rsi,%rcx,4)
incq %rcx
jmp 0x820a
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/extractors.cpp
// Function: extractOK(iArray*, dArray*)
dArray *extractOK(iArray *okList,dArray *array){
  dArray *returnArray = allocDoubleArray(okList->x);
  int extractIndex;
  double var;
  for(int j=0;j<okList->x;j++){
    extractIndex = okList->array[j];
    var = array->array[extractIndex];
    returnArray->array[j] = var;
  }
  return returnArray;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
movl (%rdi), %edi
callq 0x97cc
movslq (%r14), %rcx
xorl %edx, %edx
cmpq %rcx, %rdx
jge 0x826f
movq 0x8(%r14), %rsi
movslq (%rsi,%rdx,4), %rsi
movq 0x8(%rbx), %rdi
movsd (%rdi,%rsi,8), %xmm0
movq 0x8(%rax), %rsi
movsd %xmm0, (%rsi,%rdx,8)
incq %rdx
jmp 0x824b
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/extractors.cpp
// Function: extractOK(bArray*, dArray*)
dArray *extractOK(bArray *okList,dArray *array){
  dArray *returnArray = allocDoubleArray(okList->numTrue);
  int inPlace = 0;
  for(int j=0 ; j<okList->x ; j++){
    if(okList->array[j] == 1){
      returnArray->array[inPlace] = array->array[j];
      inPlace++;
    }
  }
  return returnArray;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
movl 0x4(%rdi), %edi
callq 0x97cc
movslq (%r14), %rcx
xorl %edx, %edx
xorl %esi, %esi
cmpq %rcx, %rdx
jge 0x82bb
movq 0x8(%r14), %rdi
cmpl $0x1, (%rdi,%rdx,4)
jne 0x82b6
movq 0x8(%rbx), %rdi
movsd (%rdi,%rdx,8), %xmm0
movq 0x8(%rax), %rdi
movslq %esi, %rsi
movsd %xmm0, (%rdi,%rsi,8)
incl %esi
incq %rdx
jmp 0x8290
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_cpp_makefile_star2_O2/GenisGE[P]evalAdmix/extractors.cpp
// Function: extractOK(bArray*, iArray*)
iArray *extractOK(bArray *okList,iArray *array){
  iArray *returnArray = allocIntArray(okList->numTrue);
  int inPlace = 0;
  for(int j=0 ; j<okList->x ; j++){
    if(okList->array[j] == 1){
      returnArray->array[inPlace] = array->array[j];
      inPlace++;
    }
  }
  return returnArray;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %rbx
movq %rdi, %r14
movslq 0x4(%rdi), %rdi
callq 0x967f
xorl %ecx, %ecx
xorl %edx, %edx
movslq (%r14), %rsi
cmpq %rsi, %rcx
jge 0x8304
movq 0x8(%r14), %rsi
cmpl $0x1, (%rsi,%rcx,4)
jne 0x82ff
movq 0x8(%rbx), %rsi
movl (%rsi,%rcx,4), %esi
movq 0x8(%rax), %rdi
movslq %edx, %rdx
movl %esi, (%rdi,%rdx,4)
incl %edx
incq %rcx
jmp 0x82da
addq $0x8, %rsp
popq %rbx
popq %r14
retq