int main(int argc, char** argv) {
if (argc==2&&strcmp("passwd",argv[1])==0)
callsystem();
write(STDOUT_FILENO, "Hello, World\n", 13);
vulnerable_function();
}
static int call_damapper(libmaus2::util::ArgParser const & arg, libmaus2::util::ArgInfo const & arginfo)
{
unsigned int const damapper_arg_k = arg.uniqueArgPresent("k") ? arg.getUnsignedNumericArg<uint64_t>("k") : 20;
int const damapper_arg_t = arg.uniqueArgPresent("t") ? arg.getParsedArg<int>("t") : -1;
int const damapper_arg_M = arg.uniqueArgPresent("M") ? arg.getParsedArg<int>("M") : -1;
double const damapper_arg_e = arg.uniqueArgPresent("e") ? arg.getParsedArg<double>("e") : std::numeric_limits<double>::min();
int const damapper_arg_s = arg.uniqueArgPresent("s") ? arg.getParsedArg<int>("s") : -1;
double const damapper_arg_n = arg.uniqueArgPresent("n") ? arg.getParsedArg<double>("n") : std::numeric_limits<double>::min();
int const damapper_arg_B = arg.uniqueArgPresent("B") ? arg.getParsedArg<int>("B") : -1;
int const damapper_arg_T = arg.uniqueArgPresent("T") ? arg.getParsedArg<int>("T") : -1;
int const damapper_arg_b = arg.uniqueArgPresent("b") ? 1 : 0; // comp bias
int const damapper_arg_v = arg.uniqueArgPresent("v") ? 1 : 0; // verbose
int const damapper_arg_p = arg.uniqueArgPresent("p") ? 1 : 0; // repeat profile (not used)
unsigned int const numthreads = damapper_arg_T < 0 ? 4 : damapper_arg_T;
unsigned int const refblocksize = arg.uniqueArgPresent("refblocksize") ? arg.getUnsignedNumericArg<uint64_t>("refblocksize") : 250;
unsigned int const readblocksize = arg.uniqueArgPresent("readblocksize") ? arg.getUnsignedNumericArg<uint64_t>("readblocksize") : 250;
std::string const argindexdir = arg.uniqueArgPresent("I") ? arg["I"] : std::string();
std::string const argworkdir = arg.uniqueArgPresent("W") ? arg["W"] : std::string();
std::string const workdir = makeAbsolute(argworkdir.size() ? argworkdir : ".");
mkdirP(workdir);
unsigned int const fastacolwidth = 80;
bool const reformatref = true;
bool const reformatreads = true;
std::string progname = arg.progname;
ProgramDescriptor PD_fasta2DAM("fasta2DAM",progname);
ProgramDescriptor PD_DBsplit("DBsplit",progname);
ProgramDescriptor PD_HPC_damapper("HPC.damapper",progname);
ProgramDescriptor PD_damapper("damapper",progname);
ProgramDescriptor PD_lascat("lascat",progname);
ProgramDescriptor PD_laschainsort("laschainsort",progname);
ProgramDescriptor PD_lastobam("lastobam",progname);
ProgramDescriptor PD_LAsort("LAsort",progname);
ProgramDescriptor PD_LAcat("LAcat",progname);
ProgramDescriptor PD_LAmerge("LAmerge",progname);
std::vector<std::string> Vpathadd;
Vpathadd.push_back(PD_LAsort.dir);
Vpathadd.push_back(PD_LAcat.dir);
Vpathadd.push_back(PD_LAmerge.dir);
std::sort(Vpathadd.begin(),Vpathadd.end());
Vpathadd.resize ( std::unique(Vpathadd.begin(),Vpathadd.end()) - Vpathadd.begin() );
std::ostringstream npathstr;
npathstr << getenv("PATH");
for ( uint64_t i = 0; i < Vpathadd.size(); ++i )
npathstr << ":" << Vpathadd[i];
std::string const npath = npathstr.str();
libmaus2::util::WriteableString Wnpath(npath);
setenv("PATH",Wnpath.A.begin(),1 /* overwrite */);
std::string const reffn = arg[0];
if ( ! libmaus2::util::GetFileSize::fileExists(reffn) )
{
libmaus2::exception::LibMausException lme;
lme.getStream() << "call.damapper: reference file " << reffn << " does not exist" << std::endl;
lme.finish();
throw lme;
}
static char const * faend[] = { ".fasta",".fa",0 };
std::string const refdir = sdirname(reffn);
std::string const indexdir = makeAbsolute(argindexdir.size() ? argindexdir : refdir);
std::string const reffile = sbasename(reffn);
std::string const reffileclipped = libmaus2::util::OutputFileNameTools::endClip(reffile,&faend[0]);
mkdirP(indexdir);
std::string const refdam = indexdir + "/" + reffileclipped + ".dam";
std::string const refidx = indexdir + "/." + reffileclipped + ".idx";
std::string const refhdr = indexdir + "/." + reffileclipped + ".hdr";
std::string const refbps = indexdir + "/." + reffileclipped + ".bps";
std::string const indexfasta = indexdir + "/" + reffileclipped + ".dam.fasta";
if (
! libmaus2::util::GetFileSize::fileExists(refdam) || libmaus2::util::GetFileSize::isOlder(refdam,reffn) ||
! libmaus2::util::GetFileSize::fileExists(refidx) || libmaus2::util::GetFileSize::isOlder(refidx,reffn) ||
! libmaus2::util::GetFileSize::fileExists(refhdr) || libmaus2::util::GetFileSize::isOlder(refhdr,reffn) ||
! libmaus2::util::GetFileSize::fileExists(refbps) || libmaus2::util::GetFileSize::isOlder(refbps,reffn) ||
! libmaus2::util::GetFileSize::fileExists(indexfasta) || libmaus2::util::GetFileSize::isOlder(indexfasta,reffn)
)
{
std::string const tmpbase = arginfo.getDefaultTmpFileName();
std::string const reffastatmp = indexdir + "/" + tmpbase + ".fasta";
std::string const refdamtmp = indexdir + "/" + tmpbase + ".dam";
std::string const refdamidxtmp = indexdir + "/." + tmpbase + ".idx";
std::string const refdamhdrtmp = indexdir + "/." + tmpbase + ".hdr";
std::string const refdambpstmp = indexdir + "/." + tmpbase + ".bps";
libmaus2::util::TempFileRemovalContainer::addTempFile(refdamtmp);
libmaus2::util::TempFileRemovalContainer::addTempFile(refdamidxtmp);
libmaus2::util::TempFileRemovalContainer::addTempFile(refdamhdrtmp);
libmaus2::util::TempFileRemovalContainer::addTempFile(refdambpstmp);
libmaus2::util::TempFileRemovalContainer::addTempFile(reffastatmp);
if ( reformatref )
{
libmaus2::fastx::FastAReader FAreader(reffn);
libmaus2::fastx::FastAReader::pattern_type pat;
libmaus2::aio::OutputStreamInstance::unique_ptr_type OSI(new libmaus2::aio::OutputStreamInstance(reffastatmp));
while ( FAreader.getNextPatternUnlocked(pat) )
pat.printMultiLine(*OSI,fastacolwidth);
OSI->flush();
OSI.reset();
}
else
{
if ( symlink(reffn.c_str(),reffastatmp.c_str()) )
{
int const error = errno;
libmaus2::exception::LibMausException lme;
lme.getStream() << "call.damapper: symlink(" << reffn << "," << reffastatmp << "): " << strerror(error) << std::endl;
lme.finish();
throw lme;
}
}
std::string const fasta2DAMcom = PD_fasta2DAM.path + " " + refdamtmp + " " + reffastatmp;
int const fasta2DAMcomres = callsystem(fasta2DAMcom.c_str());
if ( damapper_arg_v )
std::cerr << "[V] " << fasta2DAMcom << std::endl;
if ( fasta2DAMcomres != 0 )
{
libmaus2::exception::LibMausException lme;
lme.getStream() << "call.damapper: " << fasta2DAMcom << " failed" << std::endl;
lme.finish();
throw lme;
}
std::ostringstream splitstr;
splitstr << PD_DBsplit.path << " -s" << refblocksize << " -x" << damapper_arg_k << " " << refdamtmp;
std::string const splitcom = splitstr.str();
int const splitcomres = callsystem(splitcom.c_str());
if ( damapper_arg_v )
std::cerr << "[V] " << splitcom << std::endl;
if ( splitcomres != 0 )
{
libmaus2::exception::LibMausException lme;
lme.getStream() << "call.damapper: " << splitcomres << " failed" << std::endl;
lme.finish();
throw lme;
}
callrename(refdamtmp,refdam);
callrename(refdamidxtmp,refidx);
callrename(refdamhdrtmp,refhdr);
callrename(refdambpstmp,refbps);
callrename(reffastatmp,indexfasta);
}
std::string const tmpbase = arginfo.getDefaultTmpFileName();
std::string const readsfastatmp = workdir + "/" + tmpbase + "_reads" + ".fasta";
std::string const readsdamtmp = workdir + "/" + tmpbase + "_reads" + ".dam";
std::string const readsidxtmp = workdir + "/." + tmpbase + "_reads" + ".idx";
std::string const readsbpstmp = workdir + "/." + tmpbase + "_reads" + ".bps";
std::string const readshdrtmp = workdir + "/." + tmpbase + "_reads" + ".hdr";
std::string const readsdamtmpscript = workdir + "/" + tmpbase + "_reads" + ".dam.script";
std::string const readslastmp = workdir + "/" + tmpbase + "_reads" + ".las";
libmaus2::util::TempFileRemovalContainer::addTempFile(readsfastatmp);
libmaus2::util::TempFileRemovalContainer::addTempFile(readsdamtmp);
libmaus2::util::TempFileRemovalContainer::addTempFile(readsidxtmp);
libmaus2::util::TempFileRemovalContainer::addTempFile(readsbpstmp);
libmaus2::util::TempFileRemovalContainer::addTempFile(readshdrtmp);
libmaus2::util::TempFileRemovalContainer::addTempFile(readsdamtmpscript);
libmaus2::util::TempFileRemovalContainer::addTempFile(readslastmp);
libmaus2::aio::OutputStreamInstance::unique_ptr_type OSI(new libmaus2::aio::OutputStreamInstance(readsfastatmp));
if ( reformatreads )
{
libmaus2::fastx::StreamFastAReaderWrapper SFAR(std::cin);
libmaus2::fastx::StreamFastAReaderWrapper::pattern_type pat;
while ( SFAR.getNextPatternUnlocked(pat) )
pat.printMultiLine(*OSI,fastacolwidth);
}
else
{
libmaus2::autoarray::AutoArray<char> A(4096,false);
while ( std::cin )
{
std::cin.read(A.begin(),A.size());
uint64_t const r = std::cin.gcount();
OSI->write(A.begin(),r);
}
}
OSI->flush();
OSI.reset();
std::string const fasta2DAMcom = PD_fasta2DAM.path + " " + readsdamtmp + " " + readsfastatmp;
int const fasta2DAMcomres = callsystem(fasta2DAMcom.c_str());
if ( damapper_arg_v )
std::cerr << "[V] " << fasta2DAMcom << std::endl;
if ( fasta2DAMcomres != 0 )
{
libmaus2::exception::LibMausException lme;
lme.getStream() << "call.damapper: " << fasta2DAMcom << " failed" << std::endl;
lme.finish();
throw lme;
}
std::ostringstream splitstr;
splitstr << PD_DBsplit.path << " -s" << readblocksize << " -x" << damapper_arg_k << " " << readsdamtmp;
std::string const splitcom = splitstr.str();
int const splitcomres = callsystem(splitcom.c_str());
if ( damapper_arg_v )
std::cerr << "[V] " << splitcom << std::endl;
if ( splitcomres != 0 )
{
libmaus2::exception::LibMausException lme;
lme.getStream() << "call.damapper: " << splitcomres << " failed" << std::endl;
lme.finish();
throw lme;
}
std::string const calldir = getCurrentDir();
if ( chdir(workdir.c_str()) )
{
int const error = errno;
libmaus2::exception::LibMausException lme;
lme.getStream() << "call.damapper: chdir(" << workdir << "): " << strerror(error) << std::endl;
lme.finish();
throw lme;
}
std::ostringstream HPC1str;
HPC1str << PD_HPC_damapper.path;
HPC1str << " -k" << damapper_arg_k;
if ( damapper_arg_t != -1 )
HPC1str << " -t" << damapper_arg_t;
if ( damapper_arg_M != -1 )
HPC1str << " -M" << damapper_arg_M;
if ( damapper_arg_e != std::numeric_limits<double>::min() )
HPC1str << " -e" << damapper_arg_e;
if ( damapper_arg_s != -1 )
HPC1str << " -s" << damapper_arg_s;
if ( damapper_arg_n != std::numeric_limits<double>::min() )
HPC1str << " -n" << damapper_arg_n;
if ( damapper_arg_B != -1 )
HPC1str << " -B" << damapper_arg_B;
HPC1str << " -T" << numthreads;
if ( damapper_arg_b )
HPC1str << " -b";
if ( damapper_arg_v )
HPC1str << " -v";
if ( damapper_arg_p )
HPC1str << " -p";
HPC1str << " -C -N " << refdam << " " << readsdamtmp << " >" << readsdamtmpscript;
std::string const HPC1 = HPC1str.str();
int const HPC1res = system(HPC1.c_str());
if ( damapper_arg_v )
std::cerr << "[V] " << HPC1 << std::endl;
if ( HPC1res != 0 )
{
libmaus2::exception::LibMausException lme;
lme.getStream() << "call.damapper: " << HPC1 << " failed" << std::endl;
lme.finish();
throw lme;
}
std::vector<std::string> Voutput;
std::vector<std::string> Vdamapper;
libmaus2::aio::InputStreamInstance::unique_ptr_type HPCisi(new libmaus2::aio::InputStreamInstance(readsdamtmpscript));
std::string const exp = "# Catenate jobs (2)";
std::string const expdamapper = "# Damapper jobs (1)";
std::string const expsub = "LAsort -a ";
std::string const expcheck = "# Check all .las files (optional but recommended)";
std::string const expchecksub = "LAcheck -vS ";
bool activedamapper = false;
bool activeoutput = false;
bool activationfound = false;
bool activationdamapperfound = false;
while ( *HPCisi )
{
std::string line;
std::getline(*HPCisi,line);
// std::cerr << line << std::endl;
if ( line.size() )
{
if ( line[0] == '#' )
{
activeoutput = false;
activedamapper = false;
if ( line == expcheck )
{
activeoutput = true;
activationfound = true;
}
else if ( line == expdamapper )
{
activedamapper = true;
activationdamapperfound = true;
}
}
else if ( activeoutput )
{
if (
line.size() >= expchecksub.size()
&&
line.substr(0,expchecksub.size()) == expchecksub
)
{
line = line.substr(expchecksub.size());
std::vector<std::string> tokens;
uint64_t l = 0;
while ( l < line.size() )
{
while ( l < line.size() && ::std::isspace(static_cast<unsigned char>(line[l])) )
++l;
uint64_t h = l;
while ( h < line.size() && ! ::std::isspace(static_cast<unsigned char>(line[h])) )
++h;
if ( h > l )
{
tokens.push_back(line.substr(l,h-l));
// std::cerr << "token " << tokens.back() << std::endl;
}
l = h;
}
if ( tokens.size() == 3 )
{
Voutput.push_back(tokens[2] + ".las");
}
else
{
libmaus2::exception::LibMausException lme;
lme.getStream() << "call.damapper: cannot understand line " << line << std::endl;
lme.finish();
throw lme;
}
}
else
{
libmaus2::exception::LibMausException lme;
lme.getStream() << "call.damapper: cannot understand line " << line << std::endl;
lme.finish();
throw lme;
}
}
else if ( activedamapper )
{
if ( startsWith(line,"damapper ") )
{
line = line.substr(std::string("damapper ").size());
line = PD_damapper.path + " " + line;
Vdamapper.push_back(line);
}
else
{
libmaus2::exception::LibMausException lme;
lme.getStream() << "call.damapper: cannot understand line " << line << std::endl;
lme.finish();
throw lme;
}
}
}
}
HPCisi.reset();
if ( ! activationfound )
{
libmaus2::exception::LibMausException lme;
lme.getStream() << "call.damapper: activation line for cat jobs not found" << std::endl;
lme.finish();
throw lme;
}
if ( ! activationdamapperfound )
{
libmaus2::exception::LibMausException lme;
lme.getStream() << "call.damapper: activation line for damapper not found" << std::endl;
lme.finish();
throw lme;
}
for ( uint64_t i = 0; i < Voutput.size(); ++i )
libmaus2::util::TempFileRemovalContainer::addTempFile(Voutput[i]);
/* call damapper */
for ( uint64_t i = 0; i < Vdamapper.size(); ++i )
{
int const damapperret = callsystem(Vdamapper[i].c_str());
if ( damapper_arg_v )
std::cerr << "[V] " << Vdamapper[i] << std::endl;
if ( damapperret != 0 )
{
libmaus2::exception::LibMausException lme;
lme.getStream() << "call.damapper: damapper call failed" << std::endl;
lme.finish();
throw lme;
}
}
/* concatenate all output .las files */
std::ostringstream catostr;
catostr << PD_laschainsort.path << " -sba " << readslastmp;
for ( uint64_t i = 0; i < Voutput.size(); ++i )
{
catostr << " " << Voutput[i];
}
std::string const catcom = catostr.str();
if ( damapper_arg_v )
std::cerr << "[V] " << catcom << std::endl;
if ( system(catcom.c_str()) != 0 )
{
libmaus2::exception::LibMausException lme;
lme.getStream() << "call.damapper: laschainsort call " << catcom << " failed" << std::endl;
lme.finish();
throw lme;
}
for ( uint64_t i = 0; i < Voutput.size(); ++i )
::remove(Voutput[i].c_str());
/* convert .las file to BAM */
std::ostringstream lastobamstr;
lastobamstr << PD_lastobam.path << " -t" << numthreads << " -snone " << refdam << " " << indexfasta << " " << readsdamtmp << " " << readsfastatmp << " " << readslastmp;
std::string const lastobamcom = lastobamstr.str();
if ( damapper_arg_v )
std::cerr << "[V] " << lastobamcom << std::endl;
if ( system(lastobamcom.c_str()) != 0 )
{
libmaus2::exception::LibMausException lme;
lme.getStream() << "call.damapper: lastobam call " << lastobamcom << " failed" << std::endl;
lme.finish();
throw lme;
}
if ( chdir(calldir.c_str()) )
{
int const error = errno;
libmaus2::exception::LibMausException lme;
lme.getStream() << "call.damapper: chdir(" << calldir << "): " << strerror(error) << std::endl;
lme.finish();
throw lme;
}
return EXIT_SUCCESS;
}
