Path
makeRelative(const Path &path_, const Path &root_) {
Path path = makeAbsolute(path_);
Path root = makeAbsolute(root_);
boost::filesystem::path::const_iterator rootIter = root.begin();
boost::filesystem::path::const_iterator pathIter = path.begin();
// Skip past common prefix
while (rootIter!=root.end() && pathIter!=path.end() && *rootIter==*pathIter) {
++rootIter;
++pathIter;
}
// Return value must back out of remaining A components
Path retval;
while (rootIter!=root.end()) {
if (*rootIter++ != ".")
retval /= "..";
}
// Append path components
while (pathIter!=path.end())
retval /= *pathIter++;
return retval;
}
/*!
\overload
A convenience function. See data(const QString& abs_name). The
file name is given in \a abs_or_rel_name and the path is in \a
context.
*/
const QMimeSource* Q3MimeSourceFactory::data(const QString& abs_or_rel_name, const QString& context) const
{
const QMimeSource* r = data(makeAbsolute(abs_or_rel_name,context));
if (!r && !d->path.isEmpty())
r = data(abs_or_rel_name);
return r;
}
void Project::setFileName( const QString &fn, bool doClear )
{
if ( fn == filename )
return;
if ( singleProjectMode() ) {
QString qsa = QString( getenv( "HOME" ) ) + QString( "/.qsa" );
if ( !QFile::exists( qsa ) ) {
QDir d;
d.mkdir( qsa );
}
if ( fn == singleProFileName )
return;
singleProFileName = fn;
static int counter = 0;
QString str_counter = QString::number( counter++ );
str_counter = "/.qsa/" + str_counter;
LanguageInterface *iface = MetaDataBase::languageInterface( language() );
filename = QString( getenv( "HOME" ) + str_counter + QString( "tmp_" ) +
QFileInfo( fn ).baseName() + "/" + QFileInfo( fn ).baseName() + ".pro" );
removeTempProject();
if ( iface && iface->supports( LanguageInterface::CompressProject ) ) {
filename = iface->uncompressProject( makeAbsolute( singleProFileName ),
QString( getenv( "HOME" ) +
str_counter + QString( "tmp_" ) +
QFileInfo( fn ).baseName() ) );
proName = makeAbsolute( singleProFileName );
}
} else {
filename = fn;
if ( !filename.endsWith( ".pro" ) )
filename += ".pro";
proName = filename;
}
if ( proName.contains( '.' ) )
proName = proName.left( proName.find( '.' ) );
if ( !doClear )
return;
clear();
if ( QFile::exists( filename ) )
parse();
}
/*!
Sets the \a filename of the file. The name can have no path, a relative path, or an absolute path.
If the file was opened before, it will be closed. All changes made to the file will be lost, then.
*/
void KDSaveFile::setFileName( const QString& filename )
{
const QString fn = makeAbsolute( filename );
if( fn == d->filename )
return;
close();
delete d->tmpFile;
d->filename = fn;
}
bool AbstractFileManager::resolveRelativePath(const String& relativePath, const StringList& rootPaths, String& absolutePath) {
StringList::const_iterator rootIt, rootEnd;
for (rootIt = rootPaths.begin(), rootEnd = rootPaths.end(); rootIt != rootEnd; ++rootIt) {
const String& rootPath = *rootIt;
absolutePath = makeAbsolute(relativePath, rootPath);
if (exists(absolutePath))
return true;
}
return false;
}
int &
class_5d9200::sub_5d9620( int &res, const char *path )
{
int var_108;
char FileName[MAX_PATH];
struct stat st;
makeAbsolute(var_108, FileName, MAX_PATH, path);
if( dk2_stat(FileName, &st) == -1 ) return res = -1;
x10.virt14(FileName);
if( x10.get08()[x10.get04() - 1] != '\\' &&
x10.get08()[x10.get04() - 1] != '/' )
x10.virt24("\\");
return res = 0;
}
ProgramDescriptor(std::string const & rprogram, std::string const & rcall)
: program(rprogram)
{
assert ( program.size() );
assert ( program[0] != '/' );
std::string call = makeAbsolute(rcall);
if ( ! which(program,path) )
{
path = sdirname(call) + "/" + program;
if ( ! libmaus2::util::GetFileSize::fileExists(path) )
{
libmaus2::exception::LibMausException lme;
lme.getStream() << "call.damapper: unable to find program " << program << std::endl;
lme.finish();
throw lme;
}
}
path = makeAbsolute(path);
dir = dirname(path);
}
/*!
Creates a new KDSaveFile instance working on \a filename with \a parent.
*/
KDSaveFile::KDSaveFile( const QString& filename, QObject* parent )
: QIODevice( parent ),
d( new Private( makeAbsolute( filename ), this ) )
{
}
Path& Path::makeAbsolute()
{
return makeAbsolute(current());
}
void Project::loadConnections()
{
#ifndef QT_NO_SQL
if ( dbFile.isEmpty() || !QFile::exists( makeAbsolute( dbFile ) ) )
return;
QFile f( makeAbsolute( dbFile ) );
if ( f.open( IO_ReadOnly ) ) {
QDomDocument doc;
QString errMsg;
int errLine;
if ( doc.setContent( &f, &errMsg, &errLine ) ) {
QDomElement e;
e = doc.firstChild().toElement();
/* connections */
QDomNodeList connections = e.toElement().elementsByTagName( "connection" );
for ( uint i = 0; i < connections.length(); i++ ) {
QDomElement connection = connections.item(i).toElement();
QDomElement connectionName = loadSingleProperty( connection, "name" );
QDomElement connectionDriver = loadSingleProperty( connection, "driver" );
QDomElement connectionDatabase = loadSingleProperty( connection,
"database" );
QDomElement connectionUsername = loadSingleProperty( connection,
"username" );
QDomElement connectionHostname = loadSingleProperty( connection,
"hostname" );
QDomElement connectionPort = loadSingleProperty( connection,
"port" );
DatabaseConnection *conn = new DatabaseConnection( this );
conn->setName( connectionName.firstChild().firstChild().toText().data() );
conn->setDriver( connectionDriver.firstChild().firstChild().toText().data() );
conn->setDatabase( connectionDatabase.firstChild().firstChild().toText().data() );
conn->setUsername( connectionUsername.firstChild().firstChild().toText().data() );
conn->setHostname( connectionHostname.firstChild().firstChild().toText().data() );
conn->setPort( QString( connectionPort.firstChild().firstChild().toText().data() ).toInt() );
/* connection tables */
QDomNodeList tables = connection.toElement().elementsByTagName( "table" );
for ( uint j = 0; j < tables.length(); j++ ) {
QDomElement table = tables.item(j).toElement();
QDomElement tableName = loadSingleProperty( table, "name" );
conn->addTable( tableName.firstChild().firstChild().toText().data() );
/* table fields */
QStringList fieldList;
QDomNodeList fields = table.toElement().elementsByTagName( "field" );
for ( uint k = 0; k < fields.length(); k++ ) {
QDomElement field = fields.item(k).toElement();
QDomElement fieldName = loadSingleProperty( field, "name" );
fieldList.append( fieldName.firstChild().firstChild().toText().data() );
}
conn->setFields( tableName.firstChild().firstChild().toText().data(),
fieldList );
}
dbConnections.append( conn );
}
} else {
qDebug( QString("Parse error: ") + errMsg + QString(" in line %d"), errLine );
}
f.close();
}
#endif
}
void Project::saveConnections()
{
#ifndef QT_NO_SQL
if ( dbFile.isEmpty() ) {
QFileInfo fi( fileName() );
setDatabaseDescription( fi.baseName() + ".db" );
}
QFile f( makeAbsolute( dbFile ) );
if ( dbConnections.isEmpty() ) {
if ( f.exists() )
f.remove();
setDatabaseDescription( "" );
modified = TRUE;
return;
}
/* .db xml */
if ( f.open( IO_WriteOnly | IO_Translate ) ) {
QTextStream ts( &f );
ts.setCodec( QTextCodec::codecForName( "UTF-8" ) );
ts << "<!DOCTYPE DB><DB version=\"1.0\">" << endl;
/* db connections */
int indent = 0;
for ( DatabaseConnection *conn = dbConnections.first(); conn; conn = dbConnections.next() ) {
ts << makeIndent( indent ) << "<connection>" << endl;
++indent;
saveSingleProperty( ts, "name", conn->name(), indent );
saveSingleProperty( ts, "driver", conn->driver(), indent );
saveSingleProperty( ts, "database", conn->database(), indent );
saveSingleProperty( ts, "username", conn->username(), indent );
saveSingleProperty( ts, "hostname", conn->hostname(), indent );
saveSingleProperty( ts, "port", QString::number( conn->port() ), indent );
/* connection tables */
QStringList tables = conn->tables();
for ( QStringList::Iterator it = tables.begin();
it != tables.end(); ++it ) {
ts << makeIndent( indent ) << "<table>" << endl;
++indent;
saveSingleProperty( ts, "name", (*it), indent );
/* tables fields */
QStringList fields = conn->fields( *it );
for ( QStringList::Iterator it2 = fields.begin();
it2 != fields.end(); ++it2 ) {
ts << makeIndent( indent ) << "<field>" << endl;
++indent;
saveSingleProperty( ts, "name", (*it2), indent );
--indent;
ts << makeIndent( indent ) << "</field>" << endl;
}
--indent;
ts << makeIndent( indent ) << "</table>" << endl;
}
--indent;
ts << makeIndent( indent ) << "</connection>" << endl;
}
ts << "</DB>" << endl;
f.close();
}
#endif
}
void Project::save( bool onlyProjectFile )
{
bool anythingModified = FALSE;
// save sources and forms
if ( !onlyProjectFile ) {
saveConnections();
for ( SourceFile *sf = sourcefiles.first(); sf; sf = sourcefiles.next() ) {
anythingModified = anythingModified || sf->isModified();
if ( !sf->save() )
return;
}
for ( FormFile *ff = formfiles.first(); ff; ff = formfiles.next() ) {
anythingModified = anythingModified || ff->isModified();
if ( !ff->save() )
return;
}
}
if ( isDummy() || filename.isEmpty() )
return;
if ( !modified ) {
if ( singleProjectMode() ) {
LanguageInterface *iface = MetaDataBase::languageInterface( language() );
if ( iface && iface->supports( LanguageInterface::CompressProject ) )
iface->compressProject( makeAbsolute( filename ), singleProFileName, anythingModified );
}
return;
}
QFile f( filename );
QString original = "";
// read the existing file
bool hasPreviousContents = FALSE;
if ( f.open( IO_ReadOnly ) ) {
QTextStream ts( &f );
original = ts.read();
f.close();
hasPreviousContents = TRUE;
remove_contents( original, "{SOURCES+=" ); // ### compatibility with early 3.0 betas
remove_contents( original, "DBFILE" );
remove_contents( original, "LANGUAGE" );
remove_contents( original, "TEMPLATE" );
removePlatformSettings( original, "CONFIG" );
removePlatformSettings( original, "DEFINES" );
removePlatformSettings( original, "LIBS" );
removePlatformSettings( original, "INCLUDEPATH" );
removePlatformSettings( original, "SOURCES" );
removePlatformSettings( original, "HEADERS" );
remove_multiline_contents( original, "FORMS" );
remove_multiline_contents( original, "INTERFACES" ); // compatibility
remove_multiline_contents( original, "IMAGES" );
for ( QStringList::Iterator it = csList.begin(); it != csList.end(); ++it )
remove_contents( original, *it );
}
if (!original.isEmpty()) {
// Removes any new lines at the beginning of the file
while (original.startsWith("\n"))
original.remove(0, 1);
}
// the contents of the saved file
QString contents;
// template
contents += "TEMPLATE\t= " + templ + "\n";
// language
contents += "LANGUAGE\t= " + lang + "\n";
contents += "\n";
// config
writePlatformSettings( contents, "CONFIG", cfg );
LanguageInterface *iface = MetaDataBase::languageInterface( lang );
if ( iface ) {
QStringList sourceKeys;
iface->sourceProjectKeys( sourceKeys );
for ( QStringList::Iterator spit = sourceKeys.begin(); spit != sourceKeys.end(); ++spit )
remove_multiline_contents( contents, *spit );
}
// libs, defines, includes
writePlatformSettings( contents, "LIBS", lbs );
writePlatformSettings( contents, "DEFINES", defs );
writePlatformSettings( contents, "INCLUDEPATH", inclPath );
writePlatformSettings( contents, "SOURCES", sources );
writePlatformSettings( contents, "HEADERS", headers );
// unix
if ( !hasPreviousContents ) {
contents +=
"unix|os2 {\n"
" UI_DIR = .ui\n"
" MOC_DIR = .moc\n"
" OBJECTS_DIR = .obj\n"
"}\n\n";
}
// sources
if ( !sourcefiles.isEmpty() && iface ) {
QMap<QString, QStringList> sourceToKey;
for ( SourceFile *f = sourcefiles.first(); f; f = sourcefiles.next() ) {
QString key = iface->projectKeyForExtension( QFileInfo( f->fileName() ).extension() );
QStringList lst = sourceToKey[ key ];
lst << makeRelative( f->fileName() );
sourceToKey.replace( key, lst );
}
for ( QMap<QString, QStringList>::Iterator skit = sourceToKey.begin();
skit != sourceToKey.end(); ++skit ) {
QString part = skit.key() + "\t+= ";
QStringList lst = *skit;
for ( QStringList::Iterator sit = lst.begin(); sit != lst.end(); ++sit ) {
part += *sit;
part += ++sit != lst.end() ? " \\\n\t" : "";
--sit;
}
part += "\n\n";
contents += part;
}
}
// forms and interfaces
if ( !formfiles.isEmpty() ) {
contents += "FORMS\t= ";
for ( QPtrListIterator<FormFile> fit = formfiles; fit.current(); ++fit ) {
contents += fit.current()->fileName() +
(fit != formfiles.last() ? " \\\n\t" : "");
}
contents += "\n\n";
}
// images
if ( !pixCollection->isEmpty() ) {
contents += "IMAGES\t= ";
QValueList<PixmapCollection::Pixmap> pixmaps = pixCollection->pixmaps();
for ( QValueList<PixmapCollection::Pixmap>::Iterator it = pixmaps.begin();
it != pixmaps.end(); ++it ) {
contents += makeRelative( (*it).absname );
contents += ++it != pixmaps.end() ? " \\\n\t" : "";
--it;
}
contents += "\n\n";
}
// database
if ( !dbFile.isEmpty() )
contents += "DBFILE\t= " + dbFile + "\n";
// custom settings
for ( QStringList::Iterator it = csList.begin(); it != csList.end(); ++it ) {
QString val = *customSettings.find( *it );
if ( !val.isEmpty() )
contents += *it + "\t= " + val + "\n";
}
if ( !f.open( IO_WriteOnly | IO_Translate ) ) {
QMessageBox::warning( messageBoxParent(),
"Save Project Failed", "Couldn't write project file " + filename );
return;
}
QTextStream os( &f );
os << contents;
if (hasPreviousContents)
os << original;
f.close();
setModified( FALSE );
if ( singleProjectMode() ) {
LanguageInterface *iface = MetaDataBase::languageInterface( language() );
if ( iface && iface->supports( LanguageInterface::CompressProject ) )
iface->compressProject( makeAbsolute( filename ), singleProFileName, TRUE );
}
}
boost::filesystem::path FilePath::makeAbsolute(const boost::filesystem::path &p) {
UString ustring = p.string();
return path(makeAbsolute(ustring).c_str());
}
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;
}