int main(int argc, char *argv[])
{
try
{
::libmaus2::util::ArgInfo const arginfo(argc,argv);
for ( uint64_t i = 0; i < arginfo.restargs.size(); ++i )
if (
arginfo.restargs[i] == "-v"
||
arginfo.restargs[i] == "--version"
)
{
std::cerr << ::biobambam2::Licensing::license();
return EXIT_SUCCESS;
}
else if (
arginfo.restargs[i] == "-h"
||
arginfo.restargs[i] == "--help"
)
{
std::cerr << ::biobambam2::Licensing::license();
std::cerr << std::endl;
std::cerr << "Key=Value pairs:" << std::endl;
std::cerr << std::endl;
std::vector< std::pair<std::string,std::string> > V;
V.push_back ( std::pair<std::string,std::string> ( "level=<["+::biobambam2::Licensing::formatNumber(getDefaultLevel())+"]>", libmaus2::bambam::BamBlockWriterBaseFactory::getBamOutputLevelHelpText() ) );
V.push_back ( std::pair<std::string,std::string> ( "verbose=<["+::biobambam2::Licensing::formatNumber(getDefaultVerbose())+"]>", "print progress report" ) );
V.push_back ( std::pair<std::string,std::string> ( "numthreads=<["+::biobambam2::Licensing::formatNumber(getDefaultNumThreads())+"]>", "number of recoding threads" ) );
V.push_back ( std::pair<std::string,std::string> ( "md5=<["+::biobambam2::Licensing::formatNumber(getDefaultMD5())+"]>", "create md5 check sum (default: 0)" ) );
V.push_back ( std::pair<std::string,std::string> ( "md5filename=<filename>", "file name for md5 check sum (default: extend output file name)" ) );
V.push_back ( std::pair<std::string,std::string> ( "index=<["+::biobambam2::Licensing::formatNumber(getDefaultIndex())+"]>", "create BAM index (default: 0)" ) );
V.push_back ( std::pair<std::string,std::string> ( "indexfilename=<filename>", "file name for BAM index file (default: extend output file name)" ) );
V.push_back ( std::pair<std::string,std::string> ( "tmpfile=<filename>", "prefix for temporary files, default: create files in current directory" ) );
::biobambam2::Licensing::printMap(std::cerr,V);
std::cerr << std::endl;
return EXIT_SUCCESS;
}
return bamrecompress(arginfo);
}
catch(std::exception const & ex)
{
std::cerr << ex.what() << std::endl;
return EXIT_FAILURE;
}
}
uint64_t bamrecompress(libmaus2::util::ArgInfo const & arginfo)
{
int const level = libmaus2::bambam::BamBlockWriterBaseFactory::checkCompressionLevel(arginfo.getValue<int>("level",getDefaultLevel()));
int const verbose = arginfo.getValue<int>("verbose",getDefaultVerbose());
int const numthreads = std::max(1,arginfo.getValue<int>("numthreads",getDefaultNumThreads()));
/*
* start index/md5 callbacks
*/
std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
std::string const tmpfileindex = tmpfilenamebase + "_index";
::libmaus2::util::TempFileRemovalContainer::addTempFile(tmpfileindex);
std::string md5filename;
std::string indexfilename;
std::vector< ::libmaus2::lz::BgzfDeflateOutputCallback * > cbs;
::libmaus2::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Pmd5cb;
if ( arginfo.getValue<unsigned int>("md5",getDefaultMD5()) )
{
if ( arginfo.hasArg("md5filename") && arginfo.getUnparsedValue("md5filename","") != "" )
md5filename = arginfo.getUnparsedValue("md5filename","");
else
std::cerr << "[V] no filename for md5 given, not creating hash" << std::endl;
if ( md5filename.size() )
{
::libmaus2::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Tmd5cb(new ::libmaus2::lz::BgzfDeflateOutputCallbackMD5);
Pmd5cb = UNIQUE_PTR_MOVE(Tmd5cb);
cbs.push_back(Pmd5cb.get());
}
}
libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
if ( arginfo.getValue<unsigned int>("index",getDefaultIndex()) )
{
if ( arginfo.hasArg("indexfilename") && arginfo.getUnparsedValue("indexfilename","") != "" )
indexfilename = arginfo.getUnparsedValue("indexfilename","");
else
std::cerr << "[V] no filename for index given, not creating index" << std::endl;
if ( indexfilename.size() )
{
libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Tindex(new libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex(tmpfileindex));
Pindex = UNIQUE_PTR_MOVE(Tindex);
cbs.push_back(Pindex.get());
}
}
/*
* end md5/index callbacks
*/
libmaus2::lz::BgzfInflateDeflateParallel::unique_ptr_type BIDP(new libmaus2::lz::BgzfInflateDeflateParallel(std::cin,std::cout,level,numthreads,4*numthreads));
for ( uint64_t i = 0; i < cbs.size(); ++i )
BIDP->registerBlockOutputCallback(cbs[i]);
libmaus2::autoarray::AutoArray<char> B(64*1024,false);
int r;
uint64_t t = 0;
uint64_t last = std::numeric_limits<uint64_t>::max();
uint64_t lcnt = 0;
uint64_t const mod = 64*1024*1024;
libmaus2::timing::RealTimeClock rtc; rtc.start();
libmaus2::timing::RealTimeClock lrtc; lrtc.start();
while ( (r = BIDP->read(B.begin(),B.size())) )
{
BIDP->write(B.begin(),r);
lcnt += r;
t += r;
if ( t/mod != last/mod )
{
if ( verbose )
{
if ( isatty(STDERR_FILENO) )
std::cerr
<< "\r" << std::string(60,' ') << "\r";
std::cerr
<< rtc.formatTime(rtc.getElapsedSeconds()) << " " << t/(1024*1024) << "MB, " << (lcnt/lrtc.getElapsedSeconds())/(1024.0*1024.0) << "MB/s";
if ( isatty(STDERR_FILENO) )
std::cerr << std::flush;
else
std::cerr << std::endl;
}
lrtc.start();
last = t;
lcnt = 0;
}
}
if ( verbose )
{
if ( isatty(STDERR_FILENO) )
std::cerr
<< "\r" << std::string(60,' ') << "\r";
std::cerr
<< rtc.formatTime(rtc.getElapsedSeconds()) << " " << t/(1024*1024) << "MB, " << (t/rtc.getElapsedSeconds())/(1024.0*1024.0) << "MB/s";
std::cerr << std::endl;
}
BIDP.reset();
if ( Pmd5cb )
{
Pmd5cb->saveDigestAsFile(md5filename);
}
if ( Pindex )
{
Pindex->flush(std::string(indexfilename));
}
return 0;
}
int bamfiltermc(libmaus2::util::ArgInfo const & arginfo)
{
bool const verbose = arginfo.getValue("verbose",getDefaultVerbose());
libmaus2::bambam::BamAlignmentDecoderWrapper::unique_ptr_type decwrapper(
libmaus2::bambam::BamMultiAlignmentDecoderFactory::construct(arginfo));
::libmaus2::bambam::BamAlignmentDecoder * ppdec = &(decwrapper->getDecoder());
::libmaus2::bambam::BamAlignmentDecoder & dec = *ppdec;
::libmaus2::bambam::BamHeader const & header = dec.getHeader();
::libmaus2::bambam::BamAlignment & algn = dec.getAlignment();
std::string const tmpfilenamebase = arginfo.getUnparsedValue("tmpfile",arginfo.getDefaultTmpFileName());
uint64_t const numthreads = arginfo.getValueUnsignedNumeric<uint64_t>("numthreads",getDefaultNumThreads());
/*
* start index/md5 callbacks
*/
std::string const tmpfileindex = tmpfilenamebase + "_index";
::libmaus2::util::TempFileRemovalContainer::addTempFile(tmpfileindex);
std::string md5filename;
std::string indexfilename;
std::vector< ::libmaus2::lz::BgzfDeflateOutputCallback * > cbs;
::libmaus2::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Pmd5cb;
if ( arginfo.getValue<unsigned int>("md5",getDefaultMD5()) )
{
if ( libmaus2::bambam::BamBlockWriterBaseFactory::getMD5FileName(arginfo) != std::string() )
md5filename = libmaus2::bambam::BamBlockWriterBaseFactory::getMD5FileName(arginfo);
else
std::cerr << "[V] no filename for md5 given, not creating hash" << std::endl;
if ( md5filename.size() )
{
::libmaus2::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Tmd5cb(new ::libmaus2::lz::BgzfDeflateOutputCallbackMD5);
Pmd5cb = UNIQUE_PTR_MOVE(Tmd5cb);
cbs.push_back(Pmd5cb.get());
}
}
libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
if ( arginfo.getValue<unsigned int>("index",getDefaultIndex()) )
{
if ( libmaus2::bambam::BamBlockWriterBaseFactory::getIndexFileName(arginfo) != std::string() )
indexfilename = libmaus2::bambam::BamBlockWriterBaseFactory::getIndexFileName(arginfo);
else
std::cerr << "[V] no filename for index given, not creating index" << std::endl;
if ( indexfilename.size() )
{
libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Tindex(new libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex(tmpfileindex));
Pindex = UNIQUE_PTR_MOVE(Tindex);
cbs.push_back(Pindex.get());
}
}
std::vector< ::libmaus2::lz::BgzfDeflateOutputCallback * > * Pcbs = 0;
if ( cbs.size() )
Pcbs = &cbs;
/*
* end md5/index callbacks
*/
::libmaus2::bambam::BamHeader::unique_ptr_type genuphead(
libmaus2::bambam::BamHeaderUpdate::updateHeader(arginfo,header,"bamfiltermc",std::string(PACKAGE_VERSION))
);
libmaus2::bambam::BamBlockWriterBase::unique_ptr_type Pwriter(libmaus2::bambam::BamBlockWriterBaseFactory::construct(*genuphead,arginfo,Pcbs));
libmaus2::bambam::BamBlockWriterBase & wr = *Pwriter;
// freelist size
uint64_t const flsize = 16*1024;
libmaus2::util::FreeList < libmaus2::bambam::BamAlignment, BamAlignmentFreeListDefaultAllocator, BamAlignmentFreeListDefaultTypeInfo > FL(flsize);
libmaus2::util::SimpleQueue < libmaus2::bambam::BamAlignment::shared_ptr_type > Q;
libmaus2::bambam::BamAuxFilterVector auxvec;
auxvec.set('M','C');
uint64_t alcnt = 0;
while ( dec.readAlignment() )
{
if ( FL.empty() )
handleQueue(Q,FL,wr,auxvec,numthreads);
assert ( ! FL.empty() );
libmaus2::bambam::BamAlignment::shared_ptr_type P = FL.get();
P->swap(algn);
Q.push_back(P);
if ( verbose && ((++alcnt % (1024*1024)) == 0) )
std::cerr << "[V] " << alcnt << std::endl;
}
handleQueue(Q,FL,wr,auxvec,numthreads);
// reset BAM writer
Pwriter.reset();
if ( Pmd5cb )
Pmd5cb->saveDigestAsFile(md5filename);
if ( Pindex )
Pindex->flush(std::string(indexfilename));
return EXIT_SUCCESS;
}
