int bamsplit(libmaus2::util::ArgInfo const & arginfo)
{
if ( isatty(STDIN_FILENO) )
{
::libmaus2::exception::LibMausException se;
se.getStream() << "Refusing read binary data from terminal, please redirect standard input to pipe or file." << std::endl;
se.finish();
throw se;
}
int const level = libmaus2::bambam::BamBlockWriterBaseFactory::checkCompressionLevel(arginfo.getValue<int>("level",getDefaultLevel()));
int const verbose = arginfo.getValue<int>("verbose",getDefaultVerbose());
uint64_t const n = arginfo.getValue<int>("n",getDefaultN());
std::string const prefix = arginfo.getUnparsedValue("prefix",getDefaultFilePrefix(arginfo));
libmaus2::bambam::BamDecoder bamdec(std::cin);
libmaus2::bambam::BamAlignment const & algn = bamdec.getAlignment();
libmaus2::bambam::BamHeader const & header = bamdec.getHeader();
::libmaus2::bambam::BamHeader::unique_ptr_type uphead(updateHeader(arginfo,header));
libmaus2::aio::OutputStreamInstance::unique_ptr_type COS;
libmaus2::bambam::BamWriter::unique_ptr_type writer;
uint64_t c = 0;
uint64_t f = 0;
while ( bamdec.readAlignment() )
{
if ( c++ % n == 0 )
{
writer.reset();
if ( COS )
COS->flush();
COS.reset();
std::ostringstream fnostr;
fnostr << prefix << "_" << std::setw(6) << std::setfill('0') << f++ << std::setw(0) << ".bam";
std::string const fn = fnostr.str();
libmaus2::aio::OutputStreamInstance::unique_ptr_type tCOS(new libmaus2::aio::OutputStreamInstance(fn));
COS = UNIQUE_PTR_MOVE(tCOS);
libmaus2::bambam::BamWriter::unique_ptr_type twriter(new libmaus2::bambam::BamWriter(*COS,*uphead,level));
writer = UNIQUE_PTR_MOVE(twriter);
if ( verbose )
std::cerr << "[V] opened file " << fn << std::endl;
}
algn.serialise(writer->getStream());
}
writer.reset();
if ( COS )
COS->flush();
COS.reset();
return EXIT_SUCCESS;
}
/**
* constructor from bit length histogram
*
* @param hist bit length histogram storing the number of bits necessary
* to store each number in the sequence to be written by this generator
**/
Array864Generator(libmaus2::util::Histogram & hist)
:
n8(getSmallerEqual(hist,8)), n64(getSmallerEqual(hist,64)-n8), n(n8+n64),
P(Array864::unique_ptr_type(new Array864)),
p8(0), p64(0)
{
P->B = ::libmaus2::autoarray::AutoArray<data_type>((n+63)/64);
writer_type::unique_ptr_type twriter(new writer_type(P->B.begin()));
W = UNIQUE_PTR_MOVE(twriter);
P->A8 = ::libmaus2::autoarray::AutoArray<uint8_t>(n8);
P->A64 = ::libmaus2::autoarray::AutoArray<uint64_t>(n64);
P->n = n;
}
int bamsplitmod(libmaus::util::ArgInfo const & arginfo)
{
if ( isatty(STDIN_FILENO) )
{
::libmaus::exception::LibMausException se;
se.getStream() << "Refusing read binary data from terminal, please redirect standard input to pipe or file." << std::endl;
se.finish();
throw se;
}
int const level = libmaus::bambam::BamBlockWriterBaseFactory::checkCompressionLevel(arginfo.getValue<int>("level",getDefaultLevel()));
int const verbose = arginfo.getValue<int>("verbose",getDefaultVerbose());
uint64_t const div = arginfo.getValue<int>("div",getDefaultDiv());
std::string const prefix = arginfo.getUnparsedValue("prefix",getDefaultFilePrefix(arginfo));
if ( ! div )
{
::libmaus::exception::LibMausException se;
se.getStream() << "div cannot be 0." << std::endl;
se.finish();
throw se;
}
libmaus::bambam::BamDecoder bamdec(std::cin);
libmaus::bambam::BamAlignment const & algn = bamdec.getAlignment();
libmaus::bambam::BamHeader const & header = bamdec.getHeader();
::libmaus::bambam::BamHeader::unique_ptr_type uphead(updateHeader(arginfo,header));
libmaus::autoarray::AutoArray<libmaus::aio::CheckedOutputStream::unique_ptr_type> COS(div);
libmaus::autoarray::AutoArray<libmaus::bambam::BamWriter::unique_ptr_type> writers(div);
std::vector < std::string > filenames;
for ( uint64_t i = 0; i < div; ++i )
{
std::ostringstream ostr;
ostr << prefix << "_" << std::setw(6) << std::setfill('0') << i << std::setw(0) << ".bam";
libmaus::aio::CheckedOutputStream::unique_ptr_type tCOS(new libmaus::aio::CheckedOutputStream(ostr.str()));
COS[i] = UNIQUE_PTR_MOVE(tCOS);
libmaus::bambam::BamWriter::unique_ptr_type twriter(new libmaus::bambam::BamWriter(*COS[i],*uphead,level));
writers[i] = UNIQUE_PTR_MOVE(twriter);
}
uint64_t c = 0;
if ( verbose )
{
while ( bamdec.readAlignment() )
{
algn.serialise ( writers [ (c++) % div ] -> getStream() );
if ( ((c) & ((1ull<<20)-1)) == 0 )
std::cerr << "[V] " << c << std::endl;
}
std::cerr << "[V] " << c << std::endl;
}
else
{
while ( bamdec.readAlignment() )
algn.serialise ( writers [ (c++) % div ] -> getStream() );
}
for ( uint64_t i = 0; i < div; ++i )
{
writers[i].reset();
COS[i]->flush();
COS[i].reset();
}
return EXIT_SUCCESS;
}