void openNewFile()
{
if ( fileptr < idda.data.size() && blockptr < idda.data[fileptr].numentries )
{
/* open file */
istr = UNIQUE_PTR_MOVE(
::libmaus::aio::CheckedInputStream::unique_ptr_type(
new ::libmaus::aio::CheckedInputStream(idda.data[fileptr].filename)
)
);
/* seek to block */
uint64_t const pos = idda.data[fileptr].getPos(blockptr);
istr->seekg ( pos , std::ios::beg );
if ( static_cast<int64_t>(istr->tellg()) != static_cast<int64_t>(pos) )
{
::libmaus::exception::LibMausException ex;
ex.getStream() << "Failed to seek to position " << pos << " in file " << idda.data[fileptr].filename << std::endl;
ex.finish();
throw ex;
}
SGI = UNIQUE_PTR_MOVE(
::libmaus::aio::SynchronousGenericInput<uint64_t>::unique_ptr_type(
new ::libmaus::aio::SynchronousGenericInput<uint64_t>(
*istr,64*1024,
::std::numeric_limits<uint64_t>::max(),
false /* do not check for multiples of entity size */
)
)
);
GD = UNIQUE_PTR_MOVE(
::libmaus::gamma::GammaDecoder< ::libmaus::aio::SynchronousGenericInput<uint64_t> >::unique_ptr_type(
new ::libmaus::gamma::GammaDecoder< ::libmaus::aio::SynchronousGenericInput<uint64_t> >(*SGI)
)
);
}
}
static ::libmaus::aio::CheckedInputStream::unique_ptr_type openFileAtPosition(std::string const & filename, uint64_t const pos)
{
::libmaus::aio::CheckedInputStream::unique_ptr_type istr(new ::libmaus::aio::CheckedInputStream(filename));
istr->seekg(pos,std::ios::beg);
return UNIQUE_PTR_MOVE(istr);
}
bool readBlock(SimpleCompressedInputBlockConcatBlock & block)
{
block.compsize = 0;
block.uncompsize = 0;
block.currentInterval = currentInterval;
block.eof = false;
// check whether we need to open the next file
if ( (!(Pcis.get())) )
{
// skip over empty intervals
while ( intervalsIt != intervals.end() && intervalsIt->empty() )
++intervalsIt;
// check whether we are done
if ( intervalsIt == intervals.end() )
{
block.eof = true;
return true;
}
// get interval
currentInterval = &(*(intervalsIt++));
block.currentInterval = currentInterval;
// open file
libmaus::aio::CheckedInputStream::unique_ptr_type Tcis(new libmaus::aio::CheckedInputStream(currentInterval->name));
Pcis = UNIQUE_PTR_MOVE(Tcis);
// seek
Pcis->seekg(currentInterval->start.first);
streampos = currentInterval->start.first;
}
block.blockstreampos = streampos;
libmaus::util::CountPutObject CPO;
block.uncompsize = libmaus::util::UTF8::decodeUTF8(*Pcis);
::libmaus::util::UTF8::encodeUTF8(block.uncompsize,CPO);
block.compsize = ::libmaus::util::NumberSerialisation::deserialiseNumber(*Pcis);
::libmaus::util::NumberSerialisation::serialiseNumber(CPO,block.compsize);
block.metasize = CPO.c;
if ( block.compsize > block.I.size() )
block.I = libmaus::autoarray::AutoArray<uint8_t>(block.compsize,false);
Pcis->read(reinterpret_cast<char *>(block.I.begin()),block.compsize);
streampos += (block.metasize+block.compsize);
bool const gcountok = Pcis->gcount() == static_cast<int64_t>(block.compsize);
if ( block.blockstreampos == currentInterval->end.first )
{
Pcis.reset();
// skip over empty intervals
while ( intervalsIt != intervals.end() && intervalsIt->empty() )
++intervalsIt;
if ( intervalsIt == intervals.end() )
block.eof = true;
}
if ( gcountok )
return true;
else
return false;
}
