void flush()
{
if ( ! flushed )
{
flushed = true;
implicitFlush();
PSGO->flush();
PSGO.reset();
uint64_t const offset = headerlength + PSGO->getWrittenBytes();
libmaus2::util::NumberSerialisation::serialiseNumber(*PMETA,offset);
libmaus2::util::NumberSerialisation::serialiseNumber(*PMETA,valueswritten);
PMETA->flush();
PMETA.reset();
assert ( POSI->tellp() == static_cast<int64_t>(offset) );
libmaus2::aio::InputStreamInstance::unique_ptr_type METAin(new libmaus2::aio::InputStreamInstance(metafn));
while ( METAin->peek() != std::istream::traits_type::eof() )
libmaus2::util::NumberSerialisation::serialiseNumber(*POSI,libmaus2::util::NumberSerialisation::deserialiseNumber(*METAin));
METAin.reset();
libmaus2::aio::FileRemoval::removeFile(metafn);
// write index offset
libmaus2::util::NumberSerialisation::serialiseNumber(*POSI,offset);
POSI->flush();
POSI.reset();
}
}
void flush()
{
assert ( pc != pe );
if ( curcnt )
{
*(pc++) = rl_pair(cursym,curcnt);
curcnt = 0;
}
implicitFlush();
// std::cerr << "Index size " << index.size()*2*sizeof(uint64_t) << " for " << this << std::endl;;
if ( ! indexwritten )
{
writer.flushBitStream();
uint64_t const indexpos = writer.getPos();
writeIndex(writer,index,indexpos,numsyms);
indexwritten = true;
}
writer.flush();
}
void flush()
{
assert ( rc != re );
if ( currun.rlen )
{
*(rc++) = currun;
currun.rlen = 0;
currun.sym = std::numeric_limits<int64_t>::min();
}
implicitFlush();
// std::cerr << "Index size " << index.size()*2*sizeof(uint64_t) << " for " << this << std::endl;;
if ( ! indexwritten )
{
writer.flushBitStream();
uint64_t const indexpos = writer.getPos();
writeIndex(writer,index,indexpos);
indexwritten = true;
}
writer.flush();
}
void flush()
{
if ( curcnt )
{
*(pc++) = ptype(cursym,curcnt);
implicitFlush();
curcnt = 0;
}
SGO.flush();
uint64_t const indexpos = SGO.getWrittenBytes();
writeIndex(indexpos);
}
void encodeRun(SymBitRun const & SC)
{
if ( static_cast<SymBit const &>(SC) == static_cast<SymBit const &>(currun) )
{
currun.rlen += SC.rlen;
}
else
{
if ( currun.rlen )
{
*(rc++) = currun;
if ( rc == re )
implicitFlush();
}
currun = SC;
}
}
void encode(SymBit const & SC)
{
if ( SC == currun )
{
currun.rlen += 1;
}
else
{
if ( currun.rlen )
{
*(rc++) = currun;
if ( rc == re )
implicitFlush();
}
currun = SC;
currun.rlen = 1;
}
}
void encode(uint64_t const sym)
{
if ( sym == cursym )
{
curcnt++;
}
else if ( curcnt )
{
*(pc++) = ptype(cursym,curcnt);
if ( pc == pe )
implicitFlush();
cursym = sym;
curcnt = 1;
}
else
{
assert ( sym != cursym );
cursym = sym;
curcnt = 1;
}
}
void encode(uint64_t const v)
{
*(pc++) = v;
if ( pc == pe )
implicitFlush();
}
