// encode sequence of run symbols
void encodeSymSeq(::libmaus2::util::Histogram & symhist)
{
// get symbol/freq vectors
std::vector < std::pair<uint64_t,uint64_t > > const symfreqs = symhist.getFreqSymVector();
assert ( ! ::libmaus2::huffman::EscapeCanonicalEncoder::needEscape(symfreqs) );
::libmaus2::huffman::CanonicalEncoder symenc(symhist.getByType<int64_t>());
// serialise symbol encoder
symenc.serialise(writer);
// write symbol values
for ( SymBitRun * t = ra; t != rc; ++t )
symenc.encode(writer,t->sym);
}
void implicitFlush()
{
if ( pc != pa )
{
writer.flushBitStream();
uint64_t const blockpos = writer.getPos();
uint64_t numsyms = 0;
::libmaus2::util::Histogram symhist;
::libmaus2::util::Histogram cnthist;
for ( rl_pair * pi = pa; pi != pc; ++pi )
{
symhist(pi->first);
cnthist(pi->second);
globalhist(pi->second);
numsyms += pi->second;
}
if ( ! numsyms )
{
::libmaus2::exception::LibMausException se;
se.getStream() << "numsyms=" << numsyms << " for pc-pa=" << pc-pa << " in RLEncoder::implicitFlush()" << std::endl;
se.finish();
throw se;
}
index.push_back(IndexEntry(blockpos,pc-pa,numsyms));
std::vector < std::pair<uint64_t,uint64_t > > const symfreqs = symhist.getFreqSymVector();
std::vector < std::pair<uint64_t,uint64_t > > const cntfreqs = cnthist.getFreqSymVector();
assert ( ! ::libmaus2::huffman::EscapeCanonicalEncoder::needEscape(symfreqs) );
::libmaus2::huffman::CanonicalEncoder symenc(symhist.getByType<int64_t>());
::libmaus2::huffman::EscapeCanonicalEncoder::unique_ptr_type esccntenc;
::libmaus2::huffman::CanonicalEncoder::unique_ptr_type cntenc;
bool const cntesc = ::libmaus2::huffman::EscapeCanonicalEncoder::needEscape(cntfreqs);
if ( cntesc )
{
::libmaus2::huffman::EscapeCanonicalEncoder::unique_ptr_type tesccntenc(new ::libmaus2::huffman::EscapeCanonicalEncoder(cntfreqs));
esccntenc = UNIQUE_PTR_MOVE(tesccntenc);
}
else
{
::libmaus2::huffman::CanonicalEncoder::unique_ptr_type tcntenc(new ::libmaus2::huffman::CanonicalEncoder(cnthist.getByType<int64_t>()));
cntenc = UNIQUE_PTR_MOVE(tcntenc);
}
// std::cerr << "Writing block of size " << (pc-pa) << std::endl;
writer.writeElias2(pc-pa);
writer.writeBit(cntesc);
symenc.serialise(writer);
if ( esccntenc )
esccntenc->serialise(writer);
else
cntenc->serialise(writer);
writer.flushBitStream();
for ( rl_pair * pi = pa; pi != pc; ++pi )
symenc.encode(writer,pi->first);
writer.flushBitStream();
if ( cntesc )
for ( rl_pair * pi = pa; pi != pc; ++pi )
esccntenc->encode(writer,pi->second);
else
for ( rl_pair * pi = pa; pi != pc; ++pi )
cntenc->encode(writer,pi->second);
writer.flushBitStream();
}
pc = pa;
}
