static std::pair<int64_t,int64_t> getLinearMaxChunk(stream_type & stream)
{
int64_t refid = -1;
int64_t maxpos = 0;
::libmaus2::bambam::BamIndexLinearChunk LC;
while ( stream.peek() != stream_type::traits_type::eof() )
{
stream.read(reinterpret_cast<char *>(&LC),sizeof(::libmaus2::bambam::BamIndexLinearChunk));
if ( refid == -1 )
refid = LC.refid;
// put back element, if it has a different refid
if ( static_cast<int64_t>(LC.refid) != refid )
{
stream.clear();
stream.seekg(-static_cast<int64_t>(sizeof(::libmaus2::bambam::BamIndexLinearChunk)),std::ios::cur);
break;
}
maxpos = std::max(maxpos,LC.chunkid);
}
return std::pair<int64_t,int64_t>(refid,maxpos);
}
static std::pair<int64_t,uint64_t> countBinChunks(stream_type & stream)
{
int64_t bin = -1;
int64_t refid = -1;
uint64_t chunks = 0;
::libmaus2::bambam::BamIndexBinChunk BC;
while ( stream.peek() != stream_type::traits_type::eof() )
{
stream.read(reinterpret_cast<char *>(&BC),sizeof(::libmaus2::bambam::BamIndexBinChunk));
if ( refid < 0 )
refid = BC.refid;
if ( bin < 0 )
bin = BC.bin;
if (
refid != static_cast<int64_t>(BC.refid)
||
bin != static_cast<int64_t>(BC.bin)
)
{
stream.clear();
stream.seekg(-static_cast<int64_t>(sizeof(::libmaus2::bambam::BamIndexBinChunk)),std::ios::cur);
stream.clear();
break;
}
chunks++;
}
return std::pair<uint64_t,uint64_t>(bin,chunks);
}
static std::pair<int64_t,uint64_t> countLinearChunks(stream_type & stream)
{
int64_t refid = -1;
uint64_t cnt = 0;
::libmaus2::bambam::BamIndexLinearChunk LC;
while ( stream.peek() != stream_type::traits_type::eof() )
{
stream.read(reinterpret_cast<char *>(&LC),sizeof(::libmaus2::bambam::BamIndexLinearChunk));
if ( refid == -1 )
refid = LC.refid;
// put back element, if it has a different refid
if ( static_cast<int64_t>(LC.refid) != refid )
{
stream.clear();
stream.seekg(-static_cast<int64_t>(sizeof(::libmaus2::bambam::BamIndexLinearChunk)),std::ios::cur);
break;
}
cnt++;
}
return std::pair<int64_t,uint64_t>(refid,cnt);
}
static bool peekLinearChunk(stream_type & stream, uint64_t const refid, uint64_t const pos, unsigned int const posshift)
{
::libmaus2::bambam::BamIndexLinearChunk LC;
if ( stream.peek() == stream_type::traits_type::eof() )
return false;
stream.read(reinterpret_cast<char *>(&LC),sizeof(::libmaus2::bambam::BamIndexLinearChunk));
stream.clear();
stream.seekg(-static_cast<int64_t>(sizeof(::libmaus2::bambam::BamIndexLinearChunk)),std::ios::cur);
return (LC.refid == refid) && ((LC.pos >> posshift)==(pos>>posshift));
}
static bool peekLinearChunk(stream_type & stream, uint64_t const refid, int64_t const chunkid)
{
::libmaus2::bambam::BamIndexLinearChunk LC;
if ( stream.peek() == stream_type::traits_type::eof() )
return false;
stream.read(reinterpret_cast<char *>(&LC),sizeof(::libmaus2::bambam::BamIndexLinearChunk));
stream.clear();
stream.seekg(-static_cast<int64_t>(sizeof(::libmaus2::bambam::BamIndexLinearChunk)),std::ios::cur);
return LC.refid == refid && LC.chunkid == chunkid;
}
static value_type getLEInteger(stream_type & stream)
{
value_type v = 0;
for ( uint64_t i = 0; i < length; ++i )
if ( stream.peek() == stream_type::traits_type::eof() )
{
libmaus2::exception::LibMausException ex;
ex.getStream() << "Failed to little endian number of length " << length << " in BamIndex::getLEInteger." << std::endl;
ex.finish();
throw ex;
}
else
{
v |= static_cast<value_type>(stream.get()) << (8*i);
}
return v;
}
static int64_t peekBin(stream_type & stream)
{
::libmaus2::bambam::BamIndexBinChunk BC;
if ( stream.peek() == stream_type::traits_type::eof() )
return -1;
stream.read(
reinterpret_cast<char *>(&BC),
sizeof(::libmaus2::bambam::BamIndexBinChunk)
);
assert ( stream.gcount() == sizeof(::libmaus2::bambam::BamIndexBinChunk) );
stream.clear();
stream.seekg(-static_cast<int64_t>(sizeof(::libmaus2::bambam::BamIndexBinChunk)),std::ios::cur);
return BC.refid;
}
bool readBlock(stream_type & stream)
{
state = bgzfinflateblockstate_read_block;
if ( failed() )
return false;
try
{
std::pair<uint64_t,uint64_t> preblockinfo = BgzfInflateBase::readBlock(stream);
blockinfo = ::libmaus2::lz::BgzfInflateInfo(
preblockinfo.first,
preblockinfo.second,
preblockinfo.second ? false : (stream.peek() == stream_type::traits_type::eof())
);
return blockinfo.uncompressed;
}
catch(libmaus2::exception::LibMausException const & lex)
{
libmaus2::exception::LibMausException::unique_ptr_type tex(lex.uclone());
ex = UNIQUE_PTR_MOVE(tex);
return false;
}
catch(std::exception const & lex)
{
libmaus2::exception::LibMausException::unique_ptr_type tex(new libmaus2::exception::LibMausException);
ex = UNIQUE_PTR_MOVE(tex);
ex->getStream() << lex.what();
ex->finish(false);
return false;
}
catch(...)
{
libmaus2::exception::LibMausException::unique_ptr_type tex(new libmaus2::exception::LibMausException);
ex = UNIQUE_PTR_MOVE(tex);
ex->getStream() << "BgzfInflateBlock::readBlock(): unknown exception caught";
ex->finish(false);
return false;
}
}
