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; } }