Example #1
0
Try<Option<Entry> > LevelDBStorageProcess::read(const string& name)
{
  CHECK_NONE(error);

  leveldb::ReadOptions options;

  string value;

  leveldb::Status status = db->Get(options, name, &value);

  if (status.IsNotFound()) {
    return None();
  } else if (!status.ok()) {
    return Error(status.ToString());
  }

  google::protobuf::io::ArrayInputStream stream(value.data(), value.size());

  Entry entry;

  if (!entry.ParseFromZeroCopyStream(&stream)) {
    return Error("Failed to deserialize Entry");
  }

  return Some(entry);
}
Example #2
0
		void load(unsigned short bamIndex)
			{
			size_t n_reads=0;
			std::string value;
			bam1_t *b= bam_init1();
			
			index2chromNames.resize(bamIndex+1);
			WHERE(in->header);
			for(int32_t i=0;i< in->header->n_targets;++i)
				{
				string target_name(in->header->target_name[i]);
				
				index2chromNames.back().push_back(target_name);
				}
			while(samread(this->in, b) > 0) /* loop over the records */
				{
				std::auto_ptr<vector<Hit> > hits(0);
				Bam1Sequence seq(b);
				leveldb::Slice key1(seq.name());
				value.clear();
				WHERE(n_reads);
				leveldb::Status status = db->Get(this->read_options, key1, &value);
				
				if(!status.ok())
					{
					hits.reset(new vector<Hit>());
					n_reads++;
					if(n_reads%1000000UL==0)
						{
						clog <<  n_reads << endl;
						//break;//TODO
						}
					}
				else
					{
					hits=decode(value);
					}
				
				Hit hit;
				hit.bamIndex=bamIndex;
				hit.tid = seq.tid();
				hit.pos = seq.pos();
				hit.flag = seq.flag();
				hits->push_back(hit);
				
				std::auto_ptr<string> encoded = this->encode(hits.get());
				leveldb::Slice value1(encoded->data(),encoded->size());
				status = db->Put(this->write_options, key1, value1);
				if(!status.ok())
					{
					cerr << "Cannot insert into db" << endl;
					break;
					}
				}
			bam_destroy1(b);
			
			}
Example #3
0
			Status Get(const std::string& key, std::string* value)
			{
				leveldb::Status s = db->Get(leveldb::ReadOptions(), key, value);
				if (s.ok())
				{
					return Status::OK();
				}

				return Status::NotFound();
			}