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);
}
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);
}
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();
}
