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#include "BooMap.hpp"
#include "RapMapSAIndex.hpp"
#include "IndexHeader.hpp"
#include <cereal/types/unordered_map.hpp>
#include <cereal/types/vector.hpp>
#include <cereal/types/string.hpp>
#include <cereal/archives/binary.hpp>
#include <cereal/archives/json.hpp>
#include <future>
#include <thread>
// These are **free** functions that are used for loading the
// appropriate type of hash.
template <typename IndexT>
bool loadHashFromIndex(const std::string& indexDir,
google::dense_hash_map<uint64_t,
rapmap::utils::SAInterval<IndexT>,
rapmap::utils::KmerKeyHasher>& khash) {
khash.set_empty_key(std::numeric_limits<uint64_t>::max());
std::ifstream hashStream(indexDir + "hash.bin");
khash.unserialize(typename google::dense_hash_map<uint64_t,
rapmap::utils::SAInterval<IndexT>,
rapmap::utils::KmerKeyHasher>::NopointerSerializer(), &hashStream);
return true;
}
template <typename IndexT>
bool loadHashFromIndex(const std::string& indexDir,
BooMap<uint64_t, rapmap::utils::SAInterval<IndexT>> & h) {
std::string hashBase = indexDir + "hash_info";
h.load(hashBase);
return true;
}
template <typename IndexT, typename HashT>
RapMapSAIndex<IndexT, HashT>::RapMapSAIndex() {}
// Given a position, p, in the concatenated text,
// return the corresponding transcript
template <typename IndexT, typename HashT>
IndexT RapMapSAIndex<IndexT, HashT>::transcriptAtPosition(IndexT p) {
return rankDict->rank(p);
}
template <typename IndexT, typename HashT>
bool RapMapSAIndex<IndexT, HashT>::load(const std::string& indDir) {
auto logger = spdlog::get("stderrLog");
size_t n{0};
IndexHeader h;
std::ifstream indexStream(indDir + "header.json");
{
cereal::JSONInputArchive ar(indexStream);
ar(h);
}
indexStream.close();
uint32_t idxK = h.kmerLen();
// This part takes the longest, so do it in it's own asynchronous task
std::future<bool> loadingHash = std::async(std::launch::async, [this, logger, indDir]() -> bool {
if (loadHashFromIndex(indDir, khash)) {
logger->info("Successfully loaded position hash");
return true;
} else {
logger->error("Failed to load position hash!");
return false;
}
// If using a google dense hash
//this->khash.set_empty_key(std::numeric_limits<uint64_t>::max());
//uint32_t k = 31;
//std::ifstream hashStream(indDir + "hash.bin");
//{
//logger->info("Loading Position Hash");
//khash.load(hashStream);
//cereal::BinaryInputArchive hashArchive(hashStream);
//hashArchive(k);
//khash.unserialize(typename google::dense_hash_map<uint64_t,
// rapmap::utils::SAInterval<IndexT>,
// rapmap::utils::KmerKeyHasher>::NopointerSerializer(), &hashStream);
//hashArchive(khash);
//}
//hashStream.close();
//std::cerr << "had " << khash.size() << " entries\n";
//return true;
});
/*
std::ifstream intervalStream(indDir + "kintervals.bin");
{
logger->info("Loading k-mer intervals");
cereal::BinaryInputArchive intervalArchive(intervalStream);
intervalArchive(kintervals);
}
intervalStream.close();
*/
std::ifstream saStream(indDir + "sa.bin");
{
logger->info("Loading Suffix Array ");
cereal::BinaryInputArchive saArchive(saStream);
saArchive(SA);
//saArchive(LCP);
}
saStream.close();
std::ifstream seqStream(indDir + "txpInfo.bin");
{
logger->info("Loading Transcript Info ");
cereal::BinaryInputArchive seqArchive(seqStream);
seqArchive(txpNames);
seqArchive(txpOffsets);
//seqArchive(positionIDs);
seqArchive(seq);
}
seqStream.close();
/*
std::ifstream rsStream(indDir + "rsdSafe.bin", std::ios::binary);
{
logger->info("Loading Rank-Select Data");
rankDictSafe.Load(rsStream);
}
rsStream.close();
*/
std::string rsFileName = indDir + "rsd.bin";
FILE* rsFile = fopen(rsFileName.c_str(), "r");
{
logger->info("Loading Rank-Select Bit Array");
bitArray.reset(bit_array_create(0));
if (!bit_array_load(bitArray.get(), rsFile)) {
logger->error("Couldn't load bit array from {}!", rsFileName);
std::exit(1);
}
logger->info("There were {} set bits in the bit array", bit_array_num_bits_set(bitArray.get()));
rankDict.reset(new rank9b(bitArray->words, bitArray->num_of_bits));
}
fclose(rsFile);
{
logger->info("Computing transcript lengths");
txpLens.resize(txpOffsets.size());
if (txpOffsets.size() > 1) {
for(size_t i = 0; i < txpOffsets.size() - 1; ++i) {
auto nextOffset = txpOffsets[i+1];
auto currentOffset = txpOffsets[i];
txpLens[i] = (nextOffset - 1) - currentOffset;
}
}
// The last length is just the length of the suffix array - the last offset
txpLens[txpOffsets.size()-1] = (SA.size() - 1) - txpOffsets[txpOffsets.size() - 1];
}
logger->info("Waiting to finish loading hash");
loadingHash.wait();
auto hashLoadRes = loadingHash.get();
if (!hashLoadRes) {
logger->error("Failed to load hash!");
std::exit(1);
}
rapmap::utils::my_mer::k(idxK);
logger->info("Done loading index");
return true;
}
template class RapMapSAIndex<int32_t, google::dense_hash_map<uint64_t,
rapmap::utils::SAInterval<int32_t>,
rapmap::utils::KmerKeyHasher>>;
template class RapMapSAIndex<int64_t, google::dense_hash_map<uint64_t,
rapmap::utils::SAInterval<int64_t>,
rapmap::utils::KmerKeyHasher>>;
template class RapMapSAIndex<int32_t, BooMap<uint64_t, rapmap::utils::SAInterval<int32_t>>>;
template class RapMapSAIndex<int64_t, BooMap<uint64_t, rapmap::utils::SAInterval<int64_t>>>;
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