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//
// RapMap - Rapid and accurate mapping of short reads to transcriptomes using
// quasi-mapping.
// Copyright (C) 2015, 2016 Rob Patro, Avi Srivastava, Hirak Sarkar
//
// This file is part of RapMap.
//
// RapMap is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// RapMap is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with RapMap. If not, see <http://www.gnu.org/licenses/>.
//
#include "BooMap.hpp"
#include "FrugalBooMap.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>
/*
void set_empty_key(spp::sparse_hash_map<uint64_t,
rapmap::utils::SAInterval<IndexT>,
rapmap::utils::KmerKeyHasher>& khash,
uint64_t k) {
}
void set_empty_key(spp::sparse_hash_map<uint64_t,
rapmap::utils::SAInterval<IndexT>,
rapmap::utils::KmerKeyHasher>& khash,
uint64_t k) {
}
*/
// Set the SA and text pointer if this is a perfect hash
template <typename IndexT>
void setPerfectHashPointers(RegHashT<uint64_t,
rapmap::utils::SAInterval<IndexT>,
rapmap::utils::KmerKeyHasher>& khash, std::vector<IndexT>& SA, std::string& seq) {
// do nothing
}
template <typename IndexT>
void setPerfectHashPointers(PerfectHashT<uint64_t,
rapmap::utils::SAInterval<IndexT>>& khash, std::vector<IndexT>& SA, std::string& seq) {
khash.setSAPtr(&SA);
khash.setTextPtr(seq.c_str(), seq.length());
}
// These are **free** functions that are used for loading the
// appropriate type of hash.
template <typename IndexT>
bool loadHashFromIndex(const std::string& indexDir,
RegHashT<uint64_t,
rapmap::utils::SAInterval<IndexT>,
rapmap::utils::KmerKeyHasher>& khash) {
std::ifstream hashStream(indexDir + "hash.bin", std::ios::binary);
khash.unserialize(typename spp_utils::pod_hash_serializer<uint64_t, rapmap::utils::SAInterval<IndexT>>(),
&hashStream);
return true;
}
template <typename IndexT>
bool loadHashFromIndex(const std::string& indexDir,
PerfectHashT<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");
IndexHeader h;
std::ifstream indexStream(indDir + "header.json");
{
cereal::JSONInputArchive ar(indexStream);
ar(h);
}
indexStream.close();
uint32_t idxK = h.kmerLen();
rapmap::utils::my_mer::k(idxK);
// 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 {
return loadHashFromIndex(indDir, khash);
});
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);
seqArchive(txpCompleteLens);
}
seqStream.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 {:n} 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);
}
// Set the SA and text pointer if this is a perfect hash
setPerfectHashPointers(khash, SA, seq);
logger->info("Done loading index");
return true;
}
template class RapMapSAIndex<int32_t, RegHashT<uint64_t,
rapmap::utils::SAInterval<int32_t>,
rapmap::utils::KmerKeyHasher>>;
template class RapMapSAIndex<int64_t, RegHashT<uint64_t,
rapmap::utils::SAInterval<int64_t>,
rapmap::utils::KmerKeyHasher>>;
template class RapMapSAIndex<int32_t, PerfectHashT<uint64_t, rapmap::utils::SAInterval<int32_t>>>;
template class RapMapSAIndex<int64_t, PerfectHashT<uint64_t, rapmap::utils::SAInterval<int64_t>>>;
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