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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/>.
//
#ifndef __INDEX_HEADER_HPP__
#define __INDEX_HEADER_HPP__
#include "spdlog/spdlog.h"
#include <cereal/types/string.hpp>
// The different types of indices supported
enum class IndexType : uint8_t {
PSEUDO = 0,
QUASI,
INVALID
};
class IndexHeader {
public:
IndexHeader () : type_(IndexType::INVALID), versionString_("invalid"), usesKmers_(false), kmerLen_(0), perfectHash_(false) {}
IndexHeader(IndexType typeIn, const std::string& versionStringIn,
bool usesKmersIn, uint32_t kmerLenIn, bool bigSA = false, bool perfectHash = false):
type_(typeIn), versionString_(versionStringIn),
usesKmers_(usesKmersIn), kmerLen_(kmerLenIn), bigSA_(bigSA),
perfectHash_(perfectHash) {}
template <typename Archive>
void save(Archive& ar) const {
ar( cereal::make_nvp("IndexType", type_) );
ar( cereal::make_nvp("IndexVersion", versionString_) );
ar( cereal::make_nvp("UsesKmers", usesKmers_) );
ar( cereal::make_nvp("KmerLen", kmerLen_) );
ar( cereal::make_nvp("BigSA", bigSA_) );
ar( cereal::make_nvp("PerfectHash", perfectHash_) );
ar( cereal::make_nvp("SeqHash", seqHash256_) );
ar( cereal::make_nvp("NameHash", nameHash256_) );
ar( cereal::make_nvp("SeqHash512", seqHash512_) );
ar( cereal::make_nvp("NameHash512", nameHash512_) );
ar( cereal::make_nvp("DecoySeqHash", decoySeqHash256_) );
ar( cereal::make_nvp("DecoyNameHash", decoyNameHash256_) );
}
template <typename Archive>
void load(Archive& ar) {
try {
ar( cereal::make_nvp("IndexType", type_) );
ar( cereal::make_nvp("IndexVersion", versionString_) );
ar( cereal::make_nvp("UsesKmers", usesKmers_) );
ar( cereal::make_nvp("KmerLen", kmerLen_) );
ar( cereal::make_nvp("BigSA", bigSA_) );
ar( cereal::make_nvp("PerfectHash", perfectHash_) );
ar( cereal::make_nvp("SeqHash", seqHash256_) );
ar( cereal::make_nvp("NameHash", nameHash256_) );
ar( cereal::make_nvp("SeqHash512", seqHash512_) );
ar( cereal::make_nvp("NameHash512", nameHash512_) );
ar( cereal::make_nvp("DecoySeqHash", decoySeqHash256_) );
ar( cereal::make_nvp("DecoyNameHash", decoyNameHash256_) );
} catch (const cereal::Exception& e) {
auto cerrLog = spdlog::get("stderrLog");
cerrLog->error("Encountered exception [{}] when loading index.", e.what());
cerrLog->error("The index was likely build with an older (and incompatible) "
"version of RapMap. Please re-build the index with a compatible version.");
cerrLog->flush();
std::exit(1);
}
}
IndexType indexType() const { return type_; }
std::string version() const { return versionString_; }
bool usesKmers() const { return usesKmers_; }
uint32_t kmerLen() const { return kmerLen_; }
bool bigSA() const { return bigSA_; }
bool perfectHash() const { return perfectHash_; }
void setSeqHash256(const std::string& seqHash) { seqHash256_ = seqHash; }
void setNameHash256(const std::string& nameHash) { nameHash256_ = nameHash; }
std::string seqHash256() const { return seqHash256_; }
std::string nameHash256() const { return nameHash256_; }
void setDecoySeqHash256(const std::string& seqHash) { decoySeqHash256_ = seqHash; }
void setDecoyNameHash256(const std::string& nameHash) { decoyNameHash256_ = nameHash; }
std::string decoySeqHash256() const { return decoySeqHash256_; }
std::string decoyNameHash256() const { return decoyNameHash256_; }
void setSeqHash512(const std::string& seqHash) { seqHash512_ = seqHash; }
void setNameHash512(const std::string& nameHash) { nameHash512_ = nameHash; }
std::string seqHash512() const { return seqHash512_; }
std::string nameHash512() const { return nameHash512_; }
private:
// The type of index we have
IndexType type_;
// The version string for the index
std::string versionString_;
// True if this index makes use of k-mers false otherwise
// (currently, all supported indices use k-mers in some form)
bool usesKmers_;
// The length of k-mer used by the index
uint32_t kmerLen_;
// Do we have a 64-bit suffix array or not
bool bigSA_;
// Are we using a perfect hash in the index or not?
bool perfectHash_;
// Hash of sequences in txome
std::string seqHash256_;
// Hash of sequence names in txome
std::string nameHash256_;
// Hash of sequences in txome
std::string seqHash512_;
// Hash of sequence names in txome
std::string nameHash512_;
// Hash of the names of decoys
std::string decoyNameHash256_;
// Hash of the sequences of decoys
std::string decoySeqHash256_;
};
#endif // __INDEX_HEADER_HPP__
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