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#ifndef THIRD_PARTY_NUCLEUS_IO_GBZ_READER_H_
#define THIRD_PARTY_NUCLEUS_IO_GBZ_READER_H_
#include <memory>
#include <vector>
#include <string>
#include "include/gbwt/utils.h"
#include "include/gbwtgraph/gbz.h"
#include "include/gbwtgraph/subgraph.h"
#include "third_party/nucleus/core/statusor.h"
#include "third_party/nucleus/io/reader_base.h"
#include "third_party/nucleus/protos/cigar.pb.h"
#include "third_party/nucleus/protos/range.pb.h"
#include "third_party/nucleus/protos/reads.pb.h"
#include "boost/interprocess/managed_shared_memory.hpp" // NOLINT
#include "boost/interprocess/shared_memory_object.hpp" // NOLINT
#include "boost/interprocess/sync/named_mutex.hpp" // NOLINT
namespace nucleus {
using SamIterable = Iterable<nucleus::genomics::v1::Read>;
// A GBZ reader.
//
// GBZ files store information about pangenome population data.
//
// This class provides methods to iterate through a GBZ file and
// query() for only read overlapping a specific region on the genome.
//
// The objects returned by iterate() or query() are nucleus.genomics.v1.Read
// objects parsed from the GBZ records in the file.
class GbzReader : public Reader {
public:
// Creates a new GbzReader reading from the GBZ file gbz_path.
//
// gbz_path must point to an existing GBZ formatted file.
//
// Returns a StatusOr that is OK if the GbzReader could be successfully
// created or an error code indicating the error that occurred.
GbzReader(const std::string& gbz_path,
const std::string& sample_name,
int context,
const std::string& chrom_prefix = "",
const std::string& shared_memory_name = "GBZ_SHARED_MEMORY",
bool create_shared_memory = false,
bool use_loaded_shared_memory = false,
int shared_memory_size_gb = 12,
int num_processes = 0);
~GbzReader(){this->close_shared_memory();}
nucleus::StatusOr<std::vector<nucleus::genomics::v1::Read>> Query(
const nucleus::genomics::v1::Range& range);
nucleus::StatusOr<std::shared_ptr<SamIterable>> Iterate() const;
private:
// The filename of the GBZ file.
std::string gbz_filename_;
// The sample name of the sample for query.
std::string sample_name_;
// Below are the pointers to the GBZ objects in shared memory and in process
// memory. Only one of them will be used at a time.
// when shared memory is used, gbz_shared_mem_ will be used.
// when shared memory is not used, gbz_ will be used.
// (TODO mobinasri: maybe use template class later to keep only one pointer)
// Pinter to the GBZ object in shared memory.
std::unique_ptr<gbwtgraph::GBZ<gbwt::SharedMemCharAllocatorType>>
gbz_shared_mem_;
// Pinter to the GBZ object in process memory.
std::unique_ptr<gbwtgraph::GBZ<std::allocator<char>>>
gbz_;
// The PathIndex object.
std::unique_ptr<gbwtgraph::PathIndex> path_index_;
// context size
int context_;
// chrom prefix
std::string chrom_prefix_;
// shared memory
boost::interprocess::managed_shared_memory* shared_memory_;
// shared memory name
std::string shared_memory_name_;
// shared memory size
int shared_memory_size_gb_;
// If True, create shared memory
bool create_shared_memory_;
// If True, use shared memory that is created by other process
bool use_loaded_shared_memory_;
// number of processes that will use shared memory excluding the one that
// created it.
// it is used to make sure that the shared memory is not deleted before all
// processes are done using it.
int num_processes_;
void create_or_open_shared_memory();
void close_shared_memory();
std::vector<nucleus::genomics::v1::Read> reads_cache_;
int cache_start_pos_ = 0;
int cache_end_pos_ = 0;
void updateCache(const std::vector<nucleus::genomics::v1::Read>& reads);
template <typename CharAllocatorType>
static std::string GetBases(const gbwt::vector_type& path,
const gbwtgraph::GBZ<CharAllocatorType>& gbz);
static std::string GetReverseComplement(const std::string& sequence);
static nucleus::genomics::v1::Read MakeRead(
const std::string& chr, const int start, const std::string& bases,
const std::vector<std::string>& cigar_elements,
const std::string& read_name);
static genomics::v1::CigarUnit_Operation ParseCigarOpStr(const char op);
static std::vector<std::string> GetCigarElements(const std::string& input);
template <typename CharAllocatorType>
static std::vector<nucleus::genomics::v1::Read> GetReadsFromSubgraph(
const gbwtgraph::Subgraph& subgraph,
const gbwtgraph::GBZ<CharAllocatorType>& gbz,
const std::string& chrom_prefix);
};
} // namespace nucleus
#endif // THIRD_PARTY_NUCLEUS_IO_GBZ_READER_H_
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